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Rob Knight

Title(s)Professor, Pediatrics
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Other Positions
    Title(s)Affiliate Professor , Computer Science and Engineering

    Title(s), Computer Science and Engineering


    Collapse Overview 
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    Collapse Research 
    Collapse research activities and funding
    Epidemiology of the gut microbiome, prediabetes and diabetes in Latinos
    NIH R01MD011389Jul 8, 2016 - Feb 28, 2021
    Role: Principal Investigator
    A High-memory Supercomputer for Proteomics, Text Mining and Microbiome Research
    NIH S10OD012300Apr 22, 2013 - Apr 21, 2014
    Role: Principal Investigator
    New Tools for Understanding the Composition and Dynamics of Microbial Communities
    NIH R01HG004872Sep 26, 2008 - Jul 31, 2013
    Role: Principal Investigator
    Metagenomic Studies of the Gut Microbiomes of Obese and Lean Twins
    NIH P01DK078669Jul 16, 2007 - Jun 30, 2019
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Clinical Trials

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Rapid homotopic communication between human orbitofrontal subregions. Curr Biol. 2026 Feb 26. Starkweather CK, Willbrand EH, Sellers KK, Hullet P, Krystal AD, Shirvalkar P, Weiner KS, Willie JT, Brunner P, Chang EF, Knight RT. PMID: 41759515.
      View in: PubMed   Mentions:    Fields:    
    2. Scikit-bio: a fundamental Python library for biological omic data analysis. Nat Methods. 2026 Feb; 23(2):274-276. Aton M, McDonald D, Cañardo Alastuey J, Azom R, Batra P, Bezshapkin V, Bolyen E, Cagle A, Caporaso JG, Debelius JW, Gorlick K, Hamsanipally N, Hunger L, Keluskar A, Liao D, Lu YY, Navas-Molina JA, Pitman A, Rideout JR, Sazonov A, Sathappan B, Schwarzberg Lipson K, Sfiligoi I, Tapo C, Vázquez-Baeza Y, Wu Z, Xu ZZ, Ye MS, Zhao J, Knight R, Morton JT, Zhu Q. PMID: 41381898.
      View in: PubMed   Mentions:
    3. Quantitative Food Compounds Enable Dietary Ontology Referencing across 500 Foods and Human Plasma. Anal Chem. 2026 Feb 03; 98(4):3160-3176. Agongo J, Gouda H, McMaugh A, Allaband C, Aghili SM, Sala-Climent M, Xing S, Cao J, Zemlin J, Wang M, Dorrestein K, Holt T, Knight R, Boland BS, Guma M, Dorrestein PC. PMID: 41549429; PMCID: PMC12874208.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity. bioRxiv. 2026 Jan 09. Montgomery TL, Nelson EA, Downs LA, Heney ER, Lee MFJ, Martino C, McDonald D, Rahman G, Knight R, Krementsov DN. PMID: 41542584; PMCID: PMC12803115.
      View in: PubMed   Mentions:
    5. Conjunctive population coding integrates sensory evidence to guide adaptive behavior. Proc Natl Acad Sci U S A. 2025 Dec 30; 122(52):e2520444122. Terlau J, Ethofer S, Naros G, Fonken Y, Lin JJ, Knight RT, Helfrich RF. PMID: 41439712; PMCID: PMC12772193.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    6. Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats. Nat Commun. 2025 Dec 18; 16(1):10126. Tonnelé H, Chen D, Morillo F, Garcia-Calleja J, Chitre AS, Johnson BB, Sanches TM, Cheng R, Bonder MJ, Gonzalez A, Kosciolek T, George AM, Han W, Holl K, Horvath A, Ishiwari K, King CP, Lamparelli AC, Martin CD, Martinez AG, Netzley AH, Tripi JA, Wang T, Bosch E, Doris PA, Stegle O, Chen H, Flagel SB, Meyer PJ, Richards JB, Robinson TE, Solberg Woods LC, Polesskaya O, Knight R, Palmer AA, Baud A. PMID: 41413022; PMCID: PMC12715198.
      View in: PubMed   Mentions:
    7. Environmental and skin-nasal microbiome variation in South African children with atopic dermatitis. BMC Microbiol. 2025 Dec 12; 26(1):34. Chen Y, Nguyen AD, Lunjani N, Ndhlovu G, Kaul D, De Pessemier B, Nakatsuji T, Madzinga M, Sovershaeva E, Hlela C, Levin M, Mankahla A, Hightower G, Callewaert C, Knight R, Gallo RL, Dupont CL, Dube F. PMID: 41388368; PMCID: PMC12817727.
      View in: PubMed   Mentions:
    8. Antimicrobial resistance is widespread among intestinal and extra-intestinal Bacteroides fragilis strains. Infect Immun. 2025 Dec 16; 93(12):e0052925. Carrillo Terrazas M, Oles RE, Loomis LR, Hsu C-Y, Vasquez Ayala A, Lee MH, Paulchakrabarti M, Pride D, Choudhury B, Nizet V, Raffatellu M, Knight R, Chu H. PMID: 41277826; PMCID: PMC12707147.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. Calculating fast differential genome coverages among metagenomic sources using micov. Commun Biol. 2025 Nov 20; 8(1):1624. Weng Y, Guccione C, McDonald D, Oles R, Devkota S, Kopylova E, Sepich-Poore GD, Salido RA, Din MO, Song SJ, Curtius K, Chu H, Bartko A, Hasty J, Knight R. PMID: 41266796; PMCID: PMC12635244.
      View in: PubMed   Mentions: Translation:Humans
    10. Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens. Urogynecology (Phila). 2025 Nov 01; 31(11):1033-1042. Lukacz ES, McDonald D, Bryant M, Putnam S, Rudser K, Brennan C, Meister M, Fok CS, Mueller MG, Knight R, Brubaker L, Prevention of Lower Urinary Tract Symptoms (PLUS) Research Consortium. PMID: 41258692; PMCID: PMC12631036.
      View in: PubMed   Mentions:
    11. Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease. bioRxiv. 2025 Oct 29. Hensen T, Khatib L, Patel L, McDonald D, González A, MahmoudianDehkordi S, Blach C, Alzheimer Gut Microbiome Project Consortium, Knight R, Kaddurah-Daouk R, Thiele I. PMID: 41279986; PMCID: PMC12636354.
      View in: PubMed   Mentions:
    12. Brain dynamics of mental manipulation. bioRxiv. 2025 Oct 21. Quiroga-Martinez DR, He T, Fernández-Rubio G, Bonetti L, Blenkmann AO, Endestad T, Solbakk AK, Meling TR, Fabricius M, Kim-McManus O, Willie JT, Brunner P, Dastjerdi M, Lin JJ, Knight RT. PMID: 41278767; PMCID: PMC12633419.
      View in: PubMed   Mentions:
    13. Industrialization drives convergent microbial and physiological shifts in the human metaorganism. bioRxiv. 2025 Oct 20. Poyet M, Rühlemann M, Schaan AP, Ma Y, Moitinho-Silva L, Wacker EM, Jebens H, Patel L, Nguyen LTT, Zimmer A, Plichta D, McDonald D, Stevens C, Agyei A, Afihene MY, Asibey SO, Awuku YA, Badiane AS, Ching LS, Corzett C, Deme A, Dominguez-Rodrigo M, Duah A, Fezeu A, Froment A, Gibbons S, Girard C, Hooker J, Ibrahim F, Iqaluk D, Juimo V, Kettunen P, Lafosse S, Lango-Yaya E, Lehtimäki J, Lim YAL, Mabulla A, Mahachai V, Mohamed RS, Moniz K, Mwikarago IE, Nartey YA, Ndiaye D, Noel M, Onyekwere C, Pin TM, Plymoth A, Roberts L, Ruokolainen L, Rusine J, Segurel L, Shapiro BJ, Sigwazi S, Sistiaga A, Valles K, Vatanen T, Vilaichone RK, Rosenstiel P, Baines J, Franke A, Ellinghaus D, Knight R, Daly M, Xavier RJ, Alm EJ, Groussin M. PMID: 41280098; PMCID: PMC12633315.
      View in: PubMed   Mentions:
    14. The Oral Microbiome and All-Cause Mortality in a US Population-Representative Prospective Cohort. J Infect Dis. 2025 Oct 15; 232(4):790-795. Vogtmann E, Yano Y, Shi J, Wan Y, Purandare V, McLean J, Li S, Knight R, Kahle L, Hullings AG, Hua X, Graubard BI, Gillison ML, Caporaso JG, Bokulich NA, Blaser MJ, Freedman ND, Chaturvedi AK, Abnet CC. PMID: 40513117; PMCID: PMC12526875.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    15. Temporal nutrition analysis associates dietary regularity and quality with gut microbiome diversity: insights from the Food & You digital cohort. Nat Commun. 2025 Sep 30; 16(1):8635. Singh R, McDonald D, Hernandez AR, Song SJ, Bartko A, Knight R, Salathé M. PMID: 41028733; PMCID: PMC12484809.
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    16. CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments. Microbiol Resour Announc. 2025 Nov 13; 14(11):e0132324. Seitz VA, McGivern BB, Shaffer M, Borton MA, Belk AD, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel H, Xu ZZ, Nieciecki V, Zhu Q, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Joshua Chan SH, Connor M, Boyd DA, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Carter DO, Burcham ZM, Knight R, Wrighton KC, Metcalf JL. PMID: 40985699; PMCID: PMC12613977.
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    17. Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats. bioRxiv. 2025 Sep 13. Tonnele H, Chen D, Morillo F, Garcia-Calleja J, Chitre AS, Johnson BB, Sanches TM, Bonder MJ, Gonzalez A, Kosciolek T, George AM, Han W, Holl K, Horvath A, Ishiwari K, King CP, Lamparelli AC, Martin CD, Martinez AG, Netzley AH, Tripi JA, Wang T, Bosch E, Doris PA, Stegle O, Chen H, Flagel SB, Meyer PJ, Richards JB, Robinson TE, Woods LCS, Polesskaya O, Knight R, Palmer AA, Baud A. PMID: 40166210; PMCID: PMC11957159.
      View in: PubMed   Mentions:
    18. Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics. Res Sq. 2025 Sep 10. Knight R, Din MO, Salido R, Wright G, Brennan C, Ambre M, Hansen L, Boyer T, Cao J, Oles R, Patel L, Weng Y, McDonald D, Bhute S, Solini G, Karthikeyan S, Humphrey G, DeHoff P, Kralicek S, Levy J, Zeller M, Hecht G, Laurent L, Yeo G, Andersen K, Bartko A. PMID: 40964040; PMCID: PMC12440100.
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    19. Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition. Cell. 2025 Nov 13; 188(23):6666-6686.e25. Minich JJ, Allsing N, Din MO, Tisza MJ, Maleta K, McDonald D, Hartwick N, Mamerto A, Brennan C, Hansen L, Shaffer J, Murray ER, Duong T, Knight R, Stephenson K, Manary MJ, Michael TP. PMID: 40930091.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    20. Predictive encoding of auditory sequences in the human prefrontal cortex. bioRxiv. 2025 Aug 22. Asko O, Volehaugen VA, Llorens A, Funderud I, Leske SL, Ivanovic J, Meling TR, Etholm L, Larsson PG, Knight RT, Endestad T, Solbakk AK, Blenkmann AO. PMID: 40894738; PMCID: PMC12393564.
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    21. Targeted Microbial Shifts and Metabolite Profiles Were Associated with Clinical Response to an Anti-Inflammatory Diet in Osteoarthritis. Nutrients. 2025 Aug 22; 17(17). Sala-Climent M, Bu K, Coras R, Cedeno M, Zuffa S, Murillo-Saich J, Mannochio-Russo H, Allaband C, Hose MK, Quan A, Choi SI, Nguyen K, Golshan S, Blank RB, Holt T, Lane NE, Knight R, Scher J, Dorrestein P, Clemente J, Guma M. PMID: 40944120; PMCID: PMC12430150.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCTClinical Trials
    22. Cyanobacteria Join the Kahalalide Conversation: Genome and Metabolite Evidence for Structurally Related Peptides. J Am Chem Soc. 2025 Sep 03; 147(35):31800-31810. Ryu B, Avalon NE, Cuau M, Almaliti J, Din MO, Brennan C, Glukhov E, Knight R, Gerwick L, Gerwick WH. PMID: 40828982; PMCID: PMC12449831.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    23. Neural dynamics of proactive and reactive cognitive control in medial and lateral prefrontal cortex. iScience. 2025 Sep 19; 28(9):113375. Khan AU, Hoy CW, Anderson KL, Piai V, King-Stephens D, Laxer KD, Weber P, Lin JJ, Knight RT, Bentley JN. PMID: 40927674; PMCID: PMC12414904.
      View in: PubMed   Mentions: 1  
    24. Blood microbial DNA signature differentiates hepatocellular carcinoma from metastatic lesions. eGastroenterology. 2025; 3(3):e100193. Guccione C, Dantas Machado AC, Youssef F, Angeli-Pahim I, Duarte S, Warren C, Farmer S, Humphrey G, Richter RA, McDonald D, Weng Y, Burgoyne A, Loomba R, Curtius K, Zarrinpar A, Knight R, Zarrinpar A. PMID: 40843454; PMCID: PMC12366555.
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    25. High frequency broadband activity detected noninvasively in infants distinguishes wake from sleep states. bioRxiv. 2025 Aug 12. Holubecki AM, Yarbrough JB, Rangarajan V, Kuperman R, Knight RT, Johnson EL. PMID: 40832198; PMCID: PMC12363898.
      View in: PubMed   Mentions:
    26. Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis. Commun Biol. 2025 Aug 06; 8(1):1159. Myers T, Song SJ, Chen Y, De Pessemier B, Khatib L, McDonald D, Huang S, Gallo R, Callewaert C, Havulinna AS, Lahti L, Roeselers G, Laiola M, Shetty SA, Kelley ST, Knight R, Bartko A. PMID: 40770074; PMCID: PMC12328700.
      View in: PubMed   Mentions: 1  Translation:Humans
    27. Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2. medRxiv. 2025 Jul 27. Levy JI, Gangavarapu P, Pilz DA, Jesvaghane MA, Steedman A, Zeller M, Gangavarapu K, McDonald D, Libuit K, Kapsak C, Young EL, Agrawal S, Orschler L, Hölzer M, Stachler E, Park DJ, Hinrichs AS, Laurent LC, Knight R, Andersen KG. PMID: 40778124; PMCID: PMC12330420.
      View in: PubMed   Mentions:
    28. Electrophysiological Signatures of Visual Sensations Elicited by Direct Electrical Stimulation. Neurosci Bull. 2025 Sep; 41(9):1617-1629. Li YY, Zhang B, Wang J, Saalmann YB, Afrasiabi M, Lv PC, Wang HX, Xiang HH, Wang MY, Luan GM, Knight RT, Wang L. PMID: 40699543; PMCID: PMC12433393.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    29. The development of aperiodic neural activity in the human brain. Nat Hum Behav. 2025 Dec; 9(12):2548-2563. Cross ZR, Gray SM, Dede AJO, Rivera YM, Yin Q, Vahidi P, Rau EMB, Cyr C, Holubecki AM, Asano E, Lin JJ, Kim McManus O, Sattar S, Saez I, Girgis F, King-Stephens D, Weber PB, Laxer KD, Schuele SU, Rosenow JM, Wu JY, Lam SK, Raskin JS, Chang EF, Shaikhouni A, Brunner P, Roland JL, Braga RM, Knight RT, Ofen N, Johnson EL. PMID: 40670699; PMCID: PMC12818177.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    30. Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort. Nat Commun. 2025 Jul 01; 16(1):5963. Pärnänen K, Ruuskanen MO, Sommeria-Klein G, Laitinen V, Kantanen P, Méric G, Gazolla Volpiano C, Inouye M, Knight R, Salomaa V, Havulinna AS, Niiranen T, Lahti L. PMID: 40593656; PMCID: PMC12214822.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    31. Gut microbiome compositional and functional features associate with Alzheimer's disease pathology. Alzheimers Dement. 2025 Jul; 21(7):e70417. Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE, Alzheimer Gut Microbiome Project Consortium, Kaddurah-Daouk R, Knight R, Bendlin BB. PMID: 40604345; PMCID: PMC12221809.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    32. A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population. mSystems. 2025 Jul 22; 10(7):e0054425. Khatib L, Song SJ, Dilmore AH, Sanders JG, Brennan C, Hernandez AR, Myers T, Oles R, Farmer S, Cowart C, Birmingham A, Diaz EA, Nizet O, Gilbert K, Litwin N, Das P, Nowinski B, Bryant M, Tribelhorn C, Sanders-Bodai K, Chaumont S, Knol J, Roeselers G, Laiola M, Shetty SA, Veiga P, Tap J, Derrien M, Koutnikova H, Cotillard A, Lay C, Tovar AR, Torres N, Arteaga L, González A, McDonald D, Bartko A, Knight R. PMID: 40586597; PMCID: PMC12282181.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    33. The microbiota vault initiative: safeguarding Earth's microbial heritage for future generations. Nat Commun. 2025 Jun 27; 16(1):5373. Dominguez-Bello MG, Steiger D, Fankhauser M, Egli A, Vonaesch P, Bokulich NA, Lavrinienko A, Hoffmann C, Zimmermann P, Muhummed A, Sayasone S, Larbi A, Padonou SW, Zinsstag J, Tschopp R, Santivarangkna C, Albertos Torres D, Li YY, Benvenga V, Teo Y, Houngbédji M, Kwarteng A, Knight R, Gilbert JA, Blaser MJ. PMID: 40579417; PMCID: PMC12205078.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    34. Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects. Cell Host Microbe. 2025 Jul 09; 33(7):1057-1072. Ramos SF, Siguenza N, Zhong W, Mohanty I, Lingaraju A, Richter RA, Karthikeyan S, Lukowski AL, Zhu Q, Nunes WDG, Zemlin J, Xu ZZ, Hasty J, Dorrestein PC, Panda S, Knight R, Zarrinpar A. PMID: 40777923; PMCID: PMC12327816.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    35. The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids. Cell. 2025 Jul 24; 188(15):4154-4169.e19. Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Gonçalves Nunes WD, Deleray V, Ayala AV, Tanaka Y, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Chu H, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC. PMID: 40499541; PMCID: PMC12428309.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    36. Correction for Tang-Wing et al., "Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus)". mSystems. 2025 Jul 22; 10(7):e0032725. Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. PMID: 40459257; PMCID: PMC12282194.
      View in: PubMed   Mentions:    Fields:    
    37. Identifying wastewater chemicals in coastal aerosols. Sci Adv. 2025 May 30; 11(22):eads9476. Cooper A, Cancelada L, Torres RR, Belcher K, Small M, Belda-Ferre P, Morris C, Mitts B, Dinasquet J, Knight R, Slade JH, Prather KA. PMID: 40435233; PMCID: PMC12118540.
      View in: PubMed   Mentions:    Fields:    Translation:PHPublic Health
    38. Antibody Levels From High-Throughput Variant-Specific SARS-CoV-2 Anti-Spike Immunoglobulin G and Angiotensin-Converting Enzyme 2 Neutralization Assays Correlate With COVID-19 Infection Risk in a Large Population. J Infect Dis. 2025 Apr 15; 231(4):921-930. Jacobs MB, Clark AE, Goldhaber NH, Valentine HD, Rivera A, Ngo T, Barber T, Holmes J, Manfredi B, Garretson AF, Bray W, Knight R, Longhurst CA, Carlin AF, De Hoff P, Laurent LC. PMID: 39676529; PMCID: PMC11998568.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    39. Clinical translation of microbiome research. Nat Med. 2025 Apr; 31(4):1099-1113. Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R. PMID: 40217076.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    40. Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort. Eur J Nutr. 2025 Apr 11; 64(4):153. Koponen K, McDonald D, Jousilahti P, Meric G, Inouye M, Lahti L, Niiranen T, Männistö S, Havulinna A, Knight R, Salomaa V. PMID: 40214782; PMCID: PMC11991935.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    41. Distributed Intracranial Activity Underlying Human Decision-making Behavior. J Neurosci. 2025 Apr 09; 45(15). Overton JA, Moxon KA, Stickle MP, Peters LM, Lin JJ, Chang EF, Knight RT, Hsu M, Saez I. PMID: 39952668; PMCID: PMC11984080.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    42. Observed Mask Wearing and Presence of SARS-CoV-2 in School Wastewater, San Diego County, CA, 2022. Am J Public Health. 2025 Apr; 115(4):519-527. Fielding-Miller R, Gaines T, Hassani A, Le T, Omaleki V, Flores M, Majnoonian A, Wijaya FC, Knight R, Karthikeyan S, Garfein RS. PMID: 40073362; PMCID: PMC11903061.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    43. Circuit dynamics of approach-avoidance conflict in humans. bioRxiv. 2025 Mar 18. Staveland BR, Oberschulte J, Berger B, Minarik T, Kim-McManus O, Willie JT, Brunner P, Dastjerdi M, Lin JJ, Hsu M, Knight RT. PMID: 39803433; PMCID: PMC11722433.
      View in: PubMed   Mentions:
    44. Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis. Gut Microbes. 2025 Dec; 17(1):2474142. Xue J, Allaband C, Zuffa S, Poulsen O, Meadows J, Zhou D, Dorrestein PC, Knight R, Haddad GG. PMID: 40025767; PMCID: PMC11881840.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    45. Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol. Anal Chem. 2025 Mar 11; 97(9):4945-4953. Zuffa S, Charron-Lamoureux V, Brennan C, Ambre M, Knight R, Dorrestein PC. PMID: 40015251; PMCID: PMC11912123.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    46. The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns. Cell. 2025 Apr 03; 188(7):2022-2041.e23. Salido RA, Zhao HN, McDonald D, Mannochio-Russo H, Zuffa S, Oles RE, Aron AT, El Abiead Y, Farmer S, González A, Martino C, Mohanty I, Parker CW, Patel L, Portal Gomes PW, Schmid R, Schwartz T, Zhu J, Barratt MR, Rubins KH, Chu H, Karouia F, Venkateswaran K, Dorrestein PC, Knight R. PMID: 40020666; PMCID: PMC12068931.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    47. To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question. J Am Soc Mass Spectrom. 2025 Apr 02; 36(4):742-759. Krutkin DD, Thomas S, Zuffa S, Rajkumar P, Knight R, Dorrestein PC, Kelley ST. PMID: 40007142; PMCID: PMC11969646.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    48. ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias. Mol Biol Rep. 2025 Feb 21; 52(1):258. Bhute S, Sanders JG, Song SJ, Lavoie S, Swafford A, Guccione C, Patel L, Gonzalez A, Rooks MG, Knight R, Bartko A. PMID: 39982577; PMCID: PMC11845529.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    49. Neural dynamics of proactive and reactive cognitive control in medial and lateral prefrontal cortex. bioRxiv. 2025 Feb 13. Khan AU, Hoy C, Anderson KL, Piai V, KingStephens D, Laxer KD, Weber P, Lin JJ, Knight RT, Bentley JN. PMID: 39990315; PMCID: PMC11844492.
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    50. Correction for Taylor et al., "Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome". mSystems. 2025 Mar 18; 10(3):e0130524. Taylor BC, Weldon KC, Ellis RJ, Franklin D, Groth T, Gentry EC, Tripathi A, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Oliveira MF, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. PMID: 39898649; PMCID: PMC11915787.
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    51. Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data. Nat Commun. 2025 Jan 18; 16(1):825. Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Hightower G, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R. PMID: 39827261; PMCID: PMC11742726.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    52. Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma. bioRxiv. 2025 Jan 16. Guccione C, Sfiligoi I, Gonzalez A, Shaffer JP, Kazachkova M, Weng Y, McDonald D, Shah SC, Minot SS, Paulson T, Grady WM, Alexandrov LB, Knight R, Curtius K. PMID: 39868296; PMCID: PMC11760701.
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    53. Slow Oscillation-Spindle Coupling Predicts Sequence-Based Language Learning. J Neurosci. 2025 01 15; 45(3). Cross ZR, Helfrich RF, Corcoran AW, Dede AJO, Kohler MJ, Coussens SW, Zou-Williams L, Schlesewsky M, Gaskell GM, Knight RT, Bornkessel-Schlesewsky I. PMID: 39572236; PMCID: PMC11735671.
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    54. Medication use is associated with distinct microbial features in anxiety and depression. Mol Psychiatry. 2025 Jun; 30(6):2545-2557. Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R, Alzheimer Gut Microbiome Project Consortium. PMID: 39794490; PMCID: PMC12092254.
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    55. Consuming a modified Mediterranean ketogenic diet reverses the peripheral lipid signature of Alzheimer's disease in humans. Commun Med (Lond). 2025 Jan 09; 5(1):11. Neth BJ, Huynh K, Giles C, Wang T, Mellett NA, Duong T, Blach C, Schimmel L, Register TC, Blennow K, Zetterberg H, Batra R, Schweickart A, Dilmore AH, Martino C, Arnold M, Krumsiek J, Han X, Dorrestein PC, Knight R, Meikle PJ, Craft S, Kaddurah-Daouk R. PMID: 39779882; PMCID: PMC11711287.
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    56. Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution. Anim Microbiome. 2025 Jan 03; 7(1):1. Epstein HE, Brown T, Akinrinade AO, McMinds R, Pollock FJ, Sonett D, Smith S, Bourne DG, Carpenter CS, Knight R, Willis BL, Medina M, Lamb JB, Thurber RV, Zaneveld JR. PMID: 39754287; PMCID: PMC11697511.
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    57. TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies. Genome Biol. 2024 Dec 19; 25(1):317. Shi P, Martino C, Han R, Janssen S, Buck G, Serrano M, Owzar K, Knight R, Shenhav L, Zhang AR. PMID: 39696594; PMCID: PMC11657513.
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    58. Correction for Brennan et al., "Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution". mSystems. 2025 Jan 21; 10(1):e0128824. Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, Gonzalez A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R. PMID: 39670765; PMCID: PMC11748486.
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    59. Diversity of human salivary heparan sulfate. Glycobiology. 2024 Dec 10; 34(12). Spliid CB, Mehta S, Fuster MM, Martino C, Morris CL, Lee N, Florentino I, Tong K, Liu L, Ackermann G, Knight R, Esko JD, Hurtado de Mendoza T. PMID: 39361890; PMCID: PMC12098930.
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    60. The mouth of America: the oral microbiome profile of the US population. medRxiv. 2024 Dec 07. Chaturvedi AK, Vogtmann E, Shi J, Yano Y, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Graubard BI, Hua X, Hullings AG, Kahle L, Knight R, Li S, McLean J, Purandare V, Wan Y, Freedman ND, Abnet CC. PMID: 39677463; PMCID: PMC11643230.
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    61. The oral microbiome and all-cause mortality in the US population. medRxiv. 2024 Dec 05. Vogtmann E, Yano Y, Shi J, Wan Y, Purandare V, McLean J, Li S, Knight R, Kahle L, Hullings AG, Hua X, Graubard BI, Gillison ML, Caporaso JG, Bokulich NA, Blaser MJ, Freedman ND, Chaturvedi AK, Abnet CC. PMID: 39677439; PMCID: PMC11643182.
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    62. Anthelmintic Treatment Reveals Sex-Dependent Worm-Gut Microbiota Interactions. Parasite Immunol. 2024 Dec; 46(12):e70000. Sabey KA, Castro A, Song SJ, Knight R, Ezenwa VO. PMID: 39707820.
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    63. Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis. bioRxiv. 2024 Nov 19. Xue J, Allaband C, Zuffa S, Poulsen O, Meadows J, Zhou D, Dorrestein PC, Knight R, Haddad GG. PMID: 39605650; PMCID: PMC11601605.
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    64. Author Correction: Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Sci Rep. 2024 Nov 12; 14(1):27692. Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey FE, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk RF, Bendlin BB, Hertel J, Thiele I. PMID: 39532987; PMCID: PMC11557876.
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    65. Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices. Biol Rev Camb Philos Soc. 2025 Apr; 100(2):748-763. Degregori S, Wang X, Kommala A, Schulhof N, Moradi S, MacDonald A, Eblen K, Jukovich S, Smith E, Kelleher E, Suzuki K, Hall Z, Knight R, Amato KR. PMID: 39530277; PMCID: PMC11885713.
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    66. Y and mitochondrial chromosomes in the heterogeneous stock rat population. G3 (Bethesda). 2024 Nov 06; 14(11). Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Aron AT, Beeson A, Bimschleger HV, Eid M, Garcia Martinez AG, Han W, Holl K, Jackson T, Johnson BB, King CP, Kuhn BN, Lamparelli AC, Netzley AH, Nguyen KH, Peng BF, Tripi JA, Wang T, Ziegler KS, Adams DJ, Baud A, Carrette LLG, Chen H, de Guglielmo G, Dorrestein P, George O, Ishiwari K, Jablonski MM, Jhou TC, Kallupi M, Knight R, Meyer PJ, Solberg Woods LC, Polesskaya O, Palmer AA. PMID: 39250761; PMCID: PMC11540319.
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    67. The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds. bioRxiv. 2024 Nov 02. Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Nunes WDG, Deleray V, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC. PMID: 39554097; PMCID: PMC11565975.
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    68. Differential neural mechanisms underlie cortical gating of visual spatial attention mediated by alpha-band oscillations. Proc Natl Acad Sci U S A. 2024 Nov 05; 121(45):e2313304121. Yang X, Fiebelkorn IC, Jensen O, Knight RT, Kastner S. PMID: 39471220; PMCID: PMC11551340.
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    69. Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data. Res Sq. 2024 Oct 23. Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R. PMID: 39502785; PMCID: PMC11537348.
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    70. Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy". mSystems. 2024 Nov 19; 9(11):e0128924. Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim H-C, Jain M, Inouye M, Gilbert JA, Knight R. PMID: 39422474; PMCID: PMC11575157.
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    71. Correction to "Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization". Anal Chem. 2024 Oct 29; 96(43):17464. Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešic M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. PMID: 39412394; PMCID: PMC11525899.
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    72. Association Between Dietary Patterns and Subgingival Microbiota: Results From the Oral Infections, Glucose Intolerance, and Insulin Resistance Study (ORIGINS). J Clin Periodontol. 2025 Jan; 52(1):2-15. Molinsky RL, Johnson AJ, Marotz L, Roy S, Bohn B, Goh CE, Chen CY, Paster B, Knight R, Genkinger J, Papapanou PN, Jacobs DR, Demmer RT. PMID: 39394967; PMCID: PMC11671169.
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    73. Differential gut microbiota composition in β-Thalassemia patients and its correlation with iron overload. Sci Rep. 2024 10 11; 14(1):23858. Nonejuie P, Wilantho A, McDonald D, Htoo HH, Chalerm J, Tripathi A, Ngamphiw C, Tongsima S, Knight R, Paiboonsukwong K, Fucharoen S. PMID: 39394230; PMCID: PMC11470119.
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    74. Social behaviour mediates the microbiome response to antibiotic treatment in a wild mammal. Proc Biol Sci. 2024 Oct; 291(2032):20241756. Brown BRP, Williams AE, Sabey KA, Onserio A, Ewoi J, Song SJ, Knight R, Ezenwa VO. PMID: 39353556; PMCID: PMC11444789.
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    75. Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems. 2024 Oct 22; 9(10):e0098524. Brennan C, Belda-Ferre P, Zuffa S, Charron-Lamoureux V, Mohanty I, Ackermann G, Allaband C, Ambre M, Boyer T, Bryant M, Cantrell K, Gonzalez A, McDonald D, Salido RA, Song SJ, Wright G, Dorrestein PC, Knight R. PMID: 39283083; PMCID: PMC11494942.
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    76. Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology. medRxiv. 2024 Sep 05. Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Sanders K, Schwartz A, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE, Alzheimer Gut Microbiome Project Consortium, Kaddurah-Daouk R, Knight R, Bendlin BB. PMID: 39281749; PMCID: PMC11398448.
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    77. Oral Supplementation with the Short-Chain Fatty Acid Acetate Ameliorates Age-Related Arterial Dysfunction in Mice. Aging Biol. 2024; 2. Longtine AG, Greenberg NT, Gonzalez A, Lindquist A, VanDongen NS, Mahoney SA, Rahman G, Clayton ZS, Ziemba BP, Ludwig KR, Widlansky ME, Knight R, Seals DR, Brunt VE. PMID: 39897133; PMCID: PMC11785404.
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    78. Decoding reveals the neural representation of perceived and imagined musical sounds. bioRxiv. 2024 Aug 20. Quiroga Martinez DR, Fernández Rubio G, Bonetti L, Achyutuni KG, Tzovara A, Knight RT, Vuust P. PMID: 37645733; PMCID: PMC10462096.
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    79. Longitudinal assessment of the impact of COVID-19 infection on mask-wearing behaviors. BMC Public Health. 2024 08 16; 24(1):2230. Pham D, Lomeli A, Goldhaber NH, Valentine HD, Knight R, Longhurst CA, Laurent LC, Jacobs MB. PMID: 39152377; PMCID: PMC11328381.
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    80. The impact of breastfeeding on the preterm infant's microbiome and metabolome: a pilot study. Pediatr Res. 2025 Feb; 97(3):1227-1236. Schulkers Escalante K, Bai-Tong SS, Allard SM, Ecklu-Mensah G, Sanchez C, Song SJ, Gilbert J, Bode L, Dorrestein P, Knight R, Gonzalez DJ, Leibel SA, Leibel SL. PMID: 39138352; PMCID: PMC12055563.
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    81. Hebbian plasticity induced by temporally coincident BCI enhances post-stroke motor recovery. Sci Rep. 2024 08 12; 14(1):18700. Krueger J, Krauth R, Reichert C, Perdikis S, Vogt S, Huchtemann T, Dürschmid S, Sickert A, Lamprecht J, Huremovic A, Görtler M, Nasuto SJ, Tsai IC, Knight RT, Hinrichs H, Heinze HJ, Lindquist S, Sailer M, Millán JDR, Sweeney-Reed CM. PMID: 39134592; PMCID: PMC11319604.
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    82. Gaze-Based Detection of Thoughts across Naturalistic Tasks Using a PSO-Optimized Random Forest Algorithm. Bioengineering (Basel). 2024 Jul 27; 11(8). Rahnuma T, Jothiraj SN, Kuvar V, Faber M, Knight RT, Kam JWY. PMID: 39199718; PMCID: PMC11351278.
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    83. House dust metagenome and pulmonary function in a US farming population. Microbiome. 2024 Jul 18; 12(1):129. Lee M, Kaul A, Ward JM, Zhu Q, Richards M, Wang Z, González A, Parks CG, Beane Freeman LE, Umbach DM, Motsinger-Reif AA, Knight R, London SJ. PMID: 39026261; PMCID: PMC11256371.
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    84. A Comparison of Rapid Rule-Learning Strategies in Humans and Monkeys. J Neurosci. 2024 Jul 10; 44(28). Goudar V, Kim JW, Liu Y, Dede AJO, Jutras MJ, Skelin I, Ruvalcaba M, Chang W, Ram B, Fairhall AL, Lin JJ, Knight RT, Buffalo EA, Wang XJ. PMID: 38871463; PMCID: PMC11236592.
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    85. Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus). mSystems. 2024 Aug 20; 9(8):e0010824. Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. PMID: 38975760; PMCID: PMC11334461.
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    86. Feasibility of Home Collection for Urogenital Microbiome Samples. Urogynecology (Phila). 2024 11 01; 30(11):896-905. Lukacz ES, Fok CS, Bryant M, Rodriguez-Ponciano DP, Meister MR, Mueller MG, Lewis CE, Lowder JL, Smith AL, Stapleton A, Ayala A, Pakpahan R, Hortsch S, McDonald D, Putnam S, Rudser K, Song SJ, Knight R, Brubaker L, PLUS Research Consortium. PMID: 38958286; PMCID: PMC11502285.
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    87. Ventrointermediate thalamic stimulation improves motor learning in humans. Commun Biol. 2024 07 02; 7(1):798. Voegtle A, Terzic L, Farahat A, Hartong N, Galazky I, Hinrichs H, Nasuto SJ, de Oliveira Andrade A, Knight RT, Ivry RB, Voges J, Deliano M, Buentjen L, Sweeney-Reed CM. PMID: 38956172; PMCID: PMC11220095.
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    88. Time of sample collection is critical for the replicability of microbiome analyses. Nat Metab. 2024 Jul; 6(7):1282-1293. Allaband C, Lingaraju A, Flores Ramos S, Kumar T, Javaheri H, Tiu MD, Dantas Machado AC, Richter RA, Elijah E, Haddad GG, Leone VA, Dorrestein PC, Knight R, Zarrinpar A. PMID: 38951660; PMCID: PMC11309016.
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    89. Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease. NPJ Metab Health Dis. 2024; 2(1):15. Schweickart A, Batra R, Neth BJ, Martino C, Shenhav L, Zhang AR, Shi P, Karu N, Huynh K, Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach C, Dorrestein PC, Knight R, Alzheimer’s Gut Microbiome Project Consortium, Craft S, Kaddurah-Daouk R, Krumsiek J. PMID: 38962750; PMCID: PMC11216994.
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    90. Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems. 2024 Jul 23; 9(7):e0051624. Oles RE, Carrillo Terrazas M, Loomis LR, Hsu C-Y, Tribelhorn C, Belda-Ferre P, Ea AC, Bryant M, Young JA, Carrow HC, Sandborn WJ, Dulai PS, Sivagnanam M, Pride D, Knight R, Chu H. PMID: 38934546; PMCID: PMC11265264.
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    91. Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies. Lancet Microbe. 2024 09; 5(9):100864. Kullberg RFJ, Wikki I, Haak BW, Kauko A, Galenkamp H, Peters-Sengers H, Butler JM, Havulinna AS, Palmu J, McDonald D, Benchraka C, Abdel-Aziz MI, Prins M, Maitland van der Zee AH, van den Born BJ, Jousilahti P, de Vos WM, Salomaa V, Knight R, Lahti L, Nieuwdorp M, Niiranen T, Wiersinga WJ. PMID: 38909617.
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    92. Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv. 2024 Jun 19. Oles RE, Terrazas MC, Loomis LR, Neal MJ, Paulchakrabarti M, Zuffa S, Hsu CY, Vasquez Ayala A, Lee MH, Tribelhorn C, Belda-Ferre P, Bryant M, Zemlin J, Young J, Dulai P, Sandborn WJ, Sivagnanam M, Raffatellu M, Pride D, Dorrestein PC, Zengler K, Choudhury B, Knight R, Chu H. PMID: 38948766; PMCID: PMC11213024.
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    93. Effects of intensive lifestyle changes on the progression of mild cognitive impairment or early dementia due to Alzheimer's disease: a randomized, controlled clinical trial. Alzheimers Res Ther. 2024 06 07; 16(1):122. Ornish D, Madison C, Kivipelto M, Kemp C, McCulloch CE, Galasko D, Artz J, Rentz D, Lin J, Norman K, Ornish A, Tranter S, DeLamarter N, Wingers N, Richling C, Kaddurah-Daouk R, Knight R, McDonald D, Patel L, Verdin E, E Tanzi R, Arnold SE. PMID: 38849944; PMCID: PMC11157928.
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    94. A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats. Nutrients. 2024 Jun 06; 16(11). Thompson RS, Bowers SJ, Vargas F, Hopkins S, Kelley T, Gonzalez A, Lowry CA, Dorrestein PC, Vitaterna MH, Turek FW, Knight R, Wright KP, Fleshner M. PMID: 38892722; PMCID: PMC11175065.
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    95. Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinformatics. 2024 06 03; 40(6). Jiang Y, McDonald D, Perry D, Knight R, Mirarab S. PMID: 38870525; PMCID: PMC11193062.
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    96. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem. 2024 06 04; 96(22):8893-8904. Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešic M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. PMID: 38782403; PMCID: PMC11154662.
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    97. Gut Microbiome Multi-Omics and Cognitive Function in the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging. medRxiv. 2024 May 17. Palacios N, Gordon S, Wang T, Burk R, Qi Q, Huttenhower C, Gonzalez HM, Knight R, De Carli C, Daviglus M, Lamar M, Telavera G, Tarraf W, Kosciolek T, Cai J, Kaplan RC. PMID: 38798527; PMCID: PMC11118626.
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    98. Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults. Eur J Nutr. 2024 Sep; 63(6):2247-2260. Maukonen M, Koponen KK, Havulinna AS, Kaartinen NE, Niiranen T, Méric G, Pajari AM, Knight R, Salomaa V, Männistö S. PMID: 38753173; PMCID: PMC11377619.
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    99. Integrating clinical research into electronic health record workflows to support a learning health system. JAMIA Open. 2024 Jul; 7(2):ooae023. Goldhaber NH, Jacobs MB, Laurent LC, Knight R, Zhu W, Pham D, Tran A, Patel SP, Hogarth M, Longhurst CA. PMID: 38751411; PMCID: PMC11095974.
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    100. Author Correction: Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol. 2024 May; 42(5):814. Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. PMID: 37853257.
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    101. Author Correction: Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol. 2024 May; 42(5):813. McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. PMID: 37853258; PMCID: PMC11098728.
      View in: PubMed   Mentions: 8     Fields:    
    102. Correction: Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene. 2024 May; 43(20):1579. Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. PMID: 38580705; PMCID: PMC11090788.
      View in: PubMed   Mentions: 1     Fields:    
    103. Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols. Sci Rep. 2024 04 29; 14(1):9785. Forry SP, Servetas SL, Kralj JG, Soh K, Hadjithomas M, Cano R, Carlin M, Amorim MG, Auch B, Bakker MG, Bartelli TF, Bustamante JP, Cassol I, Chalita M, Dias-Neto E, Duca AD, Gohl DM, Kazantseva J, Haruna MT, Menzel P, Moda BS, Neuberger-Castillo L, Nunes DN, Patel IR, Peralta RD, Saliou A, Schwarzer R, Sevilla S, Takenaka IKTM, Wang JR, Knight R, Gevers D, Jackson SA. PMID: 38684791; PMCID: PMC11059151.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    104. Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors. bioRxiv. 2024 Apr 20. Usyk M, Hayes RB, Knight R, Gonzalez A, Li H, Osman I, Weber JS, Ahn J. PMID: 38659744; PMCID: PMC11042335.
      View in: PubMed   Mentions:
    105. Improving microbial phylogeny with citizen science within a mass-market video game. Nat Biotechnol. 2025 Jan; 43(1):76-84. Sarrazin-Gendron R, Ghasemloo Gheidari P, Butyaev A, Keding T, Cai E, Zheng J, Mutalova R, Mounthanyvong J, Zhu Y, Nazarova E, Drogaris C, Erhart K, Borderlands Science Development Team, Borderlands Science players, Brouillette A, Richard G, Pitchford R, Caisse S, Blanchette M, McDonald D, Knight R, Szantner A, Waldispühl J. PMID: 38622344; PMCID: PMC11738981.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    106. Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice. Nat Commun. 2024 Apr 08; 15(1):3009. Dokoshi T, Chen Y, Cavagnero KJ, Rahman G, Hakim D, Brinton S, Schwarz H, Brown EA, O'Neill A, Nakamura Y, Li F, Salzman NH, Knight R, Gallo RL. PMID: 38589392; PMCID: PMC11001995.
      View in: PubMed   Mentions: 30     Fields:    
    107. The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nat Rev Gastroenterol Hepatol. 2024 Jul; 21(7):493-516. Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. PMID: 38575682; PMCID: PMC12248421.
      View in: PubMed   Mentions: 48     Fields:    Translation:Humans
    108. Harnessing the power within: engineering the microbiome for enhanced gynecologic health. Reprod Fertil. 2024 04 01; 5(2). Brennan C, Chan K, Kumar T, Maissy E, Brubaker L, Dothard MI, Gilbert JA, Gilbert KE, Lewis AL, Thackray VG, Zarrinpar A, Knight R. PMID: 38513356; PMCID: PMC11046331.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    109. Integration of polygenic and gut metagenomic risk prediction for common diseases. Nat Aging. 2024 Apr; 4(4):584-594. Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, Méric G, Inouye M. PMID: 38528230; PMCID: PMC11031402.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    110. Peripheral neuronal activation shapes the microbiome and alters gut physiology. Cell Rep. 2024 04 23; 43(4):113953. Griffiths JA, Yoo BB, Thuy-Boun P, Cantu VJ, Weldon KC, Challis C, Sweredoski MJ, Chan KY, Thron TM, Sharon G, Moradian A, Humphrey G, Zhu Q, Shaffer JP, Wolan DW, Dorrestein PC, Knight R, Gradinaru V, Mazmanian SK. PMID: 38517896; PMCID: PMC11132177.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    111. Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. bioRxiv. 2024 Mar 19. Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R, Alzheimer Gut Microbiome Project Consortium. PMID: 38562901; PMCID: PMC10983923.
      View in: PubMed   Mentions:
    112. Differential Cognitive Effects of Unilateral Subthalamic Nucleus Deep Brain Stimulation for Parkinson's Disease. Ann Neurol. 2024 Jun; 95(6):1205-1219. Del Bene VA, Martin RC, Brinkerhoff SA, Olson JW, Nelson MJ, Marotta D, Gonzalez CL, Mills KA, Kamath V, Cutter G, Hurt CP, Wade M, Robinson FG, Bentley JN, Guthrie BL, Knight RT, Walker HC. PMID: 38501317; PMCID: PMC11102318.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    113. Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Sci Rep. 2024 03 13; 14(1):6095. Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey FE, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk RF, Bendlin BB, Hertel J, Thiele I. PMID: 38480804; PMCID: PMC10937638.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    114. Author Correction: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nat Genet. 2024 Mar; 56(3):554. Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brozynska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G. PMID: 38424462.
      View in: PubMed   Mentions: 8     Fields:    
    115. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene. 2024 04; 43(15):1127-1148. Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. PMID: 38396294; PMCID: PMC10997506.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    116. Predictable and unpredictable deviance detection in the human hippocampus and amygdala. Cereb Cortex. 2024 01 31; 34(2). Tzovara A, Fedele T, Sarnthein J, Ledergerber D, Lin JJ, Knight RT. PMID: 38216528; PMCID: PMC10839835.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    117. Ramping dynamics and theta oscillations reflect dissociable signatures during rule-guided human behavior. Nat Commun. 2024 Jan 20; 15(1):637. Weber J, Solbakk AK, Blenkmann AO, Llorens A, Funderud I, Leske S, Larsson PG, Ivanovic J, Knight RT, Endestad T, Helfrich RF. PMID: 38245516; PMCID: PMC10799948.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    118. Anatomical registration of intracranial electrodes. Robust model-based localization and deformable smooth brain-shift compensation methods. J Neurosci Methods. 2024 04; 404:110056. Blenkmann AO, Leske SL, Llorens A, Lin JJ, Chang EF, Brunner P, Schalk G, Ivanovic J, Larsson PG, Knight RT, Endestad T, Solbakk AK. PMID: 38224783; PMCID: PMC12244442.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    119. Differential contribution of sensorimotor cortex and subthalamic nucleus to unimanual and bimanual hand movements. Cereb Cortex. 2024 01 14; 34(1). Merrick CM, Doyle ON, Gallegos NE, Irwin ZT, Olson JW, Gonzalez CL, Knight RT, Ivry RB, Walker HC. PMID: 38124548; PMCID: PMC10793582.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    120. A multi-study analysis enables identification of potential microbial features associated with skin aging signs. Front Aging. 2023; 4:1304705. Myers T, Bouslimani A, Huang S, Hansen ST, Clavaud C, Azouaoui A, Ott A, Gueniche A, Bouez C, Zheng Q, Aguilar L, Knight R, Moreau M, Song SJ. PMID: 38362046; PMCID: PMC10868648.
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    121. Awake ripples enhance emotional memory encoding in the human brain. Nat Commun. 2024 01 03; 15(1):215. Zhang H, Skelin I, Ma S, Paff M, Mnatsakanyan L, Yassa MA, Knight RT, Lin JJ. PMID: 38172140; PMCID: PMC10764865.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    122. Asymmetric coding of reward prediction errors in human insula and dorsomedial prefrontal cortex. Nat Commun. 2023 12 21; 14(1):8520. Hoy CW, Quiroga-Martinez DR, Sandoval E, King-Stephens D, Laxer KD, Weber P, Lin JJ, Knight RT. PMID: 38129440; PMCID: PMC10739882.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    123. Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv. 2023 Dec 21. Oles RE, Terrazas MC, Loomis LR, Hsu CY, Tribelhorn C, Ferre PB, Ea A, Bryant M, Young J, Carrow HC, Sandborn WJ, Dulai P, Sivagnanam M, Pride D, Knight R, Chu H. PMID: 38187556; PMCID: PMC10769428.
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    124. Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses. Microbiol Spectr. 2024 Jan 11; 12(1):e0371223. Kumar T, Bryant M, Cantrell K, Song SJ, McDonald D, Tubb HM, Farmer S, Lewis A, Lukacz ES, Brubaker L, Knight R. PMID: 38095462; PMCID: PMC10783137.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    125. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell. 2023 12 21; 186(26):5690-5704.e20. Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. PMID: 38101407; PMCID: PMC10795731.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCellsPHPublic Health
    126. A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis. medRxiv. 2023 Nov 27. Schweickart A, Batra R, Neth BJ, Martino C, Shenhav L, Zhang AR, Shi P, Karu N, Huynh K, Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach C, Dorrestein PC, Knight R, Alzheimer’s Gut Microbiome Project Consortium, Craft S, Kaddurah-Daouk R, Krumsiek J. PMID: 38076824; PMCID: PMC10705656.
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    127. Optimizing campus-wide COVID-19 test notifications with interpretable wastewater time-series features using machine learning models. Sci Rep. 2023 11 24; 13(1):20670. Lin T, Karthikeyan S, Satterlund A, Schooley R, Knight R, De Gruttola V, Martin N, Zou J. PMID: 38001346; PMCID: PMC10673837.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansPHPublic Health
    128. Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort. Arterioscler Thromb Vasc Biol. 2024 02; 44(2):477-487. Koponen K, Kambur O, Joseph B, Ruuskanen MO, Jousilahti P, Salido R, Brennan C, Jain M, Meric G, Inouye M, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V. PMID: 37970720; PMCID: PMC10805357.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    129. Jumbo phages are active against extensively drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. Antimicrob Agents Chemother. 2023 12 14; 67(12):e0065423. Cobián Güemes AG, Ghatbale P, Blanc AN, Morgan CJ, Garcia A, Leonard J, Huang L, Kovalick G, Proost M, Chiu M, Kuo P, Oh J, Karthikeyan S, Knight R, Pogliano J, Schooley RT, Pride DT. PMID: 37931230; PMCID: PMC10720484.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    130. Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol. 2023 Nov; 41(11):1656. Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. PMID: 37853256.
      View in: PubMed   Mentions: 6     Fields:    
    131. Periodic attention deficits after frontoparietal lesions provide causal evidence for rhythmic attentional sampling. Curr Biol. 2023 11 20; 33(22):4893-4904.e3. Raposo I, Szczepanski SM, Haaland K, Endestad T, Solbakk AK, Knight RT, Helfrich RF. PMID: 37852264; PMCID: PMC10842514.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    132. Association of Subjective and Objective Measures of Sleep With Gut Microbiota Composition and Diversity in Older Men: The Osteoporotic Fractures in Men Study. J Gerontol A Biol Sci Med Sci. 2023 10 09; 78(10):1925-1932. Estaki M, Langsetmo L, Shardell M, Mischel A, Jiang L, Zhong Y, Kaufmann C, Knight R, Stone K, Kado D. PMID: 36655399; PMCID: PMC10562887.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    133. Oral fungal profiling and risk of nasopharyngeal carcinoma: a population-based case-control study. EBioMedicine. 2023 Oct; 96:104813. Chen Y, Li W, Chang ET, Debelius JW, Manoharan L, Zheng Y, Li Y, Huang G, Adami HO, Knight R, Cai Y, Zhang Z, Ye W. PMID: 37776725; PMCID: PMC10550808.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    134. Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Res Sq. 2023 Sep 06. Martinelli F, Heinken A, Henning AK, Wörheide MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston M, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey F, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk R, Bendlin BB, Hertel J, Thiele I. PMID: 37720019; PMCID: PMC10503865.
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    135. Correction: A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice. Elife. 2023 Aug 31; 12. Abdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK. PMID: 37650862; PMCID: PMC10471158.
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    136. Human REM sleep recalibrates neural activity in support of memory formation. Sci Adv. 2023 08 25; 9(34):eadj1895. Lendner JD, Niethard N, Mander BA, van Schalkwijk FJ, Schuh-Hofer S, Schmidt H, Knight RT, Born J, Walker MP, Lin JJ, Helfrich RF. PMID: 37624898; PMCID: PMC10456851.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    137. Dynamic expectations: Behavioral and electrophysiological evidence of sub-second updates in reward predictions. Commun Biol. 2023 08 24; 6(1):871. Marciano D, Bellier L, Mayer I, Ruvalcaba M, Lee S, Hsu M, Knight RT. PMID: 37620589; PMCID: PMC10449862.
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    138. Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression. Cell Rep. 2023 08 29; 42(8):112997. Fu T, Huan T, Rahman G, Zhi H, Xu Z, Oh TG, Guo J, Coulter S, Tripathi A, Martino C, McCarville JL, Zhu Q, Cayabyab F, Low B, He M, Xing S, Vargas F, Yu RT, Atkins A, Liddle C, Ayres J, Raffatellu M, Dorrestein PC, Downes M, Knight R, Evans RM. PMID: 37611587; PMCID: PMC10903535.
      View in: PubMed   Mentions: 37     Fields:    Translation:Animals
    139. Decision and response monitoring during working memory are sequentially represented in the human insula. iScience. 2023 Oct 20; 26(10):107653. Llorens A, Bellier L, Blenkmann AO, Ivanovic J, Larsson PG, Lin JJ, Endestad T, Solbakk AK, Knight RT. PMID: 37674986; PMCID: PMC10477069.
      View in: PubMed   Mentions: 10  
    140. Music can be reconstructed from human auditory cortex activity using nonlinear decoding models. PLoS Biol. 2023 08; 21(8):e3002176. Bellier L, Llorens A, Marciano D, Gunduz A, Schalk G, Brunner P, Knight RT. PMID: 37582062; PMCID: PMC10427021.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    141. Stem cells and extracellular vesicles to improve preclinical orofacial soft tissue healing. Stem Cell Res Ther. 2023 08 15; 14(1):203. Wang Z, Knight R, Stephens P, Ongkosuwito EM, Wagener FADTG, Von den Hoff JW. PMID: 37580820; PMCID: PMC10426149.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    142. Engineered bacteria detect tumor DNA. Science. 2023 08 11; 381(6658):682-686. Cooper RM, Wright JA, Ng JQ, Goyne JM, Suzuki N, Lee YK, Ichinose M, Radford G, Ryan FJ, Kumar S, Thomas EM, Vrbanac L, Knight R, Woods SL, Worthley DL, Hasty J. PMID: 37561843; PMCID: PMC10852993.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
    143. Electrophysiological signatures of inequity-dependent reward encoding in the human OFC. Cell Rep. 2023 08 29; 42(8):112865. Marciano D, Staveland BR, Lin JJ, Saez I, Hsu M, Knight RT. PMID: 37494185; PMCID: PMC12199477.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    144. Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol. 2024 May; 42(5):768-777. Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. PMID: 37500914; PMCID: PMC10818028.
      View in: PubMed   Mentions: 9     Fields:    
    145. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol. 2024 May; 42(5):715-718. McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. PMID: 37500913; PMCID: PMC10818020.
      View in: PubMed   Mentions: 237     Fields:    Translation:Cells
    146. Distinct ventral stream and prefrontal cortex representational dynamics during sustained conscious visual perception. Cell Rep. 2023 07 25; 42(7):112752. Vishne G, Gerber EM, Knight RT, Deouell LY. PMID: 37422763; PMCID: PMC10530642.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    147. Unexpected sound omissions are signaled in human posterior superior temporal gyrus: an intracranial study. Cereb Cortex. 2023 07 05; 33(14):8837-8848. Cho H, Fonken YM, Adamek M, Jimenez R, Lin JJ, Schalk G, Knight RT, Brunner P. PMID: 37280730; PMCID: PMC10350817.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    148. Subspace partitioning in the human prefrontal cortex resolves cognitive interference. Proc Natl Acad Sci U S A. 2023 07 11; 120(28):e2220523120. Weber J, Iwama G, Solbakk AK, Blenkmann AO, Larsson PG, Ivanovic J, Knight RT, Endestad T, Helfrich R. PMID: 37399398; PMCID: PMC10334727.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    149. Multiple memory systems for efficient temporal order memory. Hippocampus. 2023 10; 33(10):1154-1157. Jafarpour A, Lin JJ, Knight RT, Buffalo EA. PMID: 37365860; PMCID: PMC10543450.
      View in: PubMed   Mentions: 4     Fields:    
    150. Dietary weight loss-induced improvements in metabolic function are enhanced by exercise in people with obesity and prediabetes. Nat Metab. 2023 07; 5(7):1221-1235. Beals JW, Kayser BD, Smith GI, Schweitzer GG, Kirbach K, Kearney ML, Yoshino J, Rahman G, Knight R, Patterson BW, Klein S. PMID: 37365374; PMCID: PMC10515726.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    151. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci. 2023 07; 26(7):1208-1217. Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G. PMID: 37365313; PMCID: PMC10322709.
      View in: PubMed   Mentions: 99     Fields:    Translation:Humans
    152. Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution. mSystems. 2023 08 31; 8(4):e0000623. Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, González A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R. PMID: 37350611; PMCID: PMC10469589.
      View in: PubMed   Mentions: 10     Fields:    
    153. Metagenomics reveals novel microbial signatures of farm exposures in house dust. Front Microbiol. 2023; 14:1202194. Wang Z, Dalton KR, Lee M, Parks CG, Beane Freeman LE, Zhu Q, González A, Knight R, Zhao S, Motsinger-Reif AA, London SJ. PMID: 37415812; PMCID: PMC10321240.
      View in: PubMed   Mentions: 8  
    154. Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study. Microbiol Spectr. 2023 08 17; 11(4):e0157223. Wu Z, Pfeiffer RM, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Garcia-Closas M, Sinha R, Figueroa JD, Brinton LA, Trabert B, Vogtmann E. PMID: 37341612; PMCID: PMC10433996.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    155. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun. 2023 06 20; 14(1):3310. Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M. PMID: 37339957; PMCID: PMC10282066.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    156. Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases. Genes (Basel). 2023 06 09; 14(6). Rahman G, McDonald D, Gonzalez A, Vázquez-Baeza Y, Jiang L, Casals-Pascual C, Hakim D, Dilmore AH, Nowinski B, Peddada S, Knight R. PMID: 37372419; PMCID: PMC10297957.
      View in: PubMed   Mentions: 9     Fields:    
    157. You are what you excrete. Nat Microbiol. 2023 Jun; 8(6):1002-1003. Guccione C, McDonald D, Fielding-Miller R, Curtius K, Knight R. PMID: 37231087.
      View in: PubMed   Mentions: 2     Fields:    
    158. Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection. Microbiome. 2023 05 27; 11(1):119. Wang Z, Peters BA, Bryant M, Hanna DB, Schwartz T, Wang T, Sollecito CC, Usyk M, Grassi E, Wiek F, Peter LS, Post WS, Landay AL, Hodis HN, Weber KM, French A, Golub ET, Lazar J, Gustafson D, Sharma A, Anastos K, Clish CB, Burk RD, Kaplan RC, Knight R, Qi Q. PMID: 37237391; PMCID: PMC10224225.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    159. A rapid theta network mechanism for flexible information encoding. Nat Commun. 2023 05 19; 14(1):2872. Johnson EL, Lin JJ, King-Stephens D, Weber PB, Laxer KD, Saez I, Girgis F, D'Esposito M, Knight RT, Badre D. PMID: 37208373; PMCID: PMC10198978.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    160. Anatomical registration of intracranial electrodes. Robust model-based localization and deformable smooth brain-shift compensation methods. bioRxiv. 2023 May 11. Blenkmann AO, Leske SL, Llorens A, Lin JJ, Chang E, Brunner P, Schalk G, Ivanovic J, Larsson PG, Knight RT, Endestad T, Solbakk AK. PMID: 37214984; PMCID: PMC10197594.
      View in: PubMed   Mentions:
    161. Grasp-specific high-frequency broadband mirror neuron activity during reach-and-grasp movements in humans. Cereb Cortex. 2023 05 09; 33(10):6291-6298. Dreyer AM, Michalke L, Perry A, Chang EF, Lin JJ, Knight RT, Rieger JW. PMID: 36562997; PMCID: PMC10183732.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    162. Reuniting philosophy and science to advance cancer research. Biol Rev Camb Philos Soc. 2023 10; 98(5):1668-1686. Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. PMID: 37157910; PMCID: PMC10869205.
      View in: PubMed   Mentions: 6     Fields:    
    163. Gut microbiome and atrial fibrillation-results from a large population-based study. EBioMedicine. 2023 May; 91:104583. Palmu J, Börschel CS, Ortega-Alonso A, Markó L, Inouye M, Jousilahti P, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Gutmann F, Linz D, Salomaa V, Havulinna AS, Forslund SK, Knight R, Lahti L, Niiranen T, Schnabel RB. PMID: 37119735; PMCID: PMC10165189.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    164. Sequence-structure-function relationships in the microbial protein universe. Nat Commun. 2023 04 26; 14(1):2351. Koehler Leman J, Szczerbiak P, Renfrew PD, Gligorijevic V, Berenberg D, Vatanen T, Taylor BC, Chandler C, Janssen S, Pataki A, Carriero N, Fisk I, Xavier RJ, Knight R, Bonneau R, Kosciolek T. PMID: 37100781; PMCID: PMC10133388.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    165. Metagenomics reveals novel microbial signatures of farm exposures in house dust. medRxiv. 2023 Apr 12. Wang Z, Dalton KR, Lee M, Parks CG, Beane Freeman LE, Zhu Q, González A, Knight R, Zhao S, Motsinger-Reif AA, London SJ. PMID: 37090637; PMCID: PMC10120797.
      View in: PubMed   Mentions:
    166. Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease. Alzheimers Dement. 2023 11; 19(11):4805-4816. Dilmore AH, Martino C, Neth BJ, West KA, Zemlin J, Rahman G, Panitchpakdi M, Meehan MJ, Weldon KC, Blach C, Schimmel L, Kaddurah-Daouk R, Dorrestein PC, Knight R, Craft S, Alzheimer's Gut Microbiome Project Consortium. PMID: 37017243; PMCID: PMC10551050.
      View in: PubMed   Mentions: 50     Fields:    Translation:Humans
    167. Evolving approaches to profiling the microbiome in skin disease. Front Immunol. 2023; 14:1151527. Chen Y, Knight R, Gallo RL. PMID: 37081873; PMCID: PMC10110978.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    168. Electrocorticographic Activation Patterns of Electroencephalographic Microstates. Brain Topogr. 2024 03; 37(2):287-295. Mikutta CA, Knight RT, Sammler D, Müller TJ, Koenig T. PMID: 36939988; PMCID: PMC10884069.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    169. Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic. Microbiol Spectr. 2023 Mar 14; e0450922. Sah GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT. PMID: 36916973; PMCID: PMC10100919.
      View in: PubMed   Mentions:    Fields:    
    170. Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods. Cancer Epidemiol Biomarkers Prev. 2023 03 06; 32(3):444-451. Zouiouich S, Byrd DA, Hua X, Karwa S, Wan Y, Shi J, Humphrey GC, Ackermann GL, Knight R, Abnet CC, Vogtmann E, Sinha R. PMID: 36649143; PMCID: PMC10498478.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    171. Differential cognitive effects of unilateral left and right subthalamic nucleus deep brain stimulation for Parkinson disease. medRxiv. 2023 Mar 01. Del Bene VA, Martin RC, Brinkerhoff SA, Olson JW, Nelson MJ, Marotta D, Gonzalez CL, Mills KA, Kamath V, Bentley JN, Guthrie BL, Knight RT, Walker HC. PMID: 36909562; PMCID: PMC10002774.
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    172. The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Gastroenterology. 2023 06; 164(7):1069-1085. Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R. PMID: 36841488; PMCID: PMC10205675.
      View in: PubMed   Mentions: 74     Fields:    Translation:Humans
    173. Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis. Sci Transl Med. 2023 02 22; 15(684):eabq8476. Brewer RC, Lanz TV, Hale CR, Sepich-Poore GD, Martino C, Swafford AD, Carroll TS, Kongpachith S, Blum LK, Elliott SE, Blachere NE, Parveen S, Fak J, Yao V, Troyanskaya O, Frank MO, Bloom MS, Jahanbani S, Gomez AM, Iyer R, Ramadoss NS, Sharpe O, Chandrasekaran S, Kelmenson LB, Wang Q, Wong H, Torres HL, Wiesen M, Graves DT, Deane KD, Holers VM, Knight R, Darnell RB, Robinson WH, Orange DE. PMID: 36812347; PMCID: PMC10496947.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    174. Diet Quality and the Fecal Microbiota in Adults in the American Gut Project. J Nutr. 2023 07; 153(7):2004-2015. Baldeon AD, McDonald D, Gonzalez A, Knight R, Holscher HD. PMID: 36828255.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
    175. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg Health Am. 2023 Mar; 19:100449. Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R, SEARCH. PMID: 36844610; PMCID: PMC9939935.
      View in: PubMed   Mentions: 23  
    176. Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. Environ Microbiome. 2023 Feb 19; 18(1):10. Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM. PMID: 36805022; PMCID: PMC9938989.
      View in: PubMed   Mentions: 3  
    177. BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. bioRxiv. 2023 Feb 02. Rahman G, Morton JT, Martino C, Sepich-Poore GD, Allaband C, Guccione C, Chen Y, Hakim D, Estaki M, Knight R. PMID: 36778470; PMCID: PMC9915500.
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    178. The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin. mSystems. 2023 02 23; 8(1):e0092222. Melnik AV, Callewaert C, Dorrestein K, Broadhead R, Minich JJ, Ernst M, Humphrey G, Ackermann G, Gathercole R, Aksenov AA, Knight R, Dorrestein PC. PMID: 36722970; PMCID: PMC9948701.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    179. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project. medRxiv. 2023 Jan 25. Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. PMID: 34704096; PMCID: PMC8547528.
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    180. Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature. 2023 02; 614(7946):118-124. Handzlik MK, Gengatharan JM, Frizzi KE, McGregor GH, Martino C, Rahman G, Gonzalez A, Moreno AM, Green CR, Guernsey LS, Lin T, Tseng P, Ideguchi Y, Fallon RJ, Chaix A, Panda S, Mali P, Wallace M, Knight R, Gantner ML, Calcutt NA, Metallo CM. PMID: 36697822; PMCID: PMC9891999.
      View in: PubMed   Mentions: 84     Fields:    Translation:Animals
    181. Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome. Mov Disord. 2023 03; 38(3):399-409. Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A, Mazmanian SK. PMID: 36691982.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    182. Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies. Cell Rep Methods. 2023 01 23; 3(1):100391. Usyk M, Peters BA, Karthikeyan S, McDonald D, Sollecito CC, Vazquez-Baeza Y, Shaffer JP, Gellman MD, Talavera GA, Daviglus ML, Thyagarajan B, Knight R, Qi Q, Kaplan R, Burk RD. PMID: 36814836; PMCID: PMC9939430.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    183. Comparing rapid rule-learning strategies in humans and monkeys. bioRxiv. 2023 Jan 10. Goudar V, Kim JW, Liu Y, Dede AJO, Jutras MJ, Skelin I, Ruvalcaba M, Chang W, Fairhall AL, Lin JJ, Knight RT, Buffalo EA, Wang XJ. PMID: 36711889; PMCID: PMC9882042.
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    184. The gut microbiome is a significant risk factor for future chronic lung disease. J Allergy Clin Immunol. 2023 04; 151(4):943-952. Liu Y, Teo SM, Méric G, Tang HHF, Zhu Q, Sanders JG, Vázquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M. PMID: 36587850; PMCID: PMC10109092.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    185. Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses. mSystems. 2023 02 23; 8(1):e0102922. Kumar T, Bryant M, Cantrell K, Song SJ, McDonald D, Tubb HM, Farmer S, Lukacz ES, Brubaker L, Knight R. PMID: 36475896; PMCID: PMC9948722.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    186. Representative oral microbiome data for the US population: the National Health and Nutrition Examination Survey. Lancet Microbe. 2023 02; 4(2):e60-e61. Vogtmann E, Chaturvedi AK, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Hua X, Hullings AG, Knight R, Purandare V, Shi J, Wan Y, Freedman ND, Abnet CC. PMID: 36455567.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    187. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nat Commun. 2022 11 17; 13(1):6978. Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE. PMID: 36396943; PMCID: PMC9671965.
      View in: PubMed   Mentions: 38     Fields:    Translation:Animals
    188. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice. Elife. 2022 11 08; 11. Abdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK. PMID: 36346385; PMCID: PMC9668333.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    189. Generation of Functional Immortalized Human Corneal Stromal Stem Cells. Int J Mol Sci. 2022 Nov 02; 23(21). Dos Santos A, Lyu N, Balayan A, Knight R, Zhuo KS, Sun Y, Xu J, Funderburgh ML, Funderburgh JL, Deng SX. PMID: 36362184; PMCID: PMC9657819.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    190. Limited microbiome differences in captive and semi-wild primate populations consuming similar diets. FEMS Microbiol Ecol. 2022 10 03; 98(10). Kuthyar S, Watson K, Huang S, Brent LJN, Platt M, Horvath J, Gonzalez-Martinez J, Martínez M, Godoy-Vitorino F, Knight R, Dominguez-Bello MG, Amato KR. PMID: 36047944; PMCID: PMC9528791.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    191. The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps. Front Nutr. 2022; 9:987216. Hanes D, Nowinski B, Lamb JJ, Larson IA, McDonald D, Knight R, Song SJ, Patno N. PMID: 36245486; PMCID: PMC9559413.
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    192. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell. 2022 09 29; 185(20):3789-3806.e17. Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R. PMID: 36179670; PMCID: PMC9567272.
      View in: PubMed   Mentions: 271     Fields:    Translation:HumansAnimals
    193. Bayesian multivariate sparse functional principal components analysis with application to longitudinal microbiome multiomics data. Ann Appl Stat. 2022 Dec; 16(4):2231-2249. Jiang L, Elrod C, Kim JJ, Swafford AD, Knight R, Thompson WK. PMID: 40969773; PMCID: PMC12442853.
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    194. Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References. mSystems. 2022 10 26; 7(5):e0075822. Hakim D, Wandro S, Zengler K, Zaramela LS, Nowinski B, Swafford A, Zhu Q, Song SJ, Gonzalez A, McDonald D, Knight R. PMID: 36073806; PMCID: PMC9600373.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    195. Distinct interacting cortical networks for stimulus-response and repetition-suppression. Commun Biol. 2022 09 05; 5(1):909. Eckert D, Reichert C, Bien CG, Heinze HJ, Knight RT, Deouell LY, Dürschmid S. PMID: 36064744; PMCID: PMC9445181.
      View in: PubMed   Mentions: 1  Translation:Humans
    196. Location-specific signatures of Crohn's disease at a multi-omics scale. Microbiome. 2022 08 24; 10(1):133. Gonzalez CG, Mills RH, Zhu Q, Sauceda C, Knight R, Dulai PS, Gonzalez DJ. PMID: 35999575; PMCID: PMC9400277.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    197. Oral Progenitor Cell Line-Derived Small Extracellular Vesicles as a Treatment for Preferential Wound Healing Outcome. Stem Cells Transl Med. 2022 08 23; 11(8):861-875. Knight R, Board-Davies E, Brown H, Clayton A, Davis T, Karatas B, Burston J, Tabi Z, Falcon-Perez JM, Paisey S, Stephens P. PMID: 35716044; PMCID: PMC9397654.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    198. Acetate reprograms gut microbiota during alcohol consumption. Nat Commun. 2022 08 08; 13(1):4630. Martino C, Zaramela LS, Gao B, Embree M, Tarasova J, Parker SJ, Wang Y, Chu H, Chen P, Lee KC, Galzerani DD, Gengatharan JM, Lekbua A, Neal M, Knight R, Tsukamoto H, Metallo CM, Schnabl B, Zengler K. PMID: 35941112; PMCID: PMC9359997.
      View in: PubMed   Mentions: 49     Fields:    Translation:Animals
    199. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell. 2022 08 18; 185(17):3263-3277.e15. Russell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A. PMID: 35931082; PMCID: PMC9464905.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    200. Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol. 2022 12; 20(12):707-720. Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R. PMID: 35906422; PMCID: PMC12875531.
      View in: PubMed   Mentions: 116     Fields:    Translation:HumansAnimalsCells
    201. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. 2022 09; 609(7925):101-108. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. PMID: 35798029; PMCID: PMC9433318.
      View in: PubMed   Mentions: 211     Fields:    Translation:HumansCellsPHPublic Health
    202. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol. 2022 12; 40(12):1774-1779. Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. PMID: 35798960; PMCID: PMC10277029.
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    203. Deep brain stimulation of the ventrointermediate nucleus of the thalamus to treat essential tremor improves motor sequence learning. Hum Brain Mapp. 2022 10 15; 43(15):4791-4799. Terzic L, Voegtle A, Farahat A, Hartong N, Galazky I, Nasuto SJ, Andrade AO, Knight RT, Ivry RB, Voges J, Buentjen L, Sweeney-Reed CM. PMID: 35792001; PMCID: PMC9491285.
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    204. Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome. Cell Rep. 2022 07 05; 40(1):111008. Dantas Machado AC, Brown SD, Lingaraju A, Sivaganesh V, Martino C, Chaix A, Zhao P, Pinto AFM, Chang MW, Richter RA, Saghatelian A, Saltiel AR, Knight R, Panda S, Zarrinpar A. PMID: 35793637; PMCID: PMC9296000.
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    205. The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study. Int J Cancer. 2022 10 15; 151(8):1248-1260. Wu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA, Vogtmann E. PMID: 35657343; PMCID: PMC9420782.
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    206. Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nat Commun. 2022 06 27; 13(1):3665. Armingol E, Baghdassarian HM, Martino C, Perez-Lopez A, Aamodt C, Knight R, Lewis NE. PMID: 35760817; PMCID: PMC9237099.
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    207. The molecular impact of life in an indoor environment. Sci Adv. 2022 Jun 24; 8(25):eabn8016. Aksenov AA, Salido RA, Melnik AV, Brennan C, Brejnrod A, Caraballo-Rodríguez AM, Gauglitz JM, Lejzerowicz F, Farmer DK, Vance ME, Knight R, Dorrestein PC. PMID: 35749501; PMCID: PMC9232106.
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    208. A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques. 2022 06; 73(1):34-46. Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R. PMID: 35713407; PMCID: PMC9361692.
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    209. Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings. mSystems. 2022 08 30; 7(4):e0010922. Cantú VJ, Sanders K, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, De Hoff P, Eisner E, Hakim A, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Plascencia A, Sathe S, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R. PMID: 35703436; PMCID: PMC9426498.
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    210. Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings. mSystems. 2022 08 30; 7(4):e0010322. Cantú VJ, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Sanders K, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, Crescini ES, De Hoff P, Eisner E, Hakim A, Kapadia B, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Sathe S, Seaver P, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R. PMID: 35703437; PMCID: PMC9426517.
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    211. Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling. Genome Res. 2022 06; 32(6):1112-1123. Hu Y, Amir A, Huang X, Li Y, Huang S, Wolfe E, Weiss S, Knight R, Xu ZZ. PMID: 35688483; PMCID: PMC9248889.
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    212. Impact of exclusive enteral nutrition on the gut microbiome of children with medical complexity. JPEN J Parenter Enteral Nutr. 2023 01; 47(1):77-86. Beauchamp-Walters J, Aleti G, Herrera L, Debelius J, Lima N, Dalal P, Hong S, Knight R, Rhee KE. PMID: 35526141.
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    213. Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase. mSystems. 2022 06 28; 7(3):e0002822. Sfiligoi I, Armstrong G, Gonzalez A, McDonald D, Knight R. PMID: 35638356; PMCID: PMC9239203.
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    214. A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats. Front Neurosci. 2022; 16:889211. Bowers SJ, Summa KC, Thompson RS, González A, Vargas F, Olker C, Jiang P, Lowry CA, Dorrestein PC, Knight R, Wright KP, Fleshner M, Turek FW, Vitaterna MH. PMID: 35685770; PMCID: PMC9172596.
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    215. Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS. J Am Heart Assoc. 2022 05 17; 11(10):e023038. Goh CE, Bohn B, Marotz C, Molinsky R, Roy S, Paster BJ, Chen CY, Rosenbaum M, Yuzefpolskaya M, Colombo PC, Desvarieux M, Papapanou PN, Jacobs DR, Knight R, Demmer RT. PMID: 35574962; PMCID: PMC9238569.
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    216. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. mSystems. 2022 06 28; 7(3):e0141121. Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Casas Maya M, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Ostrander RT, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. PMID: 35575492; PMCID: PMC9239251.
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    217. Orbitofrontal cortex governs working memory for temporal order. Curr Biol. 2022 05 09; 32(9):R410-R411. Johnson EL, Chang WK, Dewar CD, Sorensen D, Lin JJ, Solbakk AK, Endestad T, Larsson PG, Ivanovic J, Meling TR, Scabini D, Knight RT. PMID: 35537388; PMCID: PMC9169582.
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    218. Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype. mSystems. 2022 06 28; 7(3):e0005022. Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, Knight R. PMID: 35477286; PMCID: PMC9238373.
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    219. Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS. NPJ Biofilms Microbiomes. 2022 04 20; 8(1):30. Marotz C, Molinsky R, Martino C, Bohn B, Roy S, Rosenbaum M, Desvarieux M, Yuzefpolskaya M, Paster BJ, Jacobs DR, Colombo PC, Papapanou PN, Knight R, Demmer RT. PMID: 35444197; PMCID: PMC9021254.
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    220. The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study). Sci Rep. 2022 04 19; 12(1):6437. Bai-Tong SS, Thoemmes MS, Weldon KC, Motazavi D, Kitsen J, Hansen S, Furst A, Geng B, Song SJ, Gilbert JA, Bode L, Dorrestein PC, Knight R, Leibel SA, Leibel SL. PMID: 35440708; PMCID: PMC9018729.
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    221. Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos. mSystems. 2022 06 28; 7(3):e0027322. Peters BA, Lin J, Qi Q, Usyk M, Isasi CR, Mossavar-Rahmani Y, Derby CA, Santoro N, Perreira KM, Daviglus ML, Kominiarek MA, Cai J, Knight R, Burk RD, Kaplan RC. PMID: 35675542; PMCID: PMC9239235.
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    222. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems. 2022 04 26; 7(2):e0016722. Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. PMID: 35369727; PMCID: PMC9040630.
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    223. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv. 2022 Apr 04. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. PMID: 35411350; PMCID: PMC8996633.
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    224. Correction to: Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. ISME J. 2022 Apr; 16(4):1201. Zhu Q, Hou Q, Huang S, Ou Q, Huo D, Vázquez-Baeza Y, Cen C, Cantu V, Estaki M, Chang H, Belda-Ferre P, Kim HC, Chen K, Knight R, Zhang J. PMID: 35042975; PMCID: PMC8941144.
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    225. Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting. Cell Metab. 2022 05 03; 34(5):719-730.e4. Liu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vázquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M. PMID: 35354069; PMCID: PMC9097589.
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    226. Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases. mSystems. 2022 04 26; 7(2):e0137821. Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. PMID: 35293792; PMCID: PMC9040843.
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    227. Age-specific survival rates, causes of death, and allowable take of golden eagles in the western United States. Ecol Appl. 2022 04; 32(3):e2544. Millsap BA, Zimmerman GS, Kendall WL, Barnes JG, Braham MA, Bedrosian BE, Bell DA, Bloom PH, Crandall RH, Domenech R, Driscoll D, Duerr AE, Gerhardt R, Gibbs SEJ, Harmata AR, Jacobson K, Katzner TE, Knight RN, Lockhart JM, McIntyre C, Murphy RK, Slater SJ, Smith BW, Smith JP, Stahlecker DW, Watson JW. PMID: 35080801; PMCID: PMC9286660.
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    228. Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides. BMC Microbiol. 2022 03 14; 22(1):75. Aleti G, Kohn JN, Troyer EA, Weldon K, Huang S, Tripathi A, Dorrestein PC, Swafford AD, Knight R, Hong S. PMID: 35287577; PMCID: PMC8919597.
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    229. Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays. 2022 05; 44(5):e2100252. Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. PMID: 35253252; PMCID: PMC10506734.
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    230. Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. Front Bioinform. 2022; 2:821861. Armstrong G, Rahman G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R. PMID: 36304280; PMCID: PMC9580878.
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    231. The Gut Microbiome Modifies the Association Between a Mediterranean Diet and Diabetes in USA Hispanic/ Latino Population. J Clin Endocrinol Metab. 2022 02 17; 107(3):e924-e934. Wang DD, Qi Q, Wang Z, Usyk M, Sotres-Alvarez D, Mattei J, Tamez M, Gellman MD, Daviglus M, Hu FB, Stampfer MJ, Huttenhower C, Knight R, Burk RD, Kaplan RC. PMID: 34747479; PMCID: PMC8851916.
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    232. Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians. Mol Ecol. 2022 04; 31(7):2140-2156. Chen MY, Kueneman JG, González A, Humphrey G, Knight R, McKenzie VJ. PMID: 35076975.
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    233. Consciousness is supported by near-critical slow cortical electrodynamics. Proc Natl Acad Sci U S A. 2022 02 15; 119(7). Toker D, Pappas I, Lendner JD, Frohlich J, Mateos DM, Muthukumaraswamy S, Carhart-Harris R, Paff M, Vespa PM, Monti MM, Sommer FT, Knight RT, D'Esposito M. PMID: 35145021; PMCID: PMC8851554.
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    234. A gut-derived metabolite alters brain activity and anxiety behaviour in mice. Nature. 2022 02; 602(7898):647-653. Needham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geschwind DH, Holschneider DP, Fischbach MA, Mazmanian SK. PMID: 35165440; PMCID: PMC9170029.
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    235. Event segmentation reveals working memory forgetting rate. iScience. 2022 Mar 18; 25(3):103902. Jafarpour A, Buffalo EA, Knight RT, Collins AGE. PMID: 35252809; PMCID: PMC8891967.
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    236. A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am J Clin Nutr. 2022 02 09; 115(2):432-443. Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P. PMID: 34617562; PMCID: PMC8827078.
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    237. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nat Genet. 2022 02; 54(2):134-142. Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brozynska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G. PMID: 35115689; PMCID: PMC9883041.
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    238. Using All Our Genomes: Blood-based Liquid Biopsies for the Early Detection of Cancer. View (Beijing). 2022 Jan; 3(1). Adams E, Sepich-Poore GD, Miller-Montgomery S, Knight R. PMID: 35872970; PMCID: PMC9307139.
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    239. Imagined speech can be decoded from low- and cross-frequency intracranial EEG features. Nat Commun. 2022 01 10; 13(1):48. Proix T, Delgado Saa J, Christen A, Martin S, Pasley BN, Knight RT, Tian X, Poeppel D, Doyle WK, Devinsky O, Arnal LH, Mégevand P, Giraud AL. PMID: 35013268; PMCID: PMC8748882.
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    240. Stool multi-omics for the study of host-microbe interactions in inflammatory bowel disease. Gut Microbes. 2022 Jan-Dec; 14(1):2154092. Sauceda C, Bayne C, Sudqi K, Gonzalez A, Dulai PS, Knight R, Gonzalez DJ, Gonzalez CG. PMID: 36503356; PMCID: PMC9746627.
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    241. Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection. Female Pelvic Med Reconstr Surg. 2022 01 01; 28(1):20-26. Jung CE, Estaki M, Chopyk J, Taylor BC, Gonzalez A, McDonald D, Shin J, Ferrante K, Wasenda E, Lippmann Q, Knight R, Pride D, Lukacz ES. PMID: 33978602.
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    242. Antigen Receptor T Cells (CAR-T) Effectively Control Tumor Growth in a Colorectal Liver Metastasis Model. J Surg Res. 2022 04; 272:37-50. Chai LF, Hardaway JC, Heatherton KR, O'Connell KP, LaPorte JP, Guha P, Lopes MC, Rabinowitz BA, Jaroch D, Cox BF, Knight R, Katz SC. PMID: 34929499.
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    243. Class Ib MHC-Mediated Immune Interactions Play a Critical Role in Maintaining Mucosal Homeostasis in the Mammalian Large Intestine. Immunohorizons. 2021 12 15; 5(12):953-971. Dasgupta S, Maricic I, Tang J, Wandro S, Weldon K, Carpenter CS, Eckmann L, Rivera-Nieves J, Sandborn W, Knight R, Dorrestein P, Swafford AD, Kumar V. PMID: 34911745; PMCID: PMC10026853.
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    244. Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity. Genome Biol. 2021 12 10; 22(1):336. Wang Z, Usyk M, Vázquez-Baeza Y, Chen GC, Isasi CR, Williams-Nguyen JS, Hua S, McDonald D, Thyagarajan B, Daviglus ML, Cai J, North KE, Wang T, Knight R, Burk RD, Kaplan RC, Qi Q. PMID: 34893089; PMCID: PMC8665519.
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    245. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. medRxiv. 2021 Dec 07. Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Maya MC, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Ostrander RT, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. PMID: 34909793; PMCID: PMC8669860.
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    246. Clean room microbiome complexity impacts planetary protection bioburden. Microbiome. 2021 12 04; 9(1):238. Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. PMID: 34861887; PMCID: PMC8643001.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    247. The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder. mSystems. 2021 Dec 21; 6(6):e0100621. Dilmore AH, McDonald D, Nguyen TT, Adams JB, Krajmalnik-Brown R, Elijah E, Dorrestein PC, Knight R. PMID: 34846164; PMCID: PMC8631314.
      View in: PubMed   Mentions: 8     Fields:    
    248. Redrawing therapeutic boundaries: microbiota and cancer. Trends Cancer. 2022 02; 8(2):87-97. Sholl J, Sepich-Poore GD, Knight R, Pradeu T. PMID: 34844910; PMCID: PMC8770609.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    249. Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts. BMC Microbiol. 2021 11 22; 21(1):324. Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R, Vogtmann E. PMID: 34809575; PMCID: PMC8607576.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    250. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892. Mirzayi C, Renson A, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. PMID: 34789871; PMCID: PMC9105086.
      View in: PubMed   Mentions: 224     Fields:    Translation:Humans
    251. Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs. mSystems. 2021 Dec 21; 6(6):e0113621. Salido RA, Cantú VJ, Clark AE, Leibel SL, Foroughishafiei A, Saha A, Hakim A, Nouri A, Lastrella AL, Castro-Martínez A, Plascencia A, Kapadia BK, Xia B, Ruiz CA, Marotz CA, Maunder D, Lawrence ES, Smoot EW, Eisner E, Crescini ES, Kohn L, Franco Vargas L, Chacón M, Betty M, Machnicki M, Wu MY, Baer NA, Belda-Ferre P, De Hoff P, Seaver P, Ostrander RT, Tsai R, Sathe S, Aigner S, Morgan SC, Ngo TT, Barber T, Cheung W, Carlin AF, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. PMID: 34726486; PMCID: PMC8562474.
      View in: PubMed   Mentions: 12     Fields:    
    252. Skin inflammation activates intestinal stromal fibroblasts and promotes colitis. J Clin Invest. 2021 11 01; 131(21). Dokoshi T, Seidman JS, Cavagnero KJ, Li F, Liggins MC, Taylor BC, Olvera J, Knight R, Chang JT, Salzman NH, Gallo RL. PMID: 34720087; PMCID: PMC8553570.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    253. Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2. ACS Sens. 2021 11 26; 6(11):3957-3966. Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS. PMID: 34714054.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    254. Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data. mSystems. 2021 Oct 26; 6(5):e0069121. Armstrong G, Martino C, Rahman G, Gonzalez A, Vázquez-Baeza Y, Mishne G, Knight R. PMID: 34609167; PMCID: PMC8547469.
      View in: PubMed   Mentions: 45     Fields:    
    255. Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases. Biomedicines. 2021 Sep 24; 9(10). Lam S, Hartmann N, Benfeitas R, Zhang C, Arif M, Turkez H, Uhlén M, Englert C, Knight R, Mardinoglu A. PMID: 34680427; PMCID: PMC8533098.
      View in: PubMed   Mentions: 10  
    256. Markers of Gut Barrier Function and Microbial Translocation Associate with Lower Gut Microbial Diversity in People with HIV. Viruses. 2021 09 22; 13(10). Ellis RJ, Iudicello JE, Heaton RK, Isnard S, Lin J, Routy JP, Gianella S, Hoenigl M, Knight R. PMID: 34696320; PMCID: PMC8537977.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    257. Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma. Microorganisms. 2021 Sep 22; 9(10). Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. PMID: 34683324; PMCID: PMC8541168.
      View in: PubMed   Mentions: 6  
    258. Reduced Gut Microbiome Diversity in People With HIV Who Have Distal Neuropathic Pain. J Pain. 2022 02; 23(2):318-325. Ellis RJ, Heaton RK, Gianella S, Rahman G, Knight R. PMID: 34530155; PMCID: PMC9854399.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    259. Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. Genome Res. 2021 11; 31(11):2131-2137. Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck KL, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R. PMID: 34479875; PMCID: PMC8559715.
      View in: PubMed   Mentions: 20     Fields:    
    260. Automatic Sensory Predictions: A Review of Predictive Mechanisms in the Brain and Their Link to Conscious Processing. Front Hum Neurosci. 2021; 15:702520. Tivadar RI, Knight RT, Tzovara A. PMID: 34489663; PMCID: PMC8416526.
      View in: PubMed   Mentions: 11  
    261. Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus. mSystems. 2021 Aug 31; 6(4):e0079321. Karthikeyan S, Nguyen A, McDonald D, Zong Y, Ronquillo N, Ren J, Zou J, Farmer S, Humphrey G, Henderson D, Javidi T, Messer K, Anderson C, Schooley R, Martin NK, Knight R. PMID: 34374562; PMCID: PMC8409724.
      View in: PubMed   Mentions: 81     Fields:    
    262. Associations of healthy food choices with gut microbiota profiles. Am J Clin Nutr. 2021 08 02; 114(2):605-616. Koponen KK, Salosensaari A, Ruuskanen MO, Havulinna AS, Männistö S, Jousilahti P, Palmu J, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Meric G, Cheng S, Inouye M, Jain M, Niiranen TJ, Valsta LM, Knight R, Salomaa VV. PMID: 34020448; PMCID: PMC8326043.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    263. Prefrontal Lesions Disrupt Posterior Alpha-Gamma Coordination of Visual Working Memory Representations. J Cogn Neurosci. 2021 08 01; 33(9):1798-1810. Davoudi S, Parto Dezfouli M, Knight RT, Daliri MR, Johnson EL. PMID: 34375418; PMCID: PMC8428813.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    264. Detection criteria and post-field sample processing influence results and cost efficiency of occupancy-based monitoring. Ecol Appl. 2021 10; 31(7):e02404. Lonsinger RC, Knight RN, Waits LP. PMID: 34231272.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    265. Emergence of an early SARS-CoV-2 epidemic in the United States. Cell. 2021 09 16; 184(19):4939-4952.e15. Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. PMID: 34508652; PMCID: PMC8313480.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCellsPHPublic Health
    266. Single-trial modeling separates multiple overlapping prediction errors during reward processing in human EEG. Commun Biol. 2021 07 23; 4(1):910. Hoy CW, Steiner SC, Knight RT. PMID: 34302057; PMCID: PMC8302587.
      View in: PubMed   Mentions: 24  Translation:Humans
    267. Nutritional Interventions and the Gut Microbiome in Children. Annu Rev Nutr. 2021 10 11; 41:479-510. Mehta S, Huey SL, McDonald D, Knight R, Finkelstein JL. PMID: 34283919.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    268. Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. bioRxiv. 2021 Jul 19. Salido RA, Cantú VJ, Clark AE, Leibel SL, Foroughishafiei A, Saha A, Hakim A, Nouri A, Lastrella AL, Castro-Martínez A, Plascencia A, Kapadia B, Xia B, Ruiz C, Marotz CA, Maunder D, Lawrence ES, Smoot EW, Eisner E, Crescini ES, Kohn L, Vargas LF, Chacón M, Betty M, Machnicki M, Wu MY, Baer NA, Belda-Ferre P, Hoff P, Seaver P, Ostrander RT, Tsai R, Sathe S, Aigner S, Morgan SC, Ngo TT, Barber T, Cheung W, Carlin AF, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. PMID: 34312621; PMCID: PMC8312891.
      View in: PubMed   Mentions:
    269. The microbiome and prostate cancer. Prostate Cancer Prostatic Dis. 2022 02; 25(2):159-164. Javier-DesLoges J, McKay RR, Swafford AD, Sepich-Poore GD, Knight R, Parsons JK. PMID: 34267333; PMCID: PMC8767983.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    270. A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere. 2021 08 25; 6(4):e0045521. Deel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL. PMID: 34259562; PMCID: PMC8386422.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansPHPublic Health
    271. A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity. mSystems. 2021 Aug 31; 6(4):e0039421. Jing G, Zhang Y, Liu L, Wang Z, Sun Z, Knight R, Su X, Xu J. PMID: 34254819; PMCID: PMC8407412.
      View in: PubMed   Mentions: 6     Fields:    
    272. Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms. Brain Behav Immun. 2021 10; 97:150-166. Thompson RS, Gaffney M, Hopkins S, Kelley T, Gonzalez A, Bowers SJ, Vitaterna MH, Turek FW, Foxx CL, Lowry CA, Vargas F, Dorrestein PC, Wright KP, Knight R, Fleshner M. PMID: 34242738.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    273. Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome. Microbiome. 2021 06 30; 9(1):151. Huang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Belda-Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li C, Zarrinpar A, Liu YY, Knight R, Zhang J. PMID: 34193290; PMCID: PMC8247228.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    274. Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome. mSystems. 2021 Jun 29; 6(3):101128msystems0011621. Allaband C, Lingaraju A, Martino C, Russell B, Tripathi A, Poulsen O, Dantas Machado AC, Zhou D, Xue J, Elijah E, Malhotra A, Dorrestein PC, Knight R, Haddad GG, Zarrinpar A. PMID: 34184915; PMCID: PMC8269208.
      View in: PubMed   Mentions: 27     Fields:    
    275. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput Biol. 2021 06; 17(6):e1009056. Dillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, Simard A, Vázquez-Baeza Y, Ziemski M, Miwa HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler BD, Cope EK, Metcalf JL, Robeson Ii MS, Bokulich NA, Caporaso JG. PMID: 34166363; PMCID: PMC8224931.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    276. Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding. Med. 2021 08 13; 2(8):951-964.e5. Song SJ, Wang J, Martino C, Jiang L, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N, Ackley E, Nardella D, Gillihan C, Montacuti V, Schweizer W, Jay M, Combellick J, Sun H, Garcia-Mantrana I, Gil Raga F, Collado MC, Rivera-Viñas JI, Campos-Rivera M, Ruiz-Calderon JF, Knight R, Dominguez-Bello MG. PMID: 35590169; PMCID: PMC9123283.
      View in: PubMed   Mentions: 49     Fields:    Translation:Humans
    277. Aperiodic sleep networks promote memory consolidation. Trends Cogn Sci. 2021 08; 25(8):648-659. Helfrich RF, Lendner JD, Knight RT. PMID: 34127388; PMCID: PMC9017392.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    278. Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. ISME J. 2021 11; 15(11):3399-3411. Zhu Q, Hou Q, Huang S, Ou Q, Huo D, Vázquez-Baeza Y, Cen C, Cantu V, Estaki M, Chang H, Belda-Ferre P, Kim HC, Chen K, Knight R, Zhang J. PMID: 34079079; PMCID: PMC8528855.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    279. Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos. Am J Clin Nutr. 2021 06 01; 113(6):1503-1514. Mei Z, Chen GC, Wang Z, Usyk M, Yu B, Baeza YV, Humphrey G, Benitez RS, Li J, Williams-Nguyen JS, Daviglus ML, Hou L, Cai J, Zheng Y, Knight R, Burk RD, Boerwinkle E, Kaplan RC, Qi Q. PMID: 33709132; PMCID: PMC8168354.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansPHPublic Health
    280. Nonalcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet. Cell Mol Gastroenterol Hepatol. 2021; 12(3):891-920. Ganguly S, Muench GA, Shang L, Rosenthal SB, Rahman G, Wang R, Wang Y, Kwon HC, Diomino AM, Kisseleva T, Soorosh P, Hosseini M, Knight R, Schnabl B, Brenner DA, Dhar D. PMID: 34062281; PMCID: PMC8342972.
      View in: PubMed   Mentions: 29     Fields:    Translation:Animals
    281. Individuals with substance use disorders have a distinct oral microbiome pattern. Brain Behav Immun Health. 2021 Aug; 15:100271. Kosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G, Tulsa 1000 Investigators, Knight R, Paulus MP. PMID: 34589776; PMCID: PMC8474247.
      View in: PubMed   Mentions: 8  
    282. Structure-based protein function prediction using graph convolutional networks. Nat Commun. 2021 05 26; 12(1):3168. Gligorijevic V, Renfrew PD, Kosciolek T, Leman JK, Berenberg D, Vatanen T, Chandler C, Taylor BC, Fisk IM, Vlamakis H, Xavier RJ, Knight R, Cho K, Bonneau R. PMID: 34039967; PMCID: PMC8155034.
      View in: PubMed   Mentions: 345     Fields:    Translation:Cells
    283. Coupling between slow waves and sharp-wave ripples engages distributed neural activity during sleep in humans. Proc Natl Acad Sci U S A. 2021 05 25; 118(21). Skelin I, Zhang H, Zheng J, Ma S, Mander BA, Kim McManus O, Vadera S, Knight RT, McNaughton BL, Lin JJ. PMID: 34001599; PMCID: PMC8166184.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    284. Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. Biometrics. 2022 09; 78(3):1155-1167. Jiang L, Haiminen N, Carrieri AP, Huang S, Vázquez-Baeza Y, Parida L, Kim HC, Swafford AD, Knight R, Natarajan L. PMID: 33914902; PMCID: PMC9787628.
      View in: PubMed   Mentions: 4     Fields:    
    285. Electrophysiological Decoding of Spatial and Color Processing in Human Prefrontal Cortex. Neuroimage. 2021 08 15; 237:118165. Min BK, Kim HS, Ko W, Ahn MH, Suk HI, Pantazis D, Knight RT. PMID: 34000400; PMCID: PMC8344402.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    286. Challenges in benchmarking metagenomic profilers. Nat Methods. 2021 06; 18(6):618-626. Sun Z, Huang S, Zhang M, Zhu Q, Haiminen N, Carrieri AP, Vázquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YY. PMID: 33986544; PMCID: PMC8184642.
      View in: PubMed   Mentions: 75     Fields:    
    287. Taxonomic signatures of cause-specific mortality risk in human gut microbiome. Nat Commun. 2021 05 11; 12(1):2671. Salosensaari A, Laitinen V, Havulinna AS, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen T. PMID: 33976176; PMCID: PMC8113604.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCellsPHPublic Health
    288. Intratumoral bacteria generate a new class of therapeutically relevant tumor antigens in melanoma. Cancer Cell. 2021 05 10; 39(5):601-603. Sepich-Poore GD, Carter H, Knight R. PMID: 33974857.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    289. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME J. 2021 10; 15(10):3005-3018. Jiao JY, Fu L, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ. PMID: 33953361; PMCID: PMC8443620.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    290. Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res. 2021 May; 31(5):934. Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. PMID: 33941606; PMCID: PMC8092014.
      View in: PubMed   Mentions:    Fields:    
    291. Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition. mSystems. 2021 Apr 27; 6(2). Marotz C, Cavagnero KJ, Song SJ, McDonald D, Wandro S, Humphrey G, Bryant M, Ackermann G, Diaz E, Knight R. PMID: 33906915; PMCID: PMC8092129.
      View in: PubMed   Mentions: 37     Fields:    
    292. Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome. Front Physiol. 2021; 12:663950. Xue J, Allaband C, Zhou D, Poulsen O, Martino C, Jiang L, Tripathi A, Elijah E, Dorrestein PC, Knight R, Zarrinpar A, Haddad GG. PMID: 33897472; PMCID: PMC8060652.
      View in: PubMed   Mentions: 20  
    293. The microbiome and human cancer. Science. 2021 03 26; 371(6536). Sepich-Poore GD, Zitvogel L, Straussman R, Hasty J, Wargo JA, Knight R. PMID: 33766858; PMCID: PMC8767999.
      View in: PubMed   Mentions: 665     Fields:    Translation:HumansCells
    294. EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. mSystems. 2021 Mar 16; 6(2). Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R. PMID: 33727399; PMCID: PMC8546999.
      View in: PubMed   Mentions: 37     Fields:    
    295. The role of the anterior nuclei of the thalamus in human memory processing. Neurosci Biobehav Rev. 2021 07; 126:146-158. Sweeney-Reed CM, Buentjen L, Voges J, Schmitt FC, Zaehle T, Kam JWY, Kaufmann J, Heinze HJ, Hinrichs H, Knight RT, Rugg MD. PMID: 33737103.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimals
    296. Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) screening among symptom-free healthcare workers. Infect Control Hosp Epidemiol. 2022 05; 43(5):657-660. Demmer RT, Ulrich AK, Wiggen TD, Strickland A, Naumchik BM, Kulasingam S, Stovitz SD, Marotz C, Belda-Ferre P, Humphrey G, De Hoff P, Laurent L, Kline S, Knight R. PMID: 33706827; PMCID: PMC8185420.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCellsPHPublic Health
    297. Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing. Environ Sci Technol. 2021 04 20; 55(8):4899-4913. Bhagwat G, Zhu Q, O'Connor W, Subashchandrabose S, Grainge I, Knight R, Palanisami T. PMID: 33686859.
      View in: PubMed   Mentions: 18     Fields:    Translation:CellsPHPublic Health
    298. High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County. mSystems. 2021 Mar 02; 6(2). Karthikeyan S, Ronquillo N, Belda-Ferre P, Alvarado D, Javidi T, Longhurst CA, Knight R. PMID: 33653938; PMCID: PMC8546963.
      View in: PubMed   Mentions: 79     Fields:    
    299. Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study. Int J Cancer. 2021 06 01; 148(11):2712-2723. Byrd DA, Vogtmann E, Wu Z, Han Y, Wan Y, Clegg-Lamptey JN, Yarney J, Wiafe-Addai B, Wiafe S, Awuah B, Ansong D, Nyarko K, Hullings AG, Hua X, Ahearn T, Goedert JJ, Shi J, Knight R, Figueroa JD, Brinton LA, Garcia-Closas M, Sinha R. PMID: 33460452; PMCID: PMC8386185.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    300. Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the ApcMin/+ mouse model. Int J Cancer. 2021 May 15; 148(10):2594-2607. Jala VR, Bodduluri SR, Ghosh S, Chheda Z, Singh R, Smith ME, Chilton PM, Fleming CJ, Mathis SP, Sharma RK, Knight R, Yan J, Haribabu B. PMID: 33497467.
      View in: PubMed   Mentions: 7     Fields:    
    301. Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load. mSystems. 2021 Feb 16; 6(1). Marotz C, Morton JT, Navarro P, Coker J, Belda-Ferre P, Knight R, Zengler K. PMID: 33594005; PMCID: PMC8561659.
      View in: PubMed   Mentions: 23     Fields:    
    302. Prefrontal lesions disrupt oscillatory signatures of spatiotemporal integration in working memory. Cortex. 2021 05; 138:113-126. Parto Dezfouli M, Davoudi S, Knight RT, Daliri MR, Johnson EL. PMID: 33684625; PMCID: PMC8058286.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    303. Characterizing multi-word speech production using event-related potentials. Psychophysiology. 2021 05; 58(5):e13788. Ries SK, Pinet S, Nozari NB, Knight RT. PMID: 33569829; PMCID: PMC8193832.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    304. Emergence of an early SARS-CoV-2 epidemic in the United States. medRxiv. 2021 Feb 08. Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. PMID: 33564781; PMCID: PMC7872376.
      View in: PubMed   Mentions:
    305. Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. medRxiv. 2021 Feb 07. Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Barrett KMS, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu C, Suchard MA, Lu JT, Lee W, Andersen KG. PMID: 33564780; PMCID: PMC7872373.
      View in: PubMed   Mentions:
    306. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Biotechniques. 2021 03; 70(3):149-159. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33512248; PMCID: PMC7931620.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    307. Distinct electrophysiological signatures of task-unrelated and dynamic thoughts. Proc Natl Acad Sci U S A. 2021 01 26; 118(4). Kam JWY, Irving ZC, Mills C, Patel S, Gopnik A, Knight RT. PMID: 33468671; PMCID: PMC7848609.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    308. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021 01 22; 9(1):25. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 33482920; PMCID: PMC7821463.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    309. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat Methods. 2021 02; 18(2):165-169. Karst SM, Ziels RM, Kirkegaard RH, Sørensen EA, McDonald D, Zhu Q, Knight R, Albertsen M. PMID: 33432244.
      View in: PubMed   Mentions: 195     Fields:    
    310. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 2021 01 09; 10(1). Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Pogliano J, Nizet V, Feist AM, Palsson BO. PMID: 33420779; PMCID: PMC7794652.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    311. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Mar Drugs. 2021 Jan 06; 19(1). Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L. PMID: 33418911; PMCID: PMC7825088.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    312. Top-Down Attentional Modulation in Human Frontal Cortex: Differential Engagement during External and Internal Attention. Cereb Cortex. 2021 01 05; 31(2):873-883. Kam JWY, Helfrich RF, Solbakk AK, Endestad T, Larsson PG, Lin JJ, Knight RT. PMID: 33063100; PMCID: PMC7786361.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    313. Reply to: Examining microbe-metabolite correlations by linear methods. Nat Methods. 2021 01; 18(1):40-41. Morton JT, McDonald D, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. PMID: 33398188.
      View in: PubMed   Mentions: 4     Fields:    
    314. Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics. Methods Mol Biol. 2021; 2327:87-92. Marotz C, Zuniga C, Zaramela L, Knight R, Zengler K. PMID: 34410641.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    315. Links between gut microbiome composition and fatty liver disease in a large population sample. Gut Microbes. 2021 Jan-Dec; 13(1):1-22. Ruuskanen MO, Åberg F, Männistö V, Havulinna AS, Méric G, Liu Y, Loomba R, Vázquez-Baeza Y, Tripathi A, Valsta LM, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ. PMID: 33651661; PMCID: PMC7928040.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    316. Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. Gut Microbes. 2021 Jan-Dec; 13(1):1961203. Alderete TL, Jones RB, Shaffer JP, Holzhausen EA, Patterson WB, Kazemian E, Chatzi L, Knight R, Plows JF, Berger PK, Goran MI. PMID: 34424832; PMCID: PMC8386720.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    317. Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota. ISME J. 2021 05; 15(5):1359-1371. Sabey KA, Song SJ, Jolles A, Knight R, Ezenwa VO. PMID: 33328653; PMCID: PMC8115229.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    318. Frontotemporal Regulation of Subjective Value to Suppress Impulsivity in Intertemporal Choices. J Neurosci. 2021 02 24; 41(8):1727-1737. Dürschmid S, Maric A, Kehl MS, Knight RT, Hinrichs H, Heinze HJ. PMID: 33334869; PMCID: PMC8115895.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    319. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Res Sq. 2020 Dec 15. Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32839765; PMCID: PMC7444291.
      View in: PubMed   Mentions:
    320. Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection. J Exp Med. 2020 12 07; 217(12). Labarta-Bajo L, Nilsen SP, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Turner JR, Zúñiga EI. PMID: 32880630; PMCID: PMC7953738.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    321. Vitamin D metabolites and the gut microbiome in older men. Nat Commun. 2020 11 26; 11(1):5997. Thomas RL, Jiang L, Adams JS, Xu ZZ, Shen J, Janssen S, Ackermann G, Vanderschueren D, Pauwels S, Knight R, Orwoll ES, Kado DM. PMID: 33244003; PMCID: PMC7693238.
      View in: PubMed   Mentions: 73     Fields:    Translation:Humans
    322. Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. Genome Res. 2021 01; 31(1):64-74. Baker JL, Morton JT, Dinis M, Alvarez R, Tran NC, Knight R, Edlund A. PMID: 33239396; PMCID: PMC7849383.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansCells
    323. Parameterizing neural power spectra into periodic and aperiodic components. Nat Neurosci. 2020 12; 23(12):1655-1665. Donoghue T, Haller M, Peterson EJ, Varma P, Sebastian P, Gao R, Noto T, Lara AH, Wallis JD, Knight RT, Shestyuk A, Voytek B. PMID: 33230329; PMCID: PMC8106550.
      View in: PubMed   Mentions: 857     Fields:    Translation:HumansAnimals
    324. Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease. Proc Natl Acad Sci U S A. 2020 12 08; 117(49):31259-31266. Yueh MF, He F, Chen C, Vu C, Tripathi A, Knight R, Karin M, Chen S, Tukey RH. PMID: 33229553; PMCID: PMC7733785.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    325. Cell Tracking Profiler - a user-driven analysis framework for evaluating 4D live-cell imaging data. J Cell Sci. 2020 11 23; 133(22). Mitchell C, Caroff L, Solis-Lemus JA, Reyes-Aldasoro CC, Vigilante A, Warburton F, de Chaumont F, Dufour A, Dallongeville S, Olivo-Marin JC, Knight R. PMID: 33093241; PMCID: PMC7710012.
      View in: PubMed   Mentions:
    326. SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers. medRxiv. 2020 Nov 14. Demmer RT, Ulrich AK, Wiggen TD, Strickland A, Naumchik BM, Kulasingam S, Stovitz SD, Marotz C, Belda-Ferre P, Humphrey G, De Hoff P, Laurent L, Kline S, Knight R. PMID: 32793921; PMCID: PMC7418736.
      View in: PubMed   Mentions:
    327. Host variables confound gut microbiota studies of human disease. Nature. 2020 11; 587(7834):448-454. Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y. PMID: 33149306; PMCID: PMC7677204.
      View in: PubMed   Mentions: 300     Fields:    Translation:Humans
    328. Expanding magnetic organelle biogenesis in the domain Bacteria. Microbiome. 2020 10 30; 8(1):152. Lin W, Zhang W, Paterson GA, Zhu Q, Zhao X, Knight R, Bazylinski DA, Roberts AP, Pan Y. PMID: 33126926; PMCID: PMC7602337.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    329. Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients. mSystems. 2020 Oct 29; 5(6). Salido RA, Morgan SC, Rojas MI, Magallanes CG, Marotz C, DeHoff P, Belda-Ferre P, Aigner S, Kado DM, Yeo GW, Gilbert JA, Laurent L, Rohwer F, Knight R. PMID: 33127739; PMCID: PMC7743156.
      View in: PubMed   Mentions: 7     Fields:    
    330. Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk. Brain Behav Immun. 2021 01; 91:245-256. Nguyen TT, Kosciolek T, Daly RE, Vázquez-Baeza Y, Swafford A, Knight R, Jeste DV. PMID: 33098964; PMCID: PMC8023565.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    331. A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2. medRxiv. 2020 Oct 20. Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS. PMID: 33106816; PMCID: PMC7587836.
      View in: PubMed   Mentions:
    332. Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV. mSystems. 2020 Oct 13; 5(5). Taylor BC, Weldon KC, Ellis RJ, Franklin D, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Iudicello J, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. PMID: 33051377; PMCID: PMC7567581.
      View in: PubMed   Mentions: 4     Fields:    
    333. Early-life gut dysbiosis linked to juvenile mortality in ostriches. Microbiome. 2020 10 12; 8(1):147. Videvall E, Song SJ, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK. PMID: 33046114; PMCID: PMC7552511.
      View in: PubMed   Mentions: 27     Fields:    Translation:Animals
    334. Insights into human cognition from intracranial EEG: A review of audition, memory, internal cognition, and causality. J Neural Eng. 2020 10 08; 17(5):051001. Johnson EL, Kam JWY, Tzovara A, Knight RT. PMID: 32916678; PMCID: PMC7731730.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimals
    335. Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic. mSystems. 2020 Oct 06; 5(5). Vrbanac A, Patras KA, Jarmusch AK, Mills RH, Shing SR, Quinn RA, Vargas F, Gonzalez DJ, Dorrestein PC, Knight R, Nizet V. PMID: 33024048; PMCID: PMC7542558.
      View in: PubMed   Mentions: 6     Fields:    
    336. Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry. Gastroenterology. 2021 01; 160(1):183-192.e3. Kelly CR, Yen EF, Grinspan AM, Kahn SA, Atreja A, Lewis JD, Moore TA, Rubin DT, Kim AM, Serra S, Nersesova Y, Fredell L, Hunsicker D, McDonald D, Knight R, Allegretti JR, Pekow J, Absah I, Hsu R, Vincent J, Khanna S, Tangen L, Crawford CV, Mattar MC, Chen LA, Fischer M, Arsenescu RI, Feuerstadt P, Goldstein J, Kerman D, Ehrlich AC, Wu GD, Laine L. PMID: 33011173; PMCID: PMC8034505.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansCells
    337. Diverse Temporal Dynamics of Repetition Suppression Revealed by Intracranial Recordings in the Human Ventral Temporal Cortex. Cereb Cortex. 2020 10 01; 30(11):5988-6003. Rangarajan V, Jacques C, Knight RT, Weiner KS, Grill-Spector K. PMID: 32583847; PMCID: PMC7732032.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    338. Leveling up citizen science. Nat Biotechnol. 2020 10; 38(10):1124-1126. Waldispühl J, Szantner A, Knight R, Caisse S, Pitchford R. PMID: 32973359.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    339. A Distinct Microbiome Signature in Posttreatment Lyme Disease Patients. mBio. 2020 09 29; 11(5). Morrissette M, Pitt N, González A, Strandwitz P, Caboni M, Rebman AW, Knight R, D'Onofrio A, Aucott JN, Soloski MJ, Lewis K. PMID: 32994327; PMCID: PMC7527730.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    340. Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020 Sep 29; 5(5). Taylor BC, Weldon KC, Ellis RJ, Franklin D, Groth T, Gentry EC, Tripathi A, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Oliveira MF, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. PMID: 32994287; PMCID: PMC7527136.
      View in: PubMed   Mentions: 11     Fields:    
    341. Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. Cell. 2020 10 29; 183(3):666-683.e17. Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S. PMID: 32991841; PMCID: PMC7521382.
      View in: PubMed   Mentions: 216     Fields:    Translation:HumansAnimalsCells
    342. Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India. mSphere. 2020 09 23; 5(5). Huey SL, Jiang L, Fedarko MW, McDonald D, Martino C, Ali F, Russell DG, Udipi SA, Thorat A, Thakker V, Ghugre P, Potdar RD, Chopra H, Rajagopalan K, Haas JD, Finkelstein JL, Knight R, Mehta S. PMID: 32968008; PMCID: PMC7568645.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    343. CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection. Proc Natl Acad Sci U S A. 2020 10 06; 117(40):24998-25007. Labarta-Bajo L, Gramalla-Schmitz A, Gerner RR, Kazane KR, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Raffatellu M, Zúñiga EI. PMID: 32958643; PMCID: PMC7547153.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    344. Direct brain recordings reveal occipital cortex involvement in memory development. Neuropsychologia. 2020 11; 148:107625. Yin Q, Johnson EL, Tang L, Auguste KI, Knight RT, Asano E, Ofen N. PMID: 32941883; PMCID: PMC7704894.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    345. Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures. Cell. 2020 09 03; 182(5):1311-1327.e14. Wozniak JM, Mills RH, Olson J, Caldera JR, Sepich-Poore GD, Carrillo-Terrazas M, Tsai CM, Vargas F, Knight R, Dorrestein PC, Liu GY, Nizet V, Sakoulas G, Rose W, Gonzalez DJ. PMID: 32888495; PMCID: PMC7494005.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansAnimalsCells
    346. Context-aware dimensionality reduction deconvolutes gut microbial community dynamics. Nat Biotechnol. 2021 02; 39(2):165-168. Martino C, Shenhav L, Marotz CA, Armstrong G, McDonald D, Vázquez-Baeza Y, Morton JT, Jiang L, Dominguez-Bello MG, Swafford AD, Halperin E, Knight R. PMID: 32868914; PMCID: PMC7878194.
      View in: PubMed   Mentions: 61     Fields:    Translation:Humans
    347. Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort. Cancer Epidemiol Biomarkers Prev. 2020 11; 29(11):2289-2299. Loftfield E, Herzig KH, Caporaso JG, Derkach A, Wan Y, Byrd DA, Vogtmann E, Männikkö M, Karhunen V, Knight R, Gunter MJ, Järvelin MR, Sinha R. PMID: 32855266; PMCID: PMC7642019.
      View in: PubMed   Mentions:
    348. Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes. N Engl J Med. 2020 08 20; 383(8):721-732. Yoshino M, Kayser BD, Yoshino J, Stein RI, Reeds D, Eagon JC, Eckhouse SR, Watrous JD, Jain M, Knight R, Schechtman K, Patterson BW, Klein S. PMID: 32813948; PMCID: PMC7456610.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansCTClinical Trials
    349. Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium. mSystems. 2020 Aug 18; 5(4). Mu A, Carter GP, Li L, Isles NS, Vrbanac AF, Morton JT, Jarmusch AK, De Souza DP, Narayana VK, Kanojia K, Nijagal B, McConville MJ, Knight R, Howden BP, Stinear TP. PMID: 32817384; PMCID: PMC7438022.
      View in: PubMed   Mentions: 6     Fields:    
    350. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods. 2020 09; 17(9):901-904. Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. PMID: 32807955; PMCID: PMC7968862.
      View in: PubMed   Mentions: 65     Fields:    
    351. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. medRxiv. 2020 Aug 13. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32511552; PMCID: PMC7274233.
      View in: PubMed   Mentions: 1  
    352. Dissociation of broadband high-frequency activity and neuronal firing in the neocortex. Sci Adv. 2020 08; 6(33):eabb0977. Leszczynski M, Barczak A, Kajikawa Y, Ulbert I, Falchier AY, Tal I, Haegens S, Melloni L, Knight RT, Schroeder CE. PMID: 32851172; PMCID: PMC7423365.
      View in: PubMed   Mentions: 93     Fields:    Translation:Cells
    353. HITM-SURE: Hepatic immunotherapy for metastases phase Ib anti-CEA CAR-T study utilizing pressure enabled drug delivery. J Immunother Cancer. 2020 08; 8(2). Katz SC, Moody AE, Guha P, Hardaway JC, Prince E, LaPorte J, Stancu M, Slansky JE, Jordan KR, Schulick RD, Knight R, Saied A, Armenio V, Junghans RP. PMID: 32843493; PMCID: PMC7449487.
      View in: PubMed   Mentions:
    354. Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation. mSystems. 2020 Jul 28; 5(4). Malli Mohan GB, Parker CW, Urbaniak C, Singh NK, Hood A, Minich JJ, Knight R, Rucker M, Venkateswaran K. PMID: 32723791; PMCID: PMC7394354.
      View in: PubMed   Mentions: 6     Fields:    
    355. Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals. J Am Heart Assoc. 2020 08 04; 9(15):e016641. Palmu J, Salosensaari A, Havulinna AS, Cheng S, Inouye M, Jain M, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Vartiainen E, Laatikainen T, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen TJ. PMID: 32691653; PMCID: PMC7792269.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    356. SHOGUN: a modular, accurate and scalable framework for microbiome quantification. Bioinformatics. 2020 07 01; 36(13):4088-4090. Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Knight R, Knights D. PMID: 32365167; PMCID: PMC7359755.
      View in: PubMed   Mentions: 37     Fields:    
    357. High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy. mSystems. 2020 Jun 23; 5(3). Raghuvanshi R, Vasco K, Vázquez-Baeza Y, Jiang L, Morton JT, Li D, Gonzalez A, DeRight Goldasich L, Humphrey G, Ackermann G, Swafford AD, Conrad D, Knight R, Dorrestein PC, Quinn RA. PMID: 32576651; PMCID: PMC7311317.
      View in: PubMed   Mentions: 49     Fields:    
    358. Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res. 2020 06; 30(6):898-909. Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. PMID: 32540955; PMCID: PMC7370886.
      View in: PubMed   Mentions: 63     Fields:    Translation:Humans
    359. Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice. Front Psychiatry. 2020; 11:518. Dethloff F, Vargas F, Elijah E, Quinn R, Park DI, Herzog DP, Müller MB, Gentry EC, Knight R, Gonzalez A, Dorrestein PC, Turck CW. PMID: 32581888; PMCID: PMC7287167.
      View in: PubMed   Mentions: 13  
    360. Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Appl Environ Microbiol. 2020 06 02; 86(12). Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE. PMID: 32303543; PMCID: PMC7267192.
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    361. QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. Curr Protoc Bioinformatics. 2020 06; 70(1):e100. Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. PMID: 32343490; PMCID: PMC9285460.
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    362. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020 05 19; 11(1):2500. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. PMID: 32427907; PMCID: PMC7237447.
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    363. Visualizing 'omic feature rankings and log-ratios using Qurro. NAR Genom Bioinform. 2020 Jun; 2(2):lqaa023. Fedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R. PMID: 32391521; PMCID: PMC7194218.
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    364. Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study. Clin Transl Sci. 2020 09; 13(5):972-984. Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM. PMID: 32216086; PMCID: PMC7485946.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    365. The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months. Am J Clin Nutr. 2020 04 01; 111(4):884-892. Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K, Agapova S, Divala O, Kaimila Y, Maleta K, Zhong C, Knight R, Trehan I, Tarr PI, Rusconi B, Manary MJ. PMID: 32047925; PMCID: PMC8287943.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    366. Comparison between a wireless dry electrode EEG system with a conventional wired wet electrode EEG system for clinical applications. Sci Rep. 2020 03 23; 10(1):5218. Hinrichs H, Scholz M, Baum AK, Kam JWY, Knight RT, Heinze HJ. PMID: 32251333; PMCID: PMC7090045.
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    367. Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020 Mar 17; 5(2). Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. PMID: 32184365; PMCID: PMC7380580.
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    368. Multiple-Disease Detection and Classification across Cohorts via Microbiome Search. mSystems. 2020 Mar 17; 5(2). Su X, Jing G, Sun Z, Liu L, Xu Z, McDonald D, Wang Z, Wang H, Gonzalez A, Zhang Y, Huang S, Huttley G, Knight R, Xu J. PMID: 32184368; PMCID: PMC7380586.
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    369. Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs. mSystems. 2020 Mar 10; 5(2). Gauglitz JM, Morton JT, Tripathi A, Hansen S, Gaffney M, Carpenter C, Weldon KC, Shah R, Parampil A, Fidgett AL, Swafford AD, Knight R, Dorrestein PC. PMID: 32156796; PMCID: PMC7065514.
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    370. Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing. Environ Int. 2020 05; 138:105604. Fouladi F, Bailey MJ, Patterson WB, Sioda M, Blakley IC, Fodor AA, Jones RB, Chen Z, Kim JS, Lurmann F, Martino C, Knight R, Gilliland FD, Alderete TL. PMID: 32135388; PMCID: PMC7181344.
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    371. Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020 03; 579(7797):123-129. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. PMID: 32103176; PMCID: PMC7252668.
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    372. Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol. 2020 Feb 25; 21(1):50. Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD. PMID: 32098632; PMCID: PMC7043042.
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    373. Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome. PLoS One. 2020; 15(2):e0229001. Bowers SJ, Vargas F, González A, He S, Jiang P, Dorrestein PC, Knight R, Wright KP, Lowry CA, Fleshner M, Vitaterna MH, Turek FW. PMID: 32078624; PMCID: PMC7032712.
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    374. Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults. Brain Behav Immun. 2020 07; 87:591-602. Kohn JN, Kosciolek T, Marotz C, Aleti G, Guay-Ross RN, Hong SH, Hansen S, Swafford A, Knight R, Hong S. PMID: 32061904; PMCID: PMC10287023.
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    375. A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice. Elife. 2020 02 11; 9. Sampson TR, Challis C, Jain N, Moiseyenko A, Ladinsky MS, Shastri GG, Thron T, Needham BD, Horvath I, Debelius JW, Janssen S, Knight R, Wittung-Stafshede P, Gradinaru V, Chapman M, Mazmanian SK. PMID: 32043464; PMCID: PMC7012599.
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    376. Human Skin, Oral, and Gut Microbiomes Predict Chronological Age. mSystems. 2020 Feb 11; 5(1). Huang S, Haiminen N, Carrieri AP, Hu R, Jiang L, Parida L, Russell B, Allaband C, Zarrinpar A, Vázquez-Baeza Y, Belda-Ferre P, Zhou H, Kim HC, Swafford AD, Knight R, Xu ZZ. PMID: 32047061; PMCID: PMC7018528.
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    377. Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study. Sci Rep. 2020 02 07; 10(1):2133. Burcham ZM, Garneau NL, Comstock SS, Tucker RM, Knight R, Metcalf JL, Genetics of Taste Lab Citizen Scientists. PMID: 32034250; PMCID: PMC7005749.
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    378. Microbial biogeography and ecology of the mouth and implications for periodontal diseases. Periodontol 2000. 2020 02; 82(1):26-41. Proctor DM, Shelef KM, Gonzalez A, Davis CL, Dethlefsen L, Burns AR, Loomer PM, Armitage GC, Ryder MI, Millman ME, Knight R, Holmes SP, Relman DA. PMID: 31850642; PMCID: PMC6924627.
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    379. Organ-level protein networks as a reference for the host effects of the microbiome. Genome Res. 2020 02; 30(2):276-286. Mills RH, Wozniak JM, Vrbanac A, Campeau A, Chassaing B, Gewirtz A, Knight R, Gonzalez DJ. PMID: 31992612; PMCID: PMC7050531.
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    380. Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations. Gastroenterology. 2020 05; 158(6):1524-1528. Casals-Pascual C, González A, Vázquez-Baeza Y, Song SJ, Jiang L, Knight R. PMID: 31930986.
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    381. Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. mBio. 2020 01 07; 11(1). Song SJ, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie VJ, Knight R. PMID: 31911491; PMCID: PMC6946802.
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    382. The emergence of microbiome centres. Nat Microbiol. 2020 01; 5(1):2-3. Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. PMID: 31857734.
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    383. Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates. mBio. 2019 12 24; 10(6). Yan Y, Maurer-Alcalá XX, Knight R, Kosakovsky Pond SL, Katz LA. PMID: 31874915; PMCID: PMC6935857.
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    384. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data. 2019 12 17; 6(1):322. Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J. PMID: 31848353; PMCID: PMC6917727.
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    385. Direct Evidence for Prediction Signals in Frontal Cortex Independent of Prediction Error. Cereb Cortex. 2019 12 17; 29(11):4530-4538. Dürschmid S, Reichert C, Hinrichs H, Heinze HJ, Kirsch HE, Knight RT, Deouell LY. PMID: 30590422; PMCID: PMC7963121.
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    386. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun. 2019 12 02; 10(1):5477. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. PMID: 31792218; PMCID: PMC6889312.
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    387. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. PLoS One. 2019; 14(11):e0224757. Byrd DA, Chen J, Vogtmann E, Hullings A, Song SJ, Amir A, Kibriya MG, Ahsan H, Chen Y, Nelson H, Knight R, Shi J, Chia N, Sinha R. PMID: 31738775; PMCID: PMC6860998.
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    388. Home chemical and microbial transitions across urbanization. Nat Microbiol. 2020 01; 5(1):108-115. McCall LI, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. PMID: 31686026; PMCID: PMC7895447.
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    389. Learning representations of microbe-metabolite interactions. Nat Methods. 2019 12; 16(12):1306-1314. Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. PMID: 31686038; PMCID: PMC6884698.
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    390. Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol. 2019 11 01; 20(1):219. Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD. PMID: 31672155; PMCID: PMC6824043.
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    391. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 10 31; 20(1):226. Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. PMID: 31672156; PMCID: PMC6822431.
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    392. Neighborhoods to Nucleotides - Advances and gaps for an obesity disparities systems epidemiology model. Curr Epidemiol Rep. 2019 Dec; 6(4):476-485. Jankowska MM, Gaulton K, Knight R, Patrick K, Sears DD. PMID: 36643055; PMCID: PMC9839192.
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    393. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst. 2019 12 18; 9(6):600-608.e4. Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. PMID: 31629686; PMCID: PMC6952069.
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    394. Species abundance information improves sequence taxonomy classification accuracy. Nat Commun. 2019 10 11; 10(1):4643. Kaehler BD, Bokulich NA, McDonald D, Knight R, Caporaso JG, Huttley GA. PMID: 31604942; PMCID: PMC6789115.
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    395. Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome Biol. 2019 10 08; 20(1):201. Amato KR, Mallott EK, McDonald D, Dominy NJ, Goldberg T, Lambert JE, Swedell L, Metcalf JL, Gomez A, Britton GAO, Stumpf RM, Leigh SR, Knight R. PMID: 31590679; PMCID: PMC6781418.
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    396. Auditory deviance detection in the human insula: An intracranial EEG study. Cortex. 2019 12; 121:189-200. Blenkmann AO, Collavini S, Lubell J, Llorens A, Funderud I, Ivanovic J, Larsson PG, Meling TR, Bekinschtein T, Kochen S, Endestad T, Knight RT, Solbakk AK. PMID: 31629197.
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    397. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems. 2019 Sep 24; 4(5). Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. PMID: 31551401; PMCID: PMC6759567.
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    398. International Federation of Clinical Neurophysiology (IFCN) - EEG research workgroup: Recommendations on frequency and topographic analysis of resting state EEG rhythms. Part 1: Applications in clinical research studies. Clin Neurophysiol. 2020 01; 131(1):285-307. Babiloni C, Barry RJ, Basar E, Blinowska KJ, Cichocki A, Drinkenburg WHIM, Klimesch W, Knight RT, Lopes da Silva F, Nunez P, Oostenveld R, Jeong J, Pascual-Marqui R, Valdes-Sosa P, Hallett M. PMID: 31501011.
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    399. Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome. Sci Rep. 2019 09 16; 9(1):13409. Jung CE, Chopyk J, Shin JH, Lukacz ES, Brubaker L, Schwanemann LK, Knight R, Wolfe AJ, Pride DT. PMID: 31527753; PMCID: PMC6746804.
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    400. Lesions to the Fronto-Parietal Network Impact Alpha-Band Phase Synchrony and Cognitive Control. Cereb Cortex. 2019 09 13; 29(10):4143-4153. Sadaghiani S, Dombert PL, Løvstad M, Funderud I, Meling TR, Endestad T, Knight RT, Solbakk AK, D'Esposito M. PMID: 30535068; PMCID: PMC6735251.
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    401. Gut microbiome in serious mental illnesses: A systematic review and critical evaluation. Schizophr Res. 2021 08; 234:24-40. Nguyen TT, Hathaway H, Kosciolek T, Knight R, Jeste DV. PMID: 31495702; PMCID: PMC7056547.
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    402. Challenges in the construction of knowledge bases for human microbiome-disease associations. Microbiome. 2019 09 05; 7(1):129. Badal VD, Wright D, Katsis Y, Kim HC, Swafford AD, Knight R, Hsu CN. PMID: 31488215; PMCID: PMC6728997.
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    403. Default network and frontoparietal control network theta connectivity supports internal attention. Nat Hum Behav. 2019 12; 3(12):1263-1270. Kam JWY, Lin JJ, Solbakk AK, Endestad T, Larsson PG, Knight RT. PMID: 31477910.
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    404. A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children. mSystems. 2019 Aug 20; 4(4). Sun Z, Huang S, Zhu P, Yue F, Zhao H, Yang M, Niu Y, Jing G, Su X, Li H, Callewaert C, Knight R, Liu J, Smith E, Wei K, Xu J. PMID: 31431508; PMCID: PMC6702293.
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    405. Bidirectional prefrontal-hippocampal dynamics organize information transfer during sleep in humans. Nat Commun. 2019 08 08; 10(1):3572. Helfrich RF, Lendner JD, Mander BA, Guillen H, Paff M, Mnatsakanyan L, Vadera S, Walker MP, Lin JJ, Knight RT. PMID: 31395890; PMCID: PMC6687745.
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    406. Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy". mBio. 2019 08 06; 10(4). Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J. PMID: 31387904; PMCID: PMC6686038.
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    407. Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment. Sleep. 2019 08 01; 42(8). Sprecher KE, Ritchie HK, Burke TM, Depner CM, Smits AN, Dorrestein PC, Fleshner M, Knight R, Lowry CA, Turek FW, Vitaterna MH, Wright KP. PMID: 31070769; PMCID: PMC6941712.
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    408. Effect of Aging on Change of Intention. Front Hum Neurosci. 2019; 13:264. Furstenberg A, Dewar CD, Sompolinsky H, Knight RT, Deouell LY. PMID: 31417383; PMCID: PMC6685419.
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    409. Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity. Mol Cell Proteomics. 2019 09; 18(9):1864-1879. Tran HQ, Mills RH, Peters NV, Holder MK, de Vries GJ, Knight R, Chassaing B, Gonzalez DJ, Gewirtz AT. PMID: 31262998; PMCID: PMC6731084.
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    410. Quantifying and Understanding Well-to-Well Contamination in Microbiome Research. mSystems. 2019 Jun 25; 4(4). Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. PMID: 31239396; PMCID: PMC6593221.
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    411. IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis. J Invest Dermatol. 2020 01; 140(1):191-202.e7. Callewaert C, Nakatsuji T, Knight R, Kosciolek T, Vrbanac A, Kotol P, Ardeleanu M, Hultsch T, Guttman-Yassky E, Bissonnette R, Silverberg JI, Krueger J, Menter A, Graham NMH, Pirozzi G, Hamilton JD, Gallo RL. PMID: 31252032; PMCID: PMC7163930.
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    412. redbiom: a Rapid Sample Discovery and Feature Characterization System. mSystems. 2019 Jun 25; 4(4). McDonald D, Kaehler B, Gonzalez A, DeReus J, Ackermann G, Marotz C, Huttley G, Knight R. PMID: 31239397; PMCID: PMC6593222.
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    413. Establishing microbial composition measurement standards with reference frames. Nat Commun. 2019 06 20; 10(1):2719. Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R. PMID: 31222023; PMCID: PMC6586903.
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    414. Sleep as a Potential Biomarker of Tau and β-Amyloid Burden in the Human Brain. J Neurosci. 2019 08 07; 39(32):6315-6324. Winer JR, Mander BA, Helfrich RF, Maass A, Harrison TM, Baker SL, Knight RT, Jagust WJ, Walker MP. PMID: 31209175; PMCID: PMC6687908.
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    415. Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes. Appl Environ Microbiol. 2019 07 01; 85(13). Thompson LR, Haroon MF, Shibl AA, Cahill MJ, Ngugi DK, Williams GJ, Morton JT, Knight R, Goodwin KD, Stingl U. PMID: 31028022; PMCID: PMC6581160.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    416. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biol. 2019 06 12; 17(1):47. Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC. PMID: 31189482; PMCID: PMC6560912.
      View in: PubMed   Mentions: 88     Fields:    Translation:Humans
    417. Ground beef microbiome changes with antimicrobial decontamination interventions and product storage. PLoS One. 2019; 14(6):e0217947. Weinroth MD, Britton BC, McCullough KR, Martin JN, Geornaras I, Knight R, Belk KE, Metcalf JL. PMID: 31166992; PMCID: PMC6550395.
      View in: PubMed   Mentions: 7     Fields:    Translation:CellsPHPublic Health
    418. Is there convergence of gut microbes in blood-feeding vertebrates? Philos Trans R Soc Lond B Biol Sci. 2019 07 22; 374(1777):20180249. Song SJ, Sanders JG, Baldassarre DT, Chaves JA, Johnson NS, Piaggio AJ, Stuckey MJ, Nováková E, Metcalf JL, Chomel BB, Aguilar-Setién A, Knight R, McKenzie VJ. PMID: 31154984; PMCID: PMC6560276.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    419. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell. 2019 05 30; 177(6):1600-1618.e17. Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. PMID: 31150625; PMCID: PMC6993574.
      View in: PubMed   Mentions: 577     Fields:    Translation:HumansAnimalsCells
    420. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 05; 569(7758):655-662. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. PMID: 31142855; PMCID: PMC6650278.
      View in: PubMed   Mentions: 1487     Fields:    Translation:HumansAnimalsCells
    421. Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary. Biotechniques. 2019 07; 67(1):29-32. Marotz C, Sharma A, Humphrey G, Gottel N, Daum C, Gilbert JA, Eloe-Fadrosh E, Knight R. PMID: 31124709; PMCID: PMC7030937.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    422. Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi. Am J Primatol. 2019 10; 81(10-11):e22989. Hale VL, Tan CL, Niu K, Yang Y, Zhang Q, Knight R, Amato KR. PMID: 31106872.
      View in: PubMed   Mentions: 49     Fields:    Translation:AnimalsCells
    423. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems. 2019 Jul-Aug; 4(4). de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG. PMID: 31098397; PMCID: PMC6517691.
      View in: PubMed   Mentions: 215     Fields:    
    424. Major shifts in gut microbiota during development and its relationship to growth in ostriches. Mol Ecol. 2019 05; 28(10):2653-2667. Videvall E, Song SJ, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK. PMID: 30916826.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    425. Early-Career Scientists Shaping the World. mSystems. 2019 May 07; 4(3). Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. PMID: 31219787; PMCID: PMC6533378.
      View in: PubMed   Mentions:    Fields:    
    426. Consent insufficient for data release-Response. Science. 2019 05 03; 364(6439):446. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. PMID: 31048484.
      View in: PubMed   Mentions:    Fields:    
    427. Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems. mSystems. 2019 Mar-Apr; 4(2). Tripathi A, Xu ZZ, Xue J, Poulsen O, Gonzalez A, Humphrey G, Meehan MJ, Melnik AV, Ackermann G, Zhou D, Malhotra A, Haddad GG, Dorrestein PC, Knight R. PMID: 31058230; PMCID: PMC6495231.
      View in: PubMed   Mentions: 22     Fields:    
    428. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data. 2019 04 26; 6(1):43. Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM. PMID: 31028276; PMCID: PMC6486602.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    429. Multiplexing of Theta and Alpha Rhythms in the Amygdala-Hippocampal Circuit Supports Pattern Separation of Emotional Information. Neuron. 2019 05 22; 102(4):887-898.e5. Zheng J, Stevenson RF, Mander BA, Mnatsakanyan L, Hsu FPK, Vadera S, Knight RT, Yassa MA, Lin JJ. PMID: 30979537; PMCID: PMC6605056.
      View in: PubMed   Mentions: 61     Fields:    Translation:Humans
    430. Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome. 2019 04 08; 7(1):50. Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich J, McDonald D, Mayer T, Knight R, Karouia F, Fox GE, Venkateswaran K. PMID: 30955503; PMCID: PMC6452512.
      View in: PubMed   Mentions: 122     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    431. A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease. Nat Commun. 2019 03 29; 10(1):1406. Caussy C, Tripathi A, Humphrey G, Bassirian S, Singh S, Faulkner C, Bettencourt R, Rizo E, Richards L, Xu ZZ, Downes MR, Evans RM, Brenner DA, Sirlin CB, Knight R, Loomba R. PMID: 30926798; PMCID: PMC6440960.
      View in: PubMed   Mentions: 180     Fields:    Translation:HumansCells
    432. The genetic basis for adaptation of model-designed syntrophic co-cultures. PLoS Comput Biol. 2019 03; 15(3):e1006213. Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM. PMID: 30822347; PMCID: PMC6415869.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    433. Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice. J Physiol. 2019 05; 597(9):2361-2378. Brunt VE, Gioscia-Ryan RA, Richey JJ, Zigler MC, Cuevas LM, Gonzalez A, Vázquez-Baeza Y, Battson ML, Smithson AT, Gilley AD, Ackermann G, Neilson AP, Weir T, Davy KP, Knight R, Seals DR. PMID: 30714619; PMCID: PMC6487935.
      View in: PubMed   Mentions: 102     Fields:    Translation:Animals
    434. Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month. Microbiome. 2019 02 27; 7(1):34. Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T, Eggesbø M. PMID: 30813950; PMCID: PMC6393990.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    435. FXR Regulates Intestinal Cancer Stem Cell Proliferation. Cell. 2019 02 21; 176(5):1098-1112.e18. Fu T, Coulter S, Yoshihara E, Oh TG, Fang S, Cayabyab F, Zhu Q, Zhang T, Leblanc M, Liu S, He M, Waizenegger W, Gasser E, Schnabl B, Atkins AR, Yu RT, Knight R, Liddle C, Downes M, Evans RM. PMID: 30794774; PMCID: PMC6701863.
      View in: PubMed   Mentions: 256     Fields:    Translation:HumansAnimalsCells
    436. Engineering the microbiome for animal health and conservation. Exp Biol Med (Maywood). 2019 04; 244(6):494-504. Jin Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. PMID: 30776908; PMCID: PMC6547002.
      View in: PubMed   Mentions: 45     Fields:    Translation:Animals
    437. Patients with basal ganglia damage show preserved learning in an economic game. Nat Commun. 2019 02 18; 10(1):802. Zhu L, Jiang Y, Scabini D, Knight RT, Hsu M. PMID: 30778070; PMCID: PMC6379550.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    438. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Microbiome. 2019 02 13; 7(1):23. Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. PMID: 30760325; PMCID: PMC6375204.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    439. A Novel Sparse Compositional Technique Reveals Microbial Perturbations. mSystems. 2019 Jan-Feb; 4(1). Martino C, Morton JT, Marotz CA, Thompson LR, Tripathi A, Knight R, Zengler K. PMID: 30801021; PMCID: PMC6372836.
      View in: PubMed   Mentions: 264     Fields:    
    440. Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. mSystems. 2019 Jan-Feb; 4(1). Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ. PMID: 30801026; PMCID: PMC6372841.
      View in: PubMed   Mentions: 32     Fields:    
    441. Calour: an Interactive, Microbe-Centric Analysis Tool. mSystems. 2019 Jan-Feb; 4(1). Xu ZZ, Amir A, Sanders J, Zhu Q, Morton JT, Bletz MC, Tripathi A, Huang S, McDonald D, Jiang L, Knight R. PMID: 30701193; PMCID: PMC6351725.
      View in: PubMed   Mentions: 25     Fields:    
    442. Toward unrestricted use of public genomic data. Science. 2019 01 25; 363(6425):350-352. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. PMID: 30679363.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    443. Role of the microbiome in human development. Gut. 2019 06; 68(6):1108-1114. Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJ. PMID: 30670574; PMCID: PMC6580755.
      View in: PubMed   Mentions: 367     Fields:    Translation:Humans
    444. Spectral Imprints of Working Memory for Everyday Associations in the Frontoparietal Network. Front Syst Neurosci. 2018; 12:65. Johnson EL, King-Stephens D, Weber PB, Laxer KD, Lin JJ, Knight RT. PMID: 30670953; PMCID: PMC6333050.
      View in: PubMed   Mentions: 17  
    445. The Microbiome and Its Potential for Pharmacology. Handb Exp Pharmacol. 2019; 260:301-326. Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R. PMID: 31820171.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    446. GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 2019 03; 4(3):396-403. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K. PMID: 30531975; PMCID: PMC6384127.
      View in: PubMed   Mentions: 541     Fields:    Translation:HumansCells
    447. Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nat Med. 2018 Dec; 24(12):1940. He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW. PMID: 30250144.
      View in: PubMed   Mentions: 12     Fields:    
    448. Neural Encoding of Auditory Features during Music Perception and Imagery. Cereb Cortex. 2018 12 01; 28(12):4222-4233. Martin S, Mikutta C, Leonard MK, Hungate D, Koelsch S, Shamma S, Chang EF, Millán JDR, Knight RT, Pasley BN. PMID: 29088345; PMCID: PMC6215461.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    449. Publisher Correction: The gut-liver axis and the intersection with the microbiome. Nat Rev Gastroenterol Hepatol. 2018 12; 15(12):785. Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R. PMID: 29785003; PMCID: PMC7133393.
      View in: PubMed   Mentions: 18     Fields:    
    450. Erratum to: The sponge microbiome project. Gigascience. 2018 12 01; 7(12). Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T. PMID: 30521034; PMCID: PMC6283209.
      View in: PubMed   Mentions: 1     Fields:    
    451. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol. 2019 02; 27(2):105-117. Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. PMID: 30497919.
      View in: PubMed   Mentions: 514     Fields:    Translation:Humans
    452. Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017. Microbiome. 2018 11 26; 6(1):210. Sinha R, Ahsan H, Blaser M, Caporaso JG, Carmical JR, Chan AT, Fodor A, Gail MH, Harris CC, Helzlsouer K, Huttenhower C, Knight R, Kong HH, Lai GY, Hutchinson DLS, Le Marchand L, Li H, Orlich MJ, Shi J, Truelove A, Verma M, Vogtmann E, White O, Willett W, Zheng W, Mahabir S, Abnet C. PMID: 30477563; PMCID: PMC6257978.
      View in: PubMed   Mentions:
    453. Temporal Dynamics and Response Modulation across the Human Visual System in a Spatial Attention Task: An ECoG Study. J Neurosci. 2019 01 09; 39(2):333-352. Martin AB, Yang X, Saalmann YB, Wang L, Shestyuk A, Lin JJ, Parvizi J, Knight RT, Kastner S. PMID: 30459219; PMCID: PMC6325255.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    454. Evaluating the Information Content of Shallow Shotgun Metagenomics. mSystems. 2018 Nov-Dec; 3(6). Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. PMID: 30443602; PMCID: PMC6234283.
      View in: PubMed   Mentions: 226     Fields:    
    455. Identifying and Predicting Novelty in Microbiome Studies. mBio. 2018 11 13; 9(6). Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J. PMID: 30425147; PMCID: PMC6234870.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    456. Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J Forensic Sci. 2019 May; 64(3):791-798. Kodama WA, Xu Z, Metcalf JL, Song SJ, Harrison N, Knight R, Carter DO, Happy CB. PMID: 30408195.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    457. Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria. mSystems. 2018 Nov-Dec; 3(6). Cekanaviciute E, Pröbstel AK, Thomann A, Runia TF, Casaccia P, Katz Sand I, Crabtree E, Singh S, Morrissey J, Barba P, Gomez R, Knight R, Mazmanian S, Graves J, Cree BAC, Zamvil SS, Baranzini SE. PMID: 30417113; PMCID: PMC6222044.
      View in: PubMed   Mentions: 44     Fields:    
    458. High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems. 2018 Nov-Dec; 3(6). Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R. PMID: 30417111; PMCID: PMC6222042.
      View in: PubMed   Mentions: 40     Fields:    
    459. Differential contributions of subthalamic beta rhythms and 1/f broadband activity to motor symptoms in Parkinson's disease. NPJ Parkinsons Dis. 2018; 4:32. Martin S, Iturrate I, Chavarriaga R, Leeb R, Sobolewski A, Li AM, Zaldivar J, Peciu-Florianu I, Pralong E, Castro-Jiménez M, Benninger D, Vingerhoets F, Knight RT, Bloch J, Millán JDR. PMID: 30417084; PMCID: PMC6218479.
      View in: PubMed   Mentions: 14  
    460. Striped UniFrac: enabling microbiome analysis at unprecedented scale. Nat Methods. 2018 11; 15(11):847-848. McDonald D, Vázquez-Baeza Y, Koslicki D, McClelland J, Reeve N, Xu Z, Gonzalez A, Knight R. PMID: 30377368; PMCID: PMC7250580.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    461. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018 11; 15(11):962-968. Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C. PMID: 30377376; PMCID: PMC6235447.
      View in: PubMed   Mentions: 829     Fields:    Translation:HumansCells
    462. Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Front Microbiol. 2018; 9:2559. Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. PMID: 30425690; PMCID: PMC6218438.
      View in: PubMed   Mentions: 33  
    463. Human posterior parietal cortex responds to visual stimuli as early as peristriate occipital cortex. Eur J Neurosci. 2018 12; 48(12):3567-3582. Regev TI, Winawer J, Gerber EM, Knight RT, Deouell LY. PMID: 30240547; PMCID: PMC6482330.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    464. Disease-modifying therapies alter gut microbial composition in MS. Neurol Neuroimmunol Neuroinflamm. 2019 01; 6(1):e517. Katz Sand I, Zhu Y, Ntranos A, Clemente JC, Cekanaviciute E, Brandstadter R, Crabtree-Hartman E, Singh S, Bencosme Y, Debelius J, Knight R, Cree BAC, Baranzini SE, Casaccia P. PMID: 30568995; PMCID: PMC6278850.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCells
    465. Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis. J Immunol. 2018 11 15; 201(10):3017-3035. Maricic I, Marrero I, Eguchi A, Nakamura R, Johnson CD, Dasgupta S, Hernandez CD, Nguyen PS, Swafford AD, Knight R, Feldstein AE, Loomba R, Kumar V. PMID: 30322964; PMCID: PMC6219905.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    466. Preserving microbial diversity. Science. 2018 Oct 05; 362(6410):33-34. Bello MGD, Knight R, Gilbert JA, Blaser MJ. PMID: 30287652.
      View in: PubMed   Mentions: 71     Fields:    Translation:Humans
    467. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018 10; 15(10):796-798. Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. PMID: 30275573; PMCID: PMC6235622.
      View in: PubMed   Mentions: 382     Fields:    Translation:Humans
    468. Comparison of Oral Collection Methods for Studies of Microbiota. Cancer Epidemiol Biomarkers Prev. 2019 01; 28(1):137-143. Vogtmann E, Chen J, Kibriya MG, Amir A, Shi J, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Barmon B, Knight R, Chia N, Ahsan H, Abnet CC, Sinha R. PMID: 30262598; PMCID: PMC6324947.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    469. Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects. Schizophr Res. 2019 02; 204:23-29. Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R, Jeste DV. PMID: 30268819; PMCID: PMC6755901.
      View in: PubMed   Mentions: 119     Fields:    Translation:Humans
    470. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci Adv. 2018 09; 4(9):eaau1908. Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. PMID: 30263961; PMCID: PMC6157970.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    471. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019 01; 17(2):218-230. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R. PMID: 30240894; PMCID: PMC6391518.
      View in: PubMed   Mentions: 149     Fields:    Translation:Humans
    472. Hippocampal CA1 gamma power predicts the precision of spatial memory judgments. Proc Natl Acad Sci U S A. 2018 10 02; 115(40):10148-10153. Stevenson RF, Zheng J, Mnatsakanyan L, Vadera S, Knight RT, Lin JJ, Yassa MA. PMID: 30224452; PMCID: PMC6176623.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCTClinical Trials
    473. Encoding of Multiple Reward-Related Computations in Transient and Sustained High-Frequency Activity in Human OFC. Curr Biol. 2018 09 24; 28(18):2889-2899.e3. Saez I, Lin J, Stolk A, Chang E, Parvizi J, Schalk G, Knight RT, Hsu M. PMID: 30220499; PMCID: PMC6590063.
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    474. Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2018 09; 561(7721):E1. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. PMID: 29973714; PMCID: PMC7871211.
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    475. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen. 2018 12; 7(6):e00716. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. PMID: 30168288; PMCID: PMC6291788.
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    476. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nat Med. 2018 10; 24(10):1532-1535. He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW. PMID: 30150716.
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    477. Neural Mechanisms of Sustained Attention Are Rhythmic. Neuron. 2018 08 22; 99(4):854-865.e5. Helfrich RF, Fiebelkorn IC, Szczepanski SM, Lin JJ, Parvizi J, Knight RT, Kastner S. PMID: 30138591; PMCID: PMC6286091.
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    478. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes. 2019; 10(2):216-227. Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL. PMID: 30118385; PMCID: PMC6546328.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsPHPublic Health
    479. Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics. Genome Biol Evol. 2018 08 01; 10(8):1927-1939. Maurer-Alcalá XX, Yan Y, Pilling OA, Knight R, Katz LA. PMID: 29945193; PMCID: PMC6101598.
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    480. Are microbiome studies ready for hypothesis-driven research? Curr Opin Microbiol. 2018 08; 44:61-69. Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R. PMID: 30059804; PMCID: PMC6153026.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    481. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun. 2018 07 20; 9(1):2872. Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S. PMID: 30030441; PMCID: PMC6054678.
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    482. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun. 2018 07 19; 9(1):2832. Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. PMID: 30026532; PMCID: PMC6053391.
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    483. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 2019 03; 13(3):576-587. Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S. PMID: 29995839; PMCID: PMC6461848.
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    484. Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus. ISME J. 2018 11; 12(11):2801-2806. Lavrinienko A, Mappes T, Tukalenko E, Mousseau TA, Møller AP, Knight R, Morton JT, Thompson LR, Watts PC. PMID: 29988064; PMCID: PMC6193954.
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    485. Integrated analysis of anatomical and electrophysiological human intracranial data. Nat Protoc. 2018 07; 13(7):1699-1723. Stolk A, Griffin S, van der Meij R, Dewar C, Saez I, Lin JJ, Piantoni G, Schoffelen JM, Knight RT, Oostenveld R. PMID: 29988107; PMCID: PMC6548463.
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    486. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018 07; 16(7):410-422. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. PMID: 29795328.
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    487. A lexical semantic hub for heteromodal naming in middle fusiform gyrus. Brain. 2018 07 01; 141(7):2112-2126. Forseth KJ, Kadipasaoglu CM, Conner CR, Hickok G, Knight RT, Tandon N. PMID: 29860298; PMCID: PMC6365955.
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    488. The gut-liver axis and the intersection with the microbiome. Nat Rev Gastroenterol Hepatol. 2018 07; 15(7):397-411. Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R. PMID: 29748586; PMCID: PMC6319369.
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    489. Low-frequency cortical activity is a neuromodulatory target that tracks recovery after stroke. Nat Med. 2018 08; 24(8):1257-1267. Ramanathan DS, Guo L, Gulati T, Davidson G, Hishinuma AK, Won SJ, Knight RT, Chang EF, Swanson RA, Ganguly K. PMID: 29915259; PMCID: PMC6093781.
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    490. Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome. mSystems. 2018 May-Jun; 3(3). Tripathi A, Melnik AV, Xue J, Poulsen O, Meehan MJ, Humphrey G, Jiang L, Ackermann G, McDonald D, Zhou D, Knight R, Dorrestein PC, Haddad GG. PMID: 29896566; PMCID: PMC5989129.
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    491. The gut microbiome of nonhuman primates: Lessons in ecology and evolution. Am J Primatol. 2018 06; 80(6):e22867. Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ. PMID: 29862519.
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    492. Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis. Eur Psychiatry. 2018 09; 53:37-45. He Y, Kosciolek T, Tang J, Zhou Y, Li Z, Ma X, Zhu Q, Yuan N, Yuan L, Li C, Jin K, Knight R, Tsuang MT, Chen X. PMID: 29870894.
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    493. Methods for phylogenetic analysis of microbiome data. Nat Microbiol. 2018 06; 3(6):652-661. Washburne AD, Morton JT, Sanders J, McDonald D, Zhu Q, Oliverio AM, Knight R. PMID: 29795540.
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    494. Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nat Commun. 2018 05 22; 9(1):2017. Michaud JM, Thompson LR, Kaul D, Espinoza JL, Richter RA, Xu ZZ, Lee C, Pham KM, Beall CM, Malfatti F, Azam F, Knight R, Burkart MD, Dupont CL, Prather KA. PMID: 29789621; PMCID: PMC5964107.
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    495. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome. 2018 05 17; 6(1):90. Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J. PMID: 29773078; PMCID: PMC5956843.
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    496. Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Cell Syst. 2018 05 23; 6(5):579-592.e4. Lapek JD, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ. PMID: 29778837; PMCID: PMC7868092.
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    497. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium , Knight R. PMID: 29795809; PMCID: PMC5954204.
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    498. Exposure to toxic metals triggers unique responses from the rat gut microbiota. Sci Rep. 2018 04 26; 8(1):6578. Richardson JB, Dancy BCR, Horton CL, Lee YS, Madejczyk MS, Xu ZZ, Ackermann G, Humphrey G, Palacios G, Knight R, Lewis JA. PMID: 29700420; PMCID: PMC5919903.
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    499. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems. 2018 May-Jun; 3(3). Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R. PMID: 29719869; PMCID: PMC5904434.
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    500. Current understanding of the human microbiome. Nat Med. 2018 04 10; 24(4):392-400. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. PMID: 29634682; PMCID: PMC7043356.
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    501. Earth Microbiome Project and Global Systems Biology. mSystems. 2018 May-Jun; 3(3). Gilbert JA, Jansson JK, Knight R. PMID: 29657969; PMCID: PMC5893859.
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    502. Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space. Breastfeed Med. 2018 04; 13(S1):S5-S6. Knight R. PMID: 29624426.
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    503. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018 May-Jun; 3(3). Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R. PMID: 29577086; PMCID: PMC5864415.
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    504. Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. PLoS Negl Trop Dis. 2018 03; 12(3):e0006344. McCall LI, Tripathi A, Vargas F, Knight R, Dorrestein PC, Siqueira-Neto JL. PMID: 29529084; PMCID: PMC5864088.
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    505. Mirroring in the Human Brain: Deciphering the Spatial-Temporal Patterns of the Human Mirror Neuron System. Cereb Cortex. 2018 03 01; 28(3):1039-1048. Perry A, Stiso J, Chang EF, Lin JJ, Parvizi J, Knight RT. PMID: 28137724; PMCID: PMC6059139.
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    506. Bacterial density rather than diversity correlates with hatching success across different avian species. FEMS Microbiol Ecol. 2018 03 01; 94(3). Peralta-Sánchez JM, Martín-Platero AM, Wegener-Parfrey L, Martínez-Bueno M, Rodríguez-Ruano S, Navas-Molina JA, Vázquez-Baeza Y, Martín-Gálvez D, Martín-Vivaldi M, Ibáñez-Álamo JD, Knight R, Soler JJ. PMID: 29438507.
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    507. Creating a 3D microbial and chemical snapshot of a human habitat. Sci Rep. 2018 02 27; 8(1):3669. Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC. PMID: 29487294; PMCID: PMC5829137.
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    508. Improving saliva shotgun metagenomics by chemical host DNA depletion. Microbiome. 2018 02 27; 6(1):42. Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. PMID: 29482639; PMCID: PMC5827986.
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    509. Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. Genes (Basel). 2018 Feb 16; 9(2). Belk A, Xu ZZ, Carter DO, Lynne A, Bucheli S, Knight R, Metcalf JL. PMID: 29462950; PMCID: PMC5852600.
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    510. Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. Proc Natl Acad Sci U S A. 2018 02 13; 115(7):1546-1551. Boast AP, Weyrich LS, Wood JR, Metcalf JL, Knight R, Cooper A. PMID: 29440415; PMCID: PMC5816151.
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    511. Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy. Methods Inf Med. 2017; 56(6):442-447. Smarr L, Hyde ER, McDonald D, Sandborn WJ, Knight R. PMID: 29582916.
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    512. Expanding our Understanding of the Role of the Microbiome in Health and Disease. Arch Med Res. 2017 11; 48(8):663-665. Knight R. PMID: 29429588.
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    513. Correction for Morton et al., "Uncovering the Horseshoe Effect in Microbial Analyses". mSystems. 2018 Jan-Feb; 3(1). Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R. PMID: 29435495; PMCID: PMC5801340.
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    514. Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder. J Psychiatr Res. 2018 04; 99:50-61. Nguyen TT, Kosciolek T, Eyler LT, Knight R, Jeste DV. PMID: 29407287; PMCID: PMC5849533.
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    515. Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. mSystems. 2018 Jan-Feb; 3(1). Zhou Y, Xu ZZ, He Y, Yang Y, Liu L, Lin Q, Nie Y, Li M, Zhi F, Liu S, Amir A, González A, Tripathi A, Chen M, Wu GD, Knight R, Zhou H, Chen Y. PMID: 29404425; PMCID: PMC5790872.
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    516. Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). mBio. 2018 01 09; 9(1). Maurer-Alcalá XX, Knight R, Katz LA. PMID: 29317511; PMCID: PMC5760741.
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    517. The human microbiome in evolution. BMC Biol. 2017 12 27; 15(1):127. Davenport ER, Sanders JG, Song SJ, Amato KR, Clark AG, Knight R. PMID: 29282061; PMCID: PMC5744394.
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    518. Persistent neuronal activity in human prefrontal cortex links perception and action. Nat Hum Behav. 2018 Jan; 2(1):80-91. Haller M, Case J, Crone NE, Chang EF, King-Stephens D, Laxer KD, Weber PB, Parvizi J, Knight RT, Shestyuk AY. PMID: 29963646; PMCID: PMC6022844.
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    519. Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. J Anim Ecol. 2018 03; 87(2):388-399. Raulo A, Ruokolainen L, Lane A, Amato K, Knight R, Leigh S, Stumpf R, White B, Nelson KE, Baden AL, Tecot SR. PMID: 29205327.
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    520. Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2017 12 21; 552(7685):430. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. PMID: 29168501; PMCID: PMC8594569.
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    521. Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes. mSystems. 2017 Nov-Dec; 2(6). Jiang L, Amir A, Morton JT, Heller R, Arias-Castro E, Knight R. PMID: 29181446; PMCID: PMC5698492.
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    522. Evaluating the impact of domestication and captivity on the horse gut microbiome. Sci Rep. 2017 11 14; 7(1):15497. Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L. PMID: 29138485; PMCID: PMC5686199.
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    523. Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2017 11 16; 551(7680):340-345. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. PMID: 29144460; PMCID: PMC5884449.
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    524. Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-Oxide. Am J Respir Cell Mol Biol. 2017 11; 57(5):581-588. Xue J, Zhou D, Poulsen O, Imamura T, Hsiao YH, Smith TH, Malhotra A, Dorrestein P, Knight R, Haddad GG. PMID: 28678519; PMCID: PMC5705907.
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    525. Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. PLoS One. 2017; 12(10):e0184336. Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, Knight R, Stigum H, Eggesbø M. PMID: 29069100; PMCID: PMC5656300.
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    526. Guiding longitudinal sampling in IBD cohorts. Gut. 2018 09; 67(9):1743-1745. Vázquez-Baeza Y, Gonzalez A, Xu ZZ, Washburne A, Herfarth HH, Sartor RB, Knight R. PMID: 29055911; PMCID: PMC6109279.
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    527. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe. 2017 Nov 08; 22(5):705-716.e4. Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC. PMID: 29056429; PMCID: PMC6267898.
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    528. Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. mBio. 2017 10 17; 8(5). Maier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, Morton JT, González A, Ackermann G, Knight R, Riedel K, Krauss RM, Schmitt-Kopplin P, Jansson JK. PMID: 29042495; PMCID: PMC5646248.
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    529. Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017 11 09; 551(7679):256. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. PMID: 29022944; PMCID: PMC7608344.
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    530. Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. mSystems. 2017 Sep-Oct; 2(5). Reddivari L, Veeramachaneni DNR, Walters WA, Lozupone C, Palmer J, Hewage MKK, Bhatnagar R, Amir A, Kennett MJ, Knight R, Vanamala JKP. PMID: 29034330; PMCID: PMC5634791.
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    531. Impacts of the Human Gut Microbiome on Therapeutics. Annu Rev Pharmacol Toxicol. 2018 01 06; 58:253-270. Vázquez-Baeza Y, Callewaert C, Debelius J, Hyde E, Marotz C, Morton JT, Swafford A, Vrbanac A, Dorrestein PC, Knight R. PMID: 28968189.
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    532. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol. 2017 Nov; 35(11):1077-1086. Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Microbiome Quality Control Project Consortium, Abnet CC, Knight R, White O, Huttenhower C. PMID: 28967885; PMCID: PMC5839636.
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    533. The Effects of Captivity on the Mammalian Gut Microbiome. Integr Comp Biol. 2017 10 01; 57(4):690-704. McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh C, Orlando L, Mendelson JR, Sanders J, Knight R. PMID: 28985326; PMCID: PMC5978021.
      View in: PubMed   Mentions: 232     Fields:    Translation:AnimalsCells
    534. The sponge microbiome project. Gigascience. 2017 10 01; 6(10):1-7. Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T. PMID: 29020741; PMCID: PMC5632291.
      View in: PubMed   Mentions: 90     Fields:    Translation:Animals
    535. Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants. Integr Comp Biol. 2017 10 01; 57(4):705-722. Sanders JG, Lukasik P, Frederickson ME, Russell JA, Koga R, Knight R, Pierce NE. PMID: 28985400.
      View in: PubMed   Mentions: 46     Fields:    Translation:Animals
    536. The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study. Psychosom Med. 2017 Oct; 79(8):936-946. Hemmings SMJ, Malan-Müller S, van den Heuvel LL, Demmitt BA, Stanislawski MA, Smith DG, Bohr AD, Stamper CE, Hyde ER, Morton JT, Marotz CA, Siebler PH, Braspenning M, Van Criekinge W, Hoisington AJ, Brenner LA, Postolache TT, McQueen MB, Krauter KS, Knight R, Seedat S, Lowry CA. PMID: 28700459; PMCID: PMC5763914.
      View in: PubMed   Mentions: 122     Fields:    Translation:Humans
    537. Encoding and Decoding Models in Cognitive Electrophysiology. Front Syst Neurosci. 2017; 11:61. Holdgraf CR, Rieger JW, Micheli C, Martin S, Knight RT, Theunissen FE. PMID: 29018336; PMCID: PMC5623038.
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    538. Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection. Anal Chem. 2017 10 03; 89(19):10414-10421. McCall LI, Morton JT, Bernatchez JA, de Siqueira-Neto JL, Knight R, Dorrestein PC, McKerrow JH. PMID: 28892370; PMCID: PMC6298790.
      View in: PubMed   Mentions: 30     Fields:    Translation:Animals
    539. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017 10 05; 550(7674):61-66. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. PMID: 28953883; PMCID: PMC5831082.
      View in: PubMed   Mentions: 665     Fields:    Translation:Humans
    540. Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. Proc Natl Acad Sci U S A. 2017 10 03; 114(40):10713-10718. Cekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, Kanner R, Bencosme Y, Lee YK, Hauser SL, Crabtree-Hartman E, Sand IK, Gacias M, Zhu Y, Casaccia P, Cree BAC, Knight R, Mazmanian SK, Baranzini SE. PMID: 28893978; PMCID: PMC5635915.
      View in: PubMed   Mentions: 538     Fields:    Translation:HumansAnimalsCells
    541. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science. 2017 08 25; 357(6353):802-806. Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL. PMID: 28839072; PMCID: PMC5891123.
      View in: PubMed   Mentions: 413     Fields:    Translation:Humans
    542. Cortical representation of persistent visual stimuli. Neuroimage. 2017 11 01; 161:67-79. Gerber EM, Golan T, Knight RT, Deouell LY. PMID: 28807872; PMCID: PMC5957542.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    543. Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. Oncoimmunology. 2017; 6(12):e1361593. Jala VR, Maturu P, Bodduluri SR, Krishnan E, Mathis S, Subbarao K, Wang M, Jenson AB, Proctor ML, Rouchka EC, Knight R, Haribabu B. PMID: 29209564; PMCID: PMC5706601.
      View in: PubMed   Mentions: 11     Fields:    
    544. Anterior Thalamic High Frequency Band Activity Is Coupled with Theta Oscillations at Rest. Front Hum Neurosci. 2017; 11:358. Sweeney-Reed CM, Zaehle T, Voges J, Schmitt FC, Buentjen L, Borchardt V, Walter M, Hinrichs H, Heinze HJ, Rugg MD, Knight RT. PMID: 28775684; PMCID: PMC5518534.
      View in: PubMed   Mentions: 15  
    545. The Microbiome and Big Data. Curr Opin Syst Biol. 2017 Aug; 4:92-96. Navas-Molina JA, Hyde ER, Sanders J, Knight R. PMID: 36937228; PMCID: PMC10019530.
      View in: PubMed   Mentions: 7  
    546. Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples. Anal Chem. 2017 07 18; 89(14):7549-7559. Melnik AV, da Silva RR, Hyde ER, Aksenov AA, Vargas F, Bouslimani A, Protsyuk I, Jarmusch AK, Tripathi A, Alexandrov T, Knight R, Dorrestein PC. PMID: 28628333.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    547. Instantaneous voltage as an alternative to power- and phase-based interpretation of oscillatory brain activity. Neuroimage. 2017 08 15; 157:545-554. Schalk G, Marple J, Knight RT, Coon WG. PMID: 28624646; PMCID: PMC5600843.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    548. Reply to Wang and Chen: An ancient origin of magnetotactic bacteria. Proc Natl Acad Sci U S A. 2017 06 27; 114(26):E5019-E5020. Lin W, Paterson GA, Zhu Q, Wang Y, Kopylova E, Li Y, Knight R, Bazylinski DA, Zhu R, Kirschvink JL, Pan Y. PMID: 28607095; PMCID: PMC5495286.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    549. Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. Cancer Prev Res (Phila). 2017 Aug; 10(8):442-450. Charepalli V, Reddivari L, Radhakrishnan S, Eriksson E, Xiao X, Kim SW, Shen F, Vijay-Kumar M, Li Q, Bhat VB, Knight R, Vanamala JKP. PMID: 28576788; PMCID: PMC6188705.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    550. DNA extraction for streamlined metagenomics of diverse environmental samples. Biotechniques. 2017 06 01; 62(6):290-293. Marotz C, Amir A, Humphrey G, Gaffney J, Gogul G, Knight R. PMID: 28625159.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansCellsPHPublic Health
    551. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems. 2017 May-Jun; 2(3). Neilson JW, Califf K, Cardona C, Copeland A, van Treuren W, Josephson KL, Knight R, Gilbert JA, Quade J, Caporaso JG, Maier RM. PMID: 28593197; PMCID: PMC5451488.
      View in: PubMed   Mentions: 73     Fields:    
    552. Spatiotemporal dynamics of word retrieval in speech production revealed by cortical high-frequency band activity. Proc Natl Acad Sci U S A. 2017 06 06; 114(23):E4530-E4538. Riès SK, Dhillon RK, Clarke A, King-Stephens D, Laxer KD, Weber PB, Kuperman RA, Auguste KI, Brunner P, Schalk G, Lin JJ, Parvizi J, Crone NE, Dronkers NF, Knight RT. PMID: 28533406; PMCID: PMC5468648.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    553. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. Microbiome. 2017 05 15; 5(1):55. Khanna S, Vazquez-Baeza Y, González A, Weiss S, Schmidt B, Muñiz-Pedrogo DA, Rainey JF, Kammer P, Nelson H, Sadowsky M, Khoruts A, Farrugia SL, Knight R, Pardi DS, Kashyap PC. PMID: 28506317; PMCID: PMC5433077.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansCells
    554. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. Elife. 2017 05 11; 6. Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. PMID: 28492366; PMCID: PMC5441867.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    555. An Elegan(t) Screen for Drug-Microbe Interactions. Cell Host Microbe. 2017 May 10; 21(5):555-556. Vrbanac A, Debelius JW, Jiang L, Morton JT, Dorrestein P, Knight R. PMID: 28494234.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    556. Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh. Appl Environ Microbiol. 2017 05 15; 83(10). Vogtmann E, Chen J, Kibriya MG, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Ahsan H, Sinha R. PMID: 28258145; PMCID: PMC5411505.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    557. Unique Strain of Rickettsia parkeri Associated with the Hard Tick Dermacentor parumapertus Neumann in the Western United States. Appl Environ Microbiol. 2017 05 01; 83(9). Paddock CD, Allerdice MEJ, Karpathy SE, Nicholson WL, Levin ML, Smith TC, Becker T, Delph RJ, Knight RN, Ritter JM, Sanders JH, Goddard J. PMID: 28213544; PMCID: PMC5394329.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    558. Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort". mSystems. 2017 Mar-Apr; 2(2). Gonzalez A, Hyde E, Sangwan N, Gilbert JA, Viirre E, Knight R. PMID: 28428981; PMCID: PMC5388783.
      View in: PubMed   Mentions: 2     Fields:    
    559. Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus. Front Microbiol. 2017; 8:526. Novakova E, Woodhams DC, Rodríguez-Ruano SM, Brucker RM, Leff JW, Maharaj A, Amir A, Knight R, Scott J. PMID: 28421042; PMCID: PMC5378795.
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    560. Microbiome Tools for Forensic Science. Trends Biotechnol. 2017 09; 35(9):814-823. Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R. PMID: 28366290.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimals
    561. Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites. Front Plant Sci. 2017; 8:429. Floros DJ, Petras D, Kapono CA, Melnik AV, Ling TJ, Knight R, Dorrestein PC. PMID: 28405197; PMCID: PMC5370242.
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    562. Neuroplasticity of language in left-hemisphere stroke: Evidence linking subsecond electrophysiology and structural connections. Hum Brain Mapp. 2017 06; 38(6):3151-3162. Piai V, Meyer L, Dronkers NF, Knight RT. PMID: 28345282; PMCID: PMC5610921.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    563. Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape. PLoS One. 2017; 12(3):e0173811. King HC, Khera-Butler T, James P, Oakley BB, Erenso G, Aseffa A, Knight R, Wellington EM, Courtenay O. PMID: 28333945; PMCID: PMC5363844.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCellsPHPublic Health
    564. Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes. Environ Microbiol. 2017 05; 19(5):1845-1856. Thompson LR, Nikolakakis K, Pan S, Reed J, Knight R, Ruby EG. PMID: 28152560; PMCID: PMC5409853.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    565. The Microbiome and Human Biology. Annu Rev Genomics Hum Genet. 2017 08 31; 18:65-86. Knight R, Callewaert C, Marotz C, Hyde ER, Debelius JW, McDonald D, Sogin ML. PMID: 28375652.
      View in: PubMed   Mentions: 169     Fields:    Translation:HumansAnimals
    566. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems. 2017 Mar-Apr; 2(2). Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R. PMID: 28289731; PMCID: PMC5340863.
      View in: PubMed   Mentions: 945     Fields:    
    567. Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping. mSystems. 2017 Mar-Apr; 2(2). Amir A, McDonald D, Navas-Molina JA, Debelius J, Morton JT, Hyde E, Robbins-Pianka A, Knight R. PMID: 28289733; PMCID: PMC5340865.
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    568. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017 03 03; 5(1):27. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. PMID: 28253908; PMCID: PMC5335496.
      View in: PubMed   Mentions: 886     Fields:    Translation:HumansCells
    569. Uncovering the Horseshoe Effect in Microbial Analyses. mSystems. 2017 Jan-Feb; 2(1). Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R. PMID: 28251186; PMCID: PMC5320001.
      View in: PubMed   Mentions: 50     Fields:    
    570. Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome. Mov Disord. 2017 05; 32(5):739-749. Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R, Payami H. PMID: 28195358; PMCID: PMC5469442.
      View in: PubMed   Mentions: 452     Fields:    Translation:HumansAnimalsCells
    571. Origin of microbial biomineralization and magnetotaxis during the Archean. Proc Natl Acad Sci U S A. 2017 02 28; 114(9):2171-2176. Lin W, Paterson GA, Zhu Q, Wang Y, Kopylova E, Li Y, Knight R, Bazylinski DA, Zhu R, Kirschvink JL, Pan Y. PMID: 28193877; PMCID: PMC5338559.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    572. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol. 2017 Feb 13; 2:17004. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. PMID: 28191884; PMCID: PMC5319707.
      View in: PubMed   Mentions: 595     Fields:    Translation:Humans
    573. Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. Microb Ecol. 2017 07; 74(1):250-258. Amato KR, Van Belle S, Di Fiore A, Estrada A, Stumpf R, White B, Nelson KE, Knight R, Leigh SR. PMID: 28124727.
      View in: PubMed   Mentions: 47     Fields:    Translation:Animals
    574. Balance Trees Reveal Microbial Niche Differentiation. mSystems. 2017 Jan-Feb; 2(1). Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R. PMID: 28144630; PMCID: PMC5264246.
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    575. Bringing the Dynamic Microbiome to Life with Animations. Cell Host Microbe. 2017 Jan 11; 21(1):7-10. Vázquez-Baeza Y, Gonzalez A, Smarr L, McDonald D, Morton JT, Navas-Molina JA, Knight R. PMID: 28081445.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    576. Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity. Front Behav Neurosci. 2016; 10:240. Thompson RS, Roller R, Mika A, Greenwood BN, Knight R, Chichlowski M, Berg BM, Fleshner M. PMID: 28119579; PMCID: PMC5223485.
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    577. Rapid tuning shifts in human auditory cortex enhance speech intelligibility. Nat Commun. 2016 12 20; 7:13654. Holdgraf CR, de Heer W, Pasley B, Rieger J, Crone N, Lin JJ, Knight RT, Theunissen FE. PMID: 27996965; PMCID: PMC5187445.
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    578. Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk. Br J Nutr. 2016 Dec; 116(12):2020-2029. Bergeron N, Williams PT, Lamendella R, Faghihnia N, Grube A, Li X, Wang Z, Knight R, Jansson JK, Hazen SL, Krauss RM. PMID: 27993177; PMCID: PMC5885763.
      View in: PubMed   Mentions: 46     Fields:    Translation:Humans
    579. Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separation. Surgery. 2017 04; 161(4):1016-1027. Schall KA, Holoyda KA, Isani M, Schlieve C, Salisbury T, Khuu T, Debelius JW, Moats RA, Pollack HA, Lien CL, Fowler K, Hou X, Knight R, Grikscheit TC. PMID: 28011012.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    580. Comparison of Collection Methods for Fecal Samples in Microbiome Studies. Am J Epidemiol. 2017 01 15; 185(2):115-123. Vogtmann E, Chen J, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Sinha R. PMID: 27986704; PMCID: PMC5253972.
      View in: PubMed   Mentions: 89     Fields:    Translation:Humans
    581. Antibiotic discovery is a walk in the park. Proc Natl Acad Sci U S A. 2016 12 20; 113(51):14477-14479. Nothias LF, Knight R, Dorrestein PC. PMID: 27940910; PMCID: PMC5187748.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    582. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Cell. 2016 Dec 01; 167(6):1469-1480.e12. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK. PMID: 27912057; PMCID: PMC5718049.
      View in: PubMed   Mentions: 1752     Fields:    Translation:HumansAnimalsCells
    583. Let researchers try new paths. Nature. 2016 10 27; 538(7626):451-453. Oni T, Sciarrino F, Adesso G, Knight R. PMID: 27786218.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    584. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biol. 2016 10 19; 17(1):217. Debelius J, Song SJ, Vazquez-Baeza Y, Xu ZZ, Gonzalez A, Knight R. PMID: 27760558; PMCID: PMC5072314.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimals
    585. Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake. Microbiome. 2016 10 19; 4(1):55. Mandal S, Godfrey KM, McDonald D, Treuren WV, Bjørnholt JV, Midtvedt T, Moen B, Rudi K, Knight R, Brantsæter AL, Peddada SD, Eggesbø M. PMID: 27756413; PMCID: PMC5070355.
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    586. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. mSystems. 2016 Sep-Oct; 1(5). Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG. PMID: 27822553; PMCID: PMC5080401.
      View in: PubMed   Mentions: 47     Fields:    
    587. Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort. mSystems. 2016 Sep-Oct; 1(5). Gonzalez A, Hyde E, Sangwan N, Gilbert JA, Viirre E, Knight R. PMID: 27822557; PMCID: PMC5080405.
      View in: PubMed   Mentions: 39     Fields:    
    588. Ripples on spikes show increased phase-amplitude coupling in mesial temporal lobe epilepsy seizure-onset zones. Epilepsia. 2016 11; 57(11):1916-1930. Weiss SA, Orosz I, Salamon N, Moy S, Wei L, Van't Klooster MA, Knight RT, Harper RM, Bragin A, Fried I, Engel J, Staba RJ. PMID: 27723936; PMCID: PMC5118142.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    589. Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks. Nat Microbiol. 2016 Oct 03; 1:16177. Vázquez-Baeza Y, Hyde ER, Suchodolski JS, Knight R. PMID: 27694806.
      View in: PubMed   Mentions: 142     Fields:    Translation:HumansAnimals
    590. Precision medicine in alcoholic and nonalcoholic fatty liver disease via modulating the gut microbiota. Am J Physiol Gastrointest Liver Physiol. 2016 12 01; 311(6):G1018-G1036. Bluemel S, Williams B, Knight R, Schnabl B. PMID: 27686615; PMCID: PMC5206291.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimals
    591. Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity. Proc Biol Sci. 2016 Sep 28; 283(1839). Kueneman JG, Woodhams DC, Harris R, Archer HM, Knight R, McKenzie VJ. PMID: 27655769; PMCID: PMC5046908.
      View in: PubMed   Mentions: 86     Fields:    Translation:Animals
    592. Culturing: Looking it up in our gut. Nat Microbiol. 2016 09 27; 1(10):16169. Marotz C, Knight R. PMID: 27670121.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    593. Effects of field conditions on fecal microbiota. J Microbiol Methods. 2016 11; 130:180-188. Hale VL, Tan CL, Niu K, Yang Y, Cui D, Zhao H, Knight R, Amato KR. PMID: 27686380.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    594. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol. 2016 Sep 26; 17(1):189. Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT. PMID: 27666579; PMCID: PMC5036307.
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    595. Direct brain recordings reveal hippocampal rhythm underpinnings of language processing. Proc Natl Acad Sci U S A. 2016 10 04; 113(40):11366-11371. Piai V, Anderson KL, Lin JJ, Dewar C, Parvizi J, Dronkers NF, Knight RT. PMID: 27647880; PMCID: PMC5056038.
      View in: PubMed   Mentions: 81     Fields:    Translation:Humans
    596. The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health. Curr Environ Health Rep. 2016 09; 3(3):270-86. Lowry CA, Smith DG, Siebler PH, Schmidt D, Stamper CE, Hassell JE, Yamashita PS, Fox JH, Reber SO, Brenner LA, Hoisington AJ, Postolache TT, Kinney KA, Marciani D, Hernandez M, Hemmings SM, Malan-Muller S, Wright KP, Knight R, Raison CL, Rook GA. PMID: 27436048; PMCID: PMC5763918.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsPHPublic Health
    597. Extreme Dysbiosis of the Microbiome in Critical Illness. mSphere. 2016 Jul-Aug; 1(4). McDonald D, Ackermann G, Khailova L, Baird C, Heyland D, Kozar R, Lemieux M, Derenski K, King J, Vis-Kampen C, Knight R, Wischmeyer PE. PMID: 27602409; PMCID: PMC5007431.
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    598. Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies. Cancer Epidemiol Biomarkers Prev. 2016 11; 25(11):1483-1490. Loftfield E, Vogtmann E, Sampson JN, Moore SC, Nelson H, Knight R, Chia N, Sinha R. PMID: 27543620; PMCID: PMC5093035.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    599. Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infect Genet Evol. 2016 11; 45:95-97. Scanlan PD, Knight R, Song SJ, Ackermann G, Cotter PD. PMID: 27545648.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimals
    600. The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems. 2016 Jul-Aug; 1(4). Hyde ER, Navas-Molina JA, Song SJ, Kueneman JG, Ackermann G, Cardona C, Humphrey G, Boyer D, Weaver T, Mendelson JR, McKenzie VJ, Gilbert JA, Knight R. PMID: 27822543; PMCID: PMC5069958.
      View in: PubMed   Mentions: 52     Fields:    
    601. Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness. Curr Opin Crit Care. 2016 08; 22(4):347-53. Wischmeyer PE, McDonald D, Knight R. PMID: 27327243; PMCID: PMC5065053.
      View in: PubMed   Mentions: 76     Fields:    Translation:Humans
    602. Metagenomic covariation along densely sampled environmental gradients in the Red Sea. ISME J. 2017 01; 11(1):138-151. Thompson LR, Williams GJ, Haroon MF, Shibl A, Larsen P, Shorenstein J, Knight R, Stingl U. PMID: 27420030; PMCID: PMC5315489.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    603. Microbiology of death. Curr Biol. 2016 07 11; 26(13):R561-R563. Metcalf JL, Carter DO, Knight R. PMID: 27404249.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsPHPublic Health
    604. Atypical Brain Mechanisms of Prediction According to Uncertainty in Autism. Front Neurosci. 2016; 10:317. Thillay A, Lemaire M, Roux S, Houy-Durand E, Barthélémy C, Knight RT, Bidet-Caulet A, Bonnet-Brilhault F. PMID: 27458337; PMCID: PMC4937033.
      View in: PubMed   Mentions: 18  
    605. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016 07 07; 535(7610):94-103. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. PMID: 27383984.
      View in: PubMed   Mentions: 341     Fields:    Translation:HumansAnimalsCells
    606. The use of intracranial recordings to decode human language: Challenges and opportunities. Brain Lang. 2019 06; 193:73-83. Martin S, Millán JDR, Knight RT, Pasley BN. PMID: 27377299; PMCID: PMC5203979.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    607. Diversity, structure and convergent evolution of the global sponge microbiome. Nat Commun. 2016 06 16; 7:11870. Thomas T, Moitinho-Silva L, Lurgi M, Björk JR, Easson C, Astudillo-García C, Olson JB, Erwin PM, López-Legentil S, Luter H, Chaves-Fonnegra A, Costa R, Schupp PJ, Steindler L, Erpenbeck D, Gilbert J, Knight R, Ackermann G, Victor Lopez J, Taylor MW, Thacker RW, Montoya JM, Hentschel U, Webster NS. PMID: 27306690; PMCID: PMC4912640.
      View in: PubMed   Mentions: 275     Fields:    Translation:Animals
    608. Clinical, neuropsychological, and pre-stimulus dorsomedial thalamic nucleus electrophysiological data in deep brain stimulation patients. Data Brief. 2016 Sep; 8:557-61. Sweeney-Reed CM, Zaehle T, Voges J, Schmitt FC, Buentjen L, Kopitzki K, Richardson-Klavehn A, Hinrichs H, Heinze HJ, Knight RT, Rugg MD. PMID: 27508216; PMCID: PMC4961763.
      View in: PubMed   Mentions: 1  
    609. Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. Gigascience. 2016 06 13; 5:27. Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG. PMID: 27296526; PMCID: PMC4906574.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    610. The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease. Surgery. 2016 08; 160(2):350-8. Wieck MM, Debelius JW, Spurrier RG, Trecartin A, Knight R, Grikscheit TC. PMID: 27302104.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    611. Stress response, gut microbial diversity and sexual signals correlate with social interactions. Biol Lett. 2016 Jun; 12(6). Levin II, Zonana DM, Fosdick BK, Song SJ, Knight R, Safran RJ. PMID: 27354713; PMCID: PMC4938059.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    612. Hierarchy of prediction errors for auditory events in human temporal and frontal cortex. Proc Natl Acad Sci U S A. 2016 06 14; 113(24):6755-60. Dürschmid S, Edwards E, Reichert C, Dewar C, Hinrichs H, Heinze HJ, Kirsch HE, Dalal SS, Deouell LY, Knight RT. PMID: 27247381; PMCID: PMC4914143.
      View in: PubMed   Mentions: 71     Fields:    Translation:Humans
    613. Pre-stimulus thalamic theta power predicts human memory formation. Neuroimage. 2016 Sep; 138:100-108. Sweeney-Reed CM, Zaehle T, Voges J, Schmitt FC, Buentjen L, Kopitzki K, Richardson-Klavehn A, Hinrichs H, Heinze HJ, Knight RT, Rugg MD. PMID: 27208861.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    614. Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice. Proc Natl Acad Sci U S A. 2016 May 31; 113(22):E3130-9. Reber SO, Siebler PH, Donner NC, Morton JT, Smith DG, Kopelman JM, Lowe KR, Wheeler KJ, Fox JH, Hassell JE, Greenwood BN, Jansch C, Lechner A, Schmidt D, Uschold-Schmidt N, Füchsl AM, Langgartner D, Walker FR, Hale MW, Lopez Perez G, Van Treuren W, González A, Halweg-Edwards AL, Fleshner M, Raison CL, Rook GA, Peddada SD, Knight R, Lowry CA. PMID: 27185913; PMCID: PMC4896712.
      View in: PubMed   Mentions: 91     Fields:    Translation:AnimalsCellsPHPublic Health
    615. Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta). Am J Primatol. 2016 Aug; 78(8):883-92. Bennett G, Malone M, Sauther ML, Cuozzo FP, White B, Nelson KE, Stumpf RM, Knight R, Leigh SR, Amato KR. PMID: 27177345.
      View in: PubMed   Mentions: 65     Fields:    Translation:Animals
    616. Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. mBio. 2016 05 13; 7(3). Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. PMID: 27178263; PMCID: PMC4895116.
      View in: PubMed   Mentions: 67     Fields:    Translation:Humans
    617. Word pair classification during imagined speech using direct brain recordings. Sci Rep. 2016 05 11; 6:25803. Martin S, Brunner P, Iturrate I, Millán Jdel R, Schalk G, Knight RT, Pasley BN. PMID: 27165452; PMCID: PMC4863149.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    618. Genetic Determinants of the Gut Microbiome in UK Twins. Cell Host Microbe. 2016 May 11; 19(5):731-43. Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C, Spector TD, Bell JT, Clark AG, Ley RE. PMID: 27173935; PMCID: PMC4915943.
      View in: PubMed   Mentions: 542     Fields:    Translation:HumansCells
    619. Microbial Skin Inhabitants: Friends Forever. Cell. 2016 May 05; 165(4):771-2. Dorrestein PC, Gallo RL, Knight R. PMID: 27153488.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    620. Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems. 2016 May-Jun; 1(3). Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R. PMID: 27822526; PMCID: PMC5069758.
      View in: PubMed   Mentions: 252     Fields:    
    621. From Sample to Multi-Omics Conclusions in under 48 Hours. mSystems. 2016 Mar-Apr; 1(2). Quinn RA, Navas-Molina JA, Hyde ER, Song SJ, Vázquez-Baeza Y, Humphrey G, Gaffney J, Minich JJ, Melnik AV, Herschend J, DeReus J, Durant A, Dutton RJ, Khosroheidari M, Green C, da Silva R, Dorrestein PC, Knight R. PMID: 27822524; PMCID: PMC5069746.
      View in: PubMed   Mentions: 29     Fields:    
    622. Geography and Location Are the Primary Drivers of Office Microbiome Composition. mSystems. 2016 Mar-Apr; 1(2). Chase J, Fouquier J, Zare M, Sonderegger DL, Knight R, Kelley ST, Siegel J, Caporaso JG. PMID: 27822521; PMCID: PMC5069741.
      View in: PubMed   Mentions: 78     Fields:    
    623. Differential Processing of Consonance and Dissonance within the Human Superior Temporal Gyrus. Front Hum Neurosci. 2016; 10:154. Foo F, King-Stephens D, Weber P, Laxer K, Parvizi J, Knight RT. PMID: 27148011; PMCID: PMC4829599.
      View in: PubMed   Mentions: 9  
    624. Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin. Front Microbiol. 2016; 7:333. Loudon AH, Venkataraman A, Van Treuren W, Woodhams DC, Parfrey LW, McKenzie VJ, Knight R, Schmidt TM, Harris RN. PMID: 27014249; PMCID: PMC4793798.
      View in: PubMed   Mentions: 38  
    625. A Cool Approach to Probing Speech Cortex. Neuron. 2016 Mar 16; 89(6):1123-1125. Flinker A, Knight RT. PMID: 26985719; PMCID: PMC4864495.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    626. Fecal Microbiome in Epidemiologic Studies-Response. Cancer Epidemiol Biomarkers Prev. 2016 05; 25(5):870-1. Sinha R, Vogtmann E, Chen J, Amir A, Shi J, Sampson J, Flores R, Knight R, Chia N. PMID: 26961994; PMCID: PMC4873434.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    627. Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project. J Microbiol Biol Educ. 2016 Mar; 17(1):46-50. Debelius JW, Vázquez-Baeza Y, McDonald D, Xu Z, Wolfe E, Knight R. PMID: 27047589; PMCID: PMC4798814.
      View in: PubMed   Mentions: 19  
    628. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome. 2016 Feb 24; 4:11. Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST. PMID: 26905735; PMCID: PMC4765138.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimals
    629. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016 07; 10(7):1669-81. Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. PMID: 26905627; PMCID: PMC4918442.
      View in: PubMed   Mentions: 323     Fields:    Translation:HumansCells
    630. Walls talk: Microbial biogeography of homes spanning urbanization. Sci Adv. 2016 Feb; 2(2):e1501061. Ruiz-Calderon JF, Cavallin H, Song SJ, Novoselac A, Pericchi LR, Hernandez JN, Rios R, Branch OH, Pereira H, Paulino LC, Blaser MJ, Knight R, Dominguez-Bello MG. PMID: 26933683; PMCID: PMC4758746.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCellsPHPublic Health
    631. Frontal and motor cortex contributions to response inhibition: evidence from electrocorticography. J Neurophysiol. 2016 Apr; 115(4):2224-36. Fonken YM, Rieger JW, Tzvi E, Crone NE, Chang E, Parvizi J, Knight RT, Krämer UM. PMID: 26864760; PMCID: PMC4869511.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    632. Open-Source Sequence Clustering Methods Improve the State Of the Art. mSystems. 2016 Jan-Feb; 1(1). Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R. PMID: 27822515; PMCID: PMC5069751.
      View in: PubMed   Mentions: 78     Fields:    
    633. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med. 2016 Mar; 22(3):250-3. Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC. PMID: 26828196; PMCID: PMC5062956.
      View in: PubMed   Mentions: 408     Fields:    Translation:HumansCells
    634. Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli. PLoS One. 2016; 11(1):e0146916. Weiss SJ, Mansell TJ, Mortazavi P, Knight R, Gill RT. PMID: 26771672; PMCID: PMC4714920.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    635. Choosing words: left hemisphere, right hemisphere, or both? Perspective on the lateralization of word retrieval. Ann N Y Acad Sci. 2016 04; 1369(1):111-31. Riès SK, Dronkers NF, Knight RT. PMID: 26766393; PMCID: PMC4874870.
      View in: PubMed   Mentions: 43     Fields:    Translation:Humans
    636. Connect MM® - the Multiple Myeloma Disease Registry: incidence of second primary malignancies in patients treated with lenalidomide. Leuk Lymphoma. 2016 09; 57(9):2228-31. Rifkin RM, Abonour R, Shah JJ, Mehta J, Narang M, Terebelo H, Gasparetto C, Toomey K, Hardin JW, Lu JJ, Kenvin L, Srinivasan S, Knight R, Nagarwala Y, Durie BG. PMID: 26766599.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    637. Tools for the Microbiome: Nano and Beyond. ACS Nano. 2016 Jan 26; 10(1):6-37. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GC, Wright AT, Young TD. PMID: 26695070.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansPHPublic Health
    638. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems. 2016 Jan-Feb; 1(1). Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R. PMID: 27822518; PMCID: PMC5069754.
      View in: PubMed   Mentions: 845     Fields:    
    639. Euphorbia plant latex is inhabited by diverse microbial communities. Am J Bot. 2015 Dec; 102(12):1966-77. Gunawardana M, Hyde ER, Lahmeyer S, Dorsey BL, La Val TP, Mullen M, Yoo J, Knight R, Baum MM. PMID: 26656131.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    640. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2016 Jan 08; 351(6269):158-62. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. PMID: 26657285.
      View in: PubMed   Mentions: 171     Fields:    Translation:AnimalsCellsPHPublic Health
    641. The microbiome quality control project: baseline study design and future directions. Genome Biol. 2015 Dec 09; 16:276. Sinha R, Abnet CC, White O, Knight R, Huttenhower C. PMID: 26653756; PMCID: PMC4674991.
      View in: PubMed   Mentions: 135     Fields:    Translation:Humans
    642. Can Your Microbiome Tell You What to Eat? Cell Metab. 2015 Dec 01; 22(6):960-1. Vanamala JK, Knight R, Spector TD. PMID: 26636494.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    643. Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies. Cancer Epidemiol Biomarkers Prev. 2016 Feb; 25(2):407-16. Sinha R, Chen J, Amir A, Vogtmann E, Shi J, Inman KS, Flores R, Sampson J, Knight R, Chia N. PMID: 26604270; PMCID: PMC4821594.
      View in: PubMed   Mentions: 111     Fields:    Translation:Humans
    644. Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia. 2016 Mar; 180(3):717-33. Amato KR, Martinez-Mota R, Righini N, Raguet-Schofield M, Corcione FP, Marini E, Humphrey G, Gogul G, Gaffney J, Lovelace E, Williams L, Luong A, Dominguez-Bello MG, Stumpf RM, White B, Nelson KE, Knight R, Leigh SR. PMID: 26597549.
      View in: PubMed   Mentions: 61     Fields:    Translation:Animals
    645. Authors' reply to Mawer and Wilcox and Mullish and Williams. BMJ. 2015 Nov 19; 351:h6132. Spector T, Knight R. PMID: 26586410.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    646. Variable responses of human and non-human primate gut microbiomes to a Western diet. Microbiome. 2015 Nov 16; 3:53. Amato KR, Yeoman CJ, Cerda G, Schmitt CA, Cramer JD, Miller ME, Gomez A, Turner TR, Wilson BA, Stumpf RM, Nelson KE, White BA, Knight R, Leigh SR. PMID: 26568112; PMCID: PMC4645477.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    647. Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas). ISME J. 2016 Apr; 10(4):934-44. Kueneman JG, Woodhams DC, Van Treuren W, Archer HM, Knight R, McKenzie VJ. PMID: 26565725; PMCID: PMC4796932.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    648. Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits. ACS Synth Biol. 2015 Nov 20; 4(11):1244-53. Freed EF, Winkler JD, Weiss SJ, Garst AD, Mutalik VK, Arkin AP, Knight R, Gill RT. PMID: 26478262.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    649. Context and the human microbiome. Microbiome. 2015 Nov 04; 3:52. McDonald D, Birmingham A, Knight R. PMID: 26530830; PMCID: PMC4632476.
      View in: PubMed   Mentions: 31     Fields:    Translation:Humans
    650. Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life. Am J Clin Nutr. 2015 Dec; 102(6):1381-8. Alderete TL, Autran C, Brekke BE, Knight R, Bode L, Goran MI, Fields DA. PMID: 26511224; PMCID: PMC6546222.
      View in: PubMed   Mentions: 101     Fields:    Translation:Humans
    651. Faecal transplants. BMJ. 2015 Oct 20; 351:h5149. Spector T, Knight R. PMID: 26487671.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    652. Age-Related Changes in 1/f Neural Electrophysiological Noise. J Neurosci. 2015 Sep 23; 35(38):13257-65. Voytek B, Kramer MA, Case J, Lepage KQ, Tempesta ZR, Knight RT, Gazzaley A. PMID: 26400953; PMCID: PMC4579381.
      View in: PubMed   Mentions: 329     Fields:    Translation:HumansPHPublic Health
    653. Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota. Cell Host Microbe. 2015 Sep 09; 18(3):296-306. Teng F, Yang F, Huang S, Bo C, Xu ZZ, Amir A, Knight R, Ling J, Xu J. PMID: 26355216.
      View in: PubMed   Mentions: 144     Fields:    Translation:Humans
    654. ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol. 2015 Oct; 33(10):1045-52. Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D. PMID: 26344404; PMCID: PMC4676274.
      View in: PubMed   Mentions: 138     Fields:    Translation:Cells
    655. Elevated synchrony in Parkinson disease detected with electroencephalography. Ann Neurol. 2015 Nov; 78(5):742-50. Swann NC, de Hemptinne C, Aron AR, Ostrem JL, Knight RT, Starr PA. PMID: 26290353; PMCID: PMC4623949.
      View in: PubMed   Mentions: 70     Fields:    Translation:Humans
    656. Genetic and environmental control of host-gut microbiota interactions. Genome Res. 2015 Oct; 25(10):1558-69. Org E, Parks BW, Joo JW, Emert B, Schwartzman W, Kang EY, Mehrabian M, Pan C, Knight R, Gunsalus R, Drake TA, Eskin E, Lusis AJ. PMID: 26260972; PMCID: PMC4579341.
      View in: PubMed   Mentions: 177     Fields:    Translation:Animals
    657. The gut microbiota in human energy homeostasis and obesity. Trends Endocrinol Metab. 2015 Sep; 26(9):493-501. Rosenbaum M, Knight R, Leibel RL. PMID: 26257300; PMCID: PMC4862197.
      View in: PubMed   Mentions: 185     Fields:    Translation:HumansAnimals
    658. Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome. 2015; 3:34. He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW. PMID: 26229598; PMCID: PMC4520016.
      View in: PubMed   Mentions: 2     Fields:    
    659. Oscillatory dynamics coordinating human frontal networks in support of goal maintenance. Nat Neurosci. 2015 Sep; 18(9):1318-24. Voytek B, Kayser AS, Badre D, Fegen D, Chang EF, Crone NE, Parvizi J, Knight RT, D'Esposito M. PMID: 26214371; PMCID: PMC4551604.
      View in: PubMed   Mentions: 112     Fields:    Translation:Humans
    660. Short Course in the Microbiome. J Circ Biomark. 2015 Jan-Dec; 4:8. Falana K, Knight R, Martin CR, Goldszmid R, Greathouse KL, Gere J, Young H, Kuo WP. PMID: 28936244; PMCID: PMC5572982.
      View in: PubMed   Mentions: 2  
    661. The UniFrac significance test is sensitive to tree topology. BMC Bioinformatics. 2015 Jul 07; 16:211. Lozupone CA, Knight R. PMID: 26150095; PMCID: PMC4492014.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    662. Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex. Appl Environ Microbiol. 2015 Sep; 81(18):6200-9. Van Treuren W, Ponnusamy L, Brinkerhoff RJ, Gonzalez A, Parobek CM, Juliano JJ, Andreadis TG, Falco RC, Ziegler LB, Hathaway N, Keeler C, Emch M, Bailey JA, Roe RM, Apperson CS, Knight R, Meshnick SR. PMID: 26150449; PMCID: PMC4542252.
      View in: PubMed   Mentions: 124     Fields:    Translation:AnimalsCells
    663. Carcass mass has little influence on the structure of gravesoil microbial communities. Int J Legal Med. 2016 Jan; 130(1):253-63. Weiss S, Carter DO, Metcalf JL, Knight R. PMID: 26024793; PMCID: PMC9645124.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCellsPHPublic Health
    664. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015; 26:27663. Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. PMID: 26028277; PMCID: PMC4450248.
      View in: PubMed   Mentions: 1072  
    665. Exercise is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats. PLoS One. 2015; 10(5):e0125889. Mika A, Van Treuren W, González A, Herrera JJ, Knight R, Fleshner M. PMID: 26016739; PMCID: PMC4446322.
      View in: PubMed   Mentions: 105     Fields:    Translation:Animals
    666. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome. 2015; 3:20. He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW. PMID: 25995836; PMCID: PMC4438525.
      View in: PubMed   Mentions: 67     Fields:    
    667. Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt. Appl Environ Microbiol. 2015 Aug; 81(15):4965-75. Bisanz JE, Enos MK, PrayGod G, Seney S, Macklaim JM, Chilton S, Willner D, Knight R, Fusch C, Fusch G, Gloor GB, Burton JP, Reid G. PMID: 25979893; PMCID: PMC4495201.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCells
    668. Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host Microbe. 2015 May 13; 17(5):603-16. Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, McHardy AC, Dangl JL, Knight R, Ley R, Schulze-Lefert P. PMID: 25974302.
      View in: PubMed   Mentions: 310     Fields:    Translation:Animals
    669. Dynamic network communication as a unifying neural basis for cognition, development, aging, and disease. Biol Psychiatry. 2015 Jun 15; 77(12):1089-97. Voytek B, Knight RT. PMID: 26005114; PMCID: PMC4443259.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansAnimalsCells
    670. Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota. ISME J. 2015 Nov; 9(11):2515-26. Smith CC, Snowberg LK, Gregory Caporaso J, Knight R, Bolnick DI. PMID: 25909977; PMCID: PMC4611514.
      View in: PubMed   Mentions: 161     Fields:    Translation:AnimalsPHPublic Health
    671. The microbiome of uncontacted Amerindians. Sci Adv. 2015 Apr 03; 1(3). Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG. PMID: 26229982; PMCID: PMC4517851.
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    672. Ribosomal RNA, the lens into life. RNA. 2015 Apr; 21(4):692-4. McDonald D, Xu Z, Hyde ER, Knight R. PMID: 25780194; PMCID: PMC4371336.
      View in: PubMed   Mentions: 2     Fields:    
    673. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome. 2015; 3:10. Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ. PMID: 25825673; PMCID: PMC4378022.
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    674. Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci U S A. 2015 Apr 28; 112(17):E2120-9. Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC. PMID: 25825778; PMCID: PMC4418856.
      View in: PubMed   Mentions: 171     Fields:    Translation:Humans
    675. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods. 2015 Jun; 113:16-26. Hale VL, Tan CL, Knight R, Amato KR. PMID: 25819008.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansAnimals
    676. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 2015 Mar 25; 6:6505. Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, Lewis CM. PMID: 25807110; PMCID: PMC4386023.
      View in: PubMed   Mentions: 270     Fields:    Translation:HumansCells
    677. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microb Ecol Health Dis. 2015; 26:26555. McDonald D, Hornig M, Lozupone C, Debelius J, Gilbert JA, Knight R. PMID: 25758371; PMCID: PMC4355505.
      View in: PubMed   Mentions: 11  
    678. Seasonal variation of postmortem microbial communities. Forensic Sci Med Pathol. 2015 Jun; 11(2):202-7. Carter DO, Metcalf JL, Bibat A, Knight R. PMID: 25737335; PMCID: PMC9636889.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsPHPublic Health
    679. Microbial endocrinology: the interplay between the microbiota and the endocrine system. FEMS Microbiol Rev. 2015 Jul; 39(4):509-21. Neuman H, Debelius JW, Knight R, Koren O. PMID: 25701044.
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    680. Redefining the role of Broca's area in speech. Proc Natl Acad Sci U S A. 2015 Mar 03; 112(9):2871-5. Flinker A, Korzeniewska A, Shestyuk AY, Franaszczuk PJ, Dronkers NF, Knight RT, Crone NE. PMID: 25730850; PMCID: PMC4352780.
      View in: PubMed   Mentions: 216     Fields:    Translation:HumansCTClinical Trials
    681. Necessary, yet dissociable contributions of the insular and ventromedial prefrontal cortices to norm adaptation: computational and lesion evidence in humans. J Neurosci. 2015 Jan 14; 35(2):467-73. Gu X, Wang X, Hula A, Wang S, Xu S, Lohrenz TM, Knight RT, Gao Z, Dayan P, Montague PR. PMID: 25589742; PMCID: PMC4293403.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    682. Sensory Deviancy Detection Measured Directly Within the Human Nucleus Accumbens. Cereb Cortex. 2016 Mar; 26(3):1168-1175. Dürschmid S, Zaehle T, Hinrichs H, Heinze HJ, Voges J, Garrido MI, Dolan RJ, Knight RT. PMID: 25576536; PMCID: PMC4737607.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    683. Tracking down the sources of experimental contamination in microbiome studies. Genome Biol. 2014 Dec 17; 15(12):564. Weiss S, Amir A, Hyde ER, Metcalf JL, Song SJ, Knight R. PMID: 25608874; PMCID: PMC4311479.
      View in: PubMed   Mentions: 100     Fields:    Translation:Humans
    684. Dietary effects on human gut microbiome diversity. Br J Nutr. 2015 Jan; 113 Suppl:S1-5. Xu Z, Knight R. PMID: 25498959; PMCID: PMC4405705.
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    685. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 2014 Dec 03; 15(12):531. Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N. PMID: 25517225; PMCID: PMC4252997.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansCells
    686. Before it is too late: professional responsibilities in late-onset Alzheimer's research and pre-symptomatic prediction. Front Hum Neurosci. 2014; 8:921. Schicktanz S, Schweda M, Ballenger JF, Fox PJ, Halpern J, Kramer JH, Micco G, Post SG, Thompson C, Knight RT, Jagust WJ. PMID: 25477802; PMCID: PMC4238325.
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    687. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water. Water Res. 2015 Feb 01; 69:30-39. Korajkic A, Parfrey LW, McMinn BR, Baeza YV, VanTeuren W, Knight R, Shanks OC. PMID: 25463929.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    688. Gut microbes and the brain: paradigm shift in neuroscience. J Neurosci. 2014 Nov 12; 34(46):15490-6. Mayer EA, Knight R, Mazmanian SK, Cryan JF, Tillisch K. PMID: 25392516; PMCID: PMC4228144.
      View in: PubMed   Mentions: 425     Fields:    Translation:HumansAnimals
    689. Human genetics shape the gut microbiome. Cell. 2014 Nov 06; 159(4):789-99. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE. PMID: 25417156; PMCID: PMC4255478.
      View in: PubMed   Mentions: 1572     Fields:    Translation:HumansAnimalsCells
    690. Specialized metabolites from the microbiome in health and disease. Cell Metab. 2014 Nov 04; 20(5):719-730. Sharon G, Garg N, Debelius J, Knight R, Dorrestein PC, Mazmanian SK. PMID: 25440054; PMCID: PMC4337795.
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    691. Proceedings of the Fifth International Workshop on Advances in Electrocorticography. Epilepsy Behav. 2014 Dec; 41:183-92. Ritaccio A, Brunner P, Gunduz A, Hermes D, Hirsch LJ, Jacobs J, Kamada K, Kastner S, Knight RT, Lesser RP, Miller K, Sejnowski T, Worrell G, Schalk G. PMID: 25461213; PMCID: PMC4268064.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    692. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 2014 Nov 17; 588(22):4223-33. Walters WA, Xu Z, Knight R. PMID: 25307765; PMCID: PMC5050012.
      View in: PubMed   Mentions: 441     Fields:    Translation:HumansAnimals
    693. Advancing the microbiome research community. Cell. 2014 Oct 09; 159(2):227-30. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, Scientists for Advancement of Microbiome Research, White O. PMID: 25303518; PMCID: PMC4221798.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimals
    694. Rethinking "enterotypes". Cell Host Microbe. 2014 Oct 08; 16(4):433-7. Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, Knight R. PMID: 25299329; PMCID: PMC5558460.
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    695. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell. 2014 Oct 09; 159(2):253-66. Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, Rey FE, Smith MI, Simon GM, Scheffrahn RH, Woebken D, Spormann AM, Van Treuren W, Ursell LK, Pirrung M, Robbins-Pianka A, Cantarel BL, Lombard V, Henrissat B, Knight R, Gordon JI. PMID: 25284151; PMCID: PMC4194163.
      View in: PubMed   Mentions: 192     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    696. Negative effects of an exotic grass invasion on small-mammal communities. PLoS One. 2014; 9(9):e108843. Freeman ED, Sharp TR, Larsen RT, Knight RN, Slater SJ, McMillan BR. PMID: 25269073; PMCID: PMC4182540.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    697. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014 Aug 29; 345(6200):1048-52. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. PMID: 25170151; PMCID: PMC4337996.
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    698. Which is more important for classifying microbial communities: who's there or what they can do? ISME J. 2014 Dec; 8(12):2357-9. Xu Z, Malmer D, Langille MG, Way SF, Knight R. PMID: 25171332; PMCID: PMC4260698.
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    699. Dynamic changes in phase-amplitude coupling facilitate spatial attention control in fronto-parietal cortex. PLoS Biol. 2014 Aug; 12(8):e1001936. Szczepanski SM, Crone NE, Kuperman RA, Auguste KI, Parvizi J, Knight RT. PMID: 25157678; PMCID: PMC4144794.
      View in: PubMed   Mentions: 92     Fields:    Translation:Humans
    700. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014; 2:e545. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG. PMID: 25177538; PMCID: PMC4145071.
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    701. HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One. 2014; 9(8):e105684. Lin P, Bach M, Asquith M, Lee AY, Akileswaran L, Stauffer P, Davin S, Pan Y, Cambronne ED, Dorris M, Debelius JW, Lauber CL, Ackermann G, Baeza YV, Gill T, Knight R, Colbert RA, Taurog JD, Van Gelder RN, Rosenbaum JT. PMID: 25140823; PMCID: PMC4139385.
      View in: PubMed   Mentions: 133     Fields:    Translation:HumansAnimals
    702. Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. mBio. 2014 Aug 12; 5(4). Eilam O, Zarecki R, Oberhardt M, Ursell LK, Kupiec M, Knight R, Gophna U, Ruppin E. PMID: 25118239; PMCID: PMC4145686.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    703. SnapShot: the human microbiome. Cell. 2014 Jul 31; 158(3):690-690.e1. González A, Vázquez-Baeza Y, Knight R. PMID: 25083877.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    704. Satellite remote sensing data can be used to model marine microbial metabolite turnover. ISME J. 2015 Jan; 9(1):166-79. Larsen PE, Scott N, Post AF, Field D, Knight R, Hamada Y, Gilbert JA. PMID: 25072414; PMCID: PMC4274419.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCellsPHPublic Health
    705. Individual diet has sex-dependent effects on vertebrate gut microbiota. Nat Commun. 2014 Jul 29; 5:4500. Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R. PMID: 25072318; PMCID: PMC4279269.
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    706. Conducting a microbiome study. Cell. 2014 Jul 17; 158(2):250-262. Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. PMID: 25036628; PMCID: PMC5074386.
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    707. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio. 2014 Jul 15; 5(4):e01371-14. Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. PMID: 25028427; PMCID: PMC4161262.
      View in: PubMed   Mentions: 265     Fields:    Translation:Cells
    708. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol. 2014; 5:298. Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. PMID: 24995004; PMCID: PMC4063188.
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    709. Finding the missing links among metabolites, microbes, and the host. Immunity. 2014 Jun 19; 40(6):824-32. Dorrestein PC, Mazmanian SK, Knight R. PMID: 24950202; PMCID: PMC4503329.
      View in: PubMed   Mentions: 168     Fields:    Translation:Humans
    710. Vertebrate decomposition is accelerated by soil microbes. Appl Environ Microbiol. 2014 Aug; 80(16):4920-9. Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R. PMID: 24907317; PMCID: PMC4135757.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCellsPHPublic Health
    711. Decoding spectrotemporal features of overt and covert speech from the human cortex. Front Neuroeng. 2014; 7:14. Martin S, Brunner P, Holdgraf C, Heinze HJ, Crone NE, Rieger J, Schalk G, Knight RT, Pasley BN. PMID: 24904404; PMCID: PMC4034498.
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    712. Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecol Lett. 2014 Aug; 17(8):979-87. Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R. PMID: 24847735; PMCID: PMC4084827.
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    713. Bacterial phylogeny structures soil resistomes across habitats. Nature. 2014 May 29; 509(7502):612-6. Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G. PMID: 24847883; PMCID: PMC4079543.
      View in: PubMed   Mentions: 345     Fields:    Translation:AnimalsCellsPHPublic Health
    714. Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness. PLoS One. 2014; 9(4):e96375. Woodhams DC, Brandt H, Baumgartner S, Kielgast J, Küpfer E, Tobler U, Davis LR, Schmidt BR, Bel C, Hodel S, Knight R, McKenzie V. PMID: 24789229; PMCID: PMC4005770.
      View in: PubMed   Mentions: 105     Fields:    Translation:Animals
    715. Spatial and temporal relationships of electrocorticographic alpha and gamma activity during auditory processing. Neuroimage. 2014 Aug 15; 97:188-95. Potes C, Brunner P, Gunduz A, Knight RT, Schalk G. PMID: 24768933; PMCID: PMC4065821.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    716. Structural basis for diversity in the SAM clan of riboswitches. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):6624-9. Trausch JJ, Xu Z, Edwards AL, Reyes FE, Ross PE, Knight R, Batey RT. PMID: 24753586; PMCID: PMC4020084.
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    717. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J. 2014 Sep; 8(9):1904-19. Tas N, Prestat E, McFarland JW, Wickland KP, Knight R, Berhe AA, Jorgenson T, Waldrop MP, Jansson JK. PMID: 24722629; PMCID: PMC4139727.
      View in: PubMed   Mentions: 50     Fields:    Translation:PHPublic Health
    718. Ancient human oral plaque preserves a wealth of biological data. Nat Genet. 2014 Apr; 46(4):321-3. Metcalf JL, Ursell LK, Knight R. PMID: 24675519.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    719. Predictive modeling of gingivitis severity and susceptibility via oral microbiota. ISME J. 2014 Sep; 8(9):1768-80. Huang S, Li R, Zeng X, He T, Zhao H, Chang A, Bo C, Chen J, Yang F, Knight R, Liu J, Davis C, Xu J. PMID: 24646694; PMCID: PMC4139724.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCellsPHPublic Health
    720. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014 Mar 12; 15(3):382-392. Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. PMID: 24629344; PMCID: PMC4059512.
      View in: PubMed   Mentions: 1721     Fields:    Translation:HumansCells
    721. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology. 2014 May; 146(6):1470-6. Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R. PMID: 24631493; PMCID: PMC4102302.
      View in: PubMed   Mentions: 168     Fields:    Translation:HumansAnimalsCells
    722. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 2014 Jul; 8(7):1464-75. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK. PMID: 24451203; PMCID: PMC4069396.
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    723. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell. 2013 Dec 19; 155(7):1446-8. Gilbert JA, Krajmalnik-Brown R, Porazinska DL, Weiss SJ, Knight R. PMID: 24360269; PMCID: PMC4166551.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimals
    724. Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings. Antiviral Res. 2014 Feb; 102:87-94. Ursell LK, Gunawardana M, Chang S, Mullen M, Moss JA, Herold BC, Keller MJ, McDonald D, González A, Knight R, Baum MM. PMID: 24361269; PMCID: PMC4006976.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    725. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). ISME J. 2014 Apr; 8(4):830-40. Loudon AH, Woodhams DC, Parfrey LW, Archer H, Knight R, McKenzie V, Harris RN. PMID: 24335825; PMCID: PMC3960541.
      View in: PubMed   Mentions: 150     Fields:    Translation:AnimalsCellsPHPublic Health
    726. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience. 2013 Nov 26; 2(1):16. Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. PMID: 24280061; PMCID: PMC4076506.
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    727. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One. 2013; 8(11):e80702. Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DP, Frank DN, Li E, Horvath S, Knight R, Braun J. PMID: 24260458; PMCID: PMC3834335.
      View in: PubMed   Mentions: 87     Fields:    Translation:Humans
    728. The amphibian skin-associated microbiome across species, space and life history stages. Mol Ecol. 2014 Mar; 23(6):1238-1250. Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ. PMID: 24171949.
      View in: PubMed   Mentions: 196     Fields:    Translation:AnimalsCellsPHPublic Health
    729. Diversity of Rickettsiales in the microbiome of the lone star tick, Amblyomma americanum. Appl Environ Microbiol. 2014 Jan; 80(1):354-9. Ponnusamy L, Gonzalez A, Van Treuren W, Weiss S, Parobek CM, Juliano JJ, Knight R, Roe RM, Apperson CS, Meshnick SR. PMID: 24162580; PMCID: PMC3910995.
      View in: PubMed   Mentions: 54     Fields:    Translation:AnimalsCells
    730. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2014 Jan; 8(1):1-3. Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. PMID: 24152717; PMCID: PMC3869023.
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    731. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. Elife. 2013 Oct 15; 2:e01104. Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R. PMID: 24137541; PMCID: PMC3796315.
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    732. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol. 2014 Mar; 23(6):1301-1317. Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R. PMID: 24118574.
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    733. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe. 2013 Sep 11; 14(3):329-39. Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, Knight R, Fontenot AP, Palmer BE. PMID: 24034618; PMCID: PMC3864811.
      View in: PubMed   Mentions: 294     Fields:    Translation:HumansCells
    734. Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere. PLoS One. 2013; 8(9):e73079. Ottesen AR, Gonzalez A, Bell R, Arce C, Rideout S, Allard M, Evans P, Strain E, Musser S, Knight R, Brown E, Pettengill JB. PMID: 24039862; PMCID: PMC3767688.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCellsPHPublic Health
    735. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013 Sep 06; 341(6150):1241214. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. PMID: 24009397; PMCID: PMC3829625.
      View in: PubMed   Mentions: 1903     Fields:    Translation:HumansAnimalsCells
    736. Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon. PLoS One. 2013; 8(8):e73140. Devine AA, Gonzalez A, Speck KE, Knight R, Helmrath M, Lund PK, Azcarate-Peril MA. PMID: 24015295; PMCID: PMC3754918.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    737. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013 Sep; 31(9):814-21. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C. PMID: 23975157; PMCID: PMC3819121.
      View in: PubMed   Mentions: 4071     Fields:    Translation:HumansCells
    738. Meta-analyses of studies of the human microbiota. Genome Res. 2013 Oct; 23(10):1704-14. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R. PMID: 23861384; PMCID: PMC3787266.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansCells
    739. Replenishing our defensive microbes. Bioessays. 2013 Sep; 35(9):810-7. Ursell LK, Van Treuren W, Metcalf JL, Pirrung M, Gewirtz A, Knight R. PMID: 23836415; PMCID: PMC4102301.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    740. The long-term stability of the human gut microbiota. Science. 2013 Jul 05; 341(6141):1237439. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI. PMID: 23828941; PMCID: PMC3791589.
      View in: PubMed   Mentions: 1051     Fields:    Translation:HumansCells
    741. Water developments and canids in two North American deserts: a test of the indirect effect of water hypothesis. PLoS One. 2013; 8(7):e67800. Hall LK, Larsen RT, Knight RN, Bunnell KD, McMillan BR. PMID: 23844097; PMCID: PMC3699512.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    742. The Ecology of Microbial Communities Associated with Macrocystis pyrifera. PLoS One. 2013; 8(6):e67480. Michelou VK, Caporaso JG, Knight R, Palumbi SR. PMID: 23840715; PMCID: PMC3686729.
      View in: PubMed   Mentions:
    743. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 2014 Mar; 63(3):401-8. Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, Azpiroz F. PMID: 23766444; PMCID: PMC3933177.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    744. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 2013 May 24; 13:114. Ottesen AR, González Peña A, White JR, Pettengill JB, Li C, Allard S, Rideout S, Allard M, Hill T, Evans P, Strain E, Musser S, Knight R, Brown E. PMID: 23705801; PMCID: PMC3680157.
      View in: PubMed   Mentions: 93     Fields:    Translation:AnimalsCells
    745. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013 Apr 16; 2:e00458. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R. PMID: 23599893; PMCID: PMC3628085.
      View in: PubMed   Mentions: 580     Fields:    Translation:HumansAnimals
    746. Meeting report: fungal its workshop (october 2012). Stand Genomic Sci. 2013 Apr 15; 8(1):118-23. Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE. PMID: 23961317; PMCID: PMC3739174.
      View in: PubMed   Mentions: 13  
    747. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 2013 Aug; 7(8):1493-506. Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N. PMID: 23575374; PMCID: PMC3721121.
      View in: PubMed   Mentions:
    748. Translating the human microbiome. Nat Biotechnol. 2013 Apr; 31(4):304-8. Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. PMID: 23563424.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimals
    749. Biphasic assembly of the murine intestinal microbiota during early development. ISME J. 2013 Jun; 7(6):1112-5. Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, Dominguez-Bello MG. PMID: 23535917; PMCID: PMC3660675.
      View in: PubMed   Mentions: 95     Fields:    Translation:AnimalsCells
    750. Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A. 2013 Mar 19; 110(12):4651-5. Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA. PMID: 23487761; PMCID: PMC3607043.
      View in: PubMed   Mentions: 94     Fields:    Translation:CellsPHPublic Health
    751. How delivery mode and feeding can shape the bacterial community in the infant gut. CMAJ. 2013 Mar 19; 185(5):373-4. Song SJ, Dominguez-Bello MG, Knight R. PMID: 23401408; PMCID: PMC3602250.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    752. From molecules to dynamic biological communities. Biol Philos. 2013 Mar; 28(2):241-259. McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R. PMID: 23483075; PMCID: PMC3586164.
      View in: PubMed   Mentions: 2  
    753. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science. 2013 Feb 01; 339(6119):548-54. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, Gordon JI. PMID: 23363771; PMCID: PMC3667500.
      View in: PubMed   Mentions: 592     Fields:    Translation:HumansAnimalsCells
    754. Bacterial diversity in two Neonatal Intensive Care Units (NICUs). PLoS One. 2013; 8(1):e54703. Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST. PMID: 23372757; PMCID: PMC3553055.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansCells
    755. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol. 2013; 9(1):e1002863. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE. PMID: 23326225; PMCID: PMC3542080.
      View in: PubMed   Mentions: 296     Fields:    Translation:HumansCells
    756. Vigilance of kit foxes at water sources: a test of competing hypotheses for a solitary carnivore subject to predation. Behav Processes. 2013 Mar; 94:76-82. Hall LK, Day CC, Westover MD, Edgel RJ, Larsen RT, Knight RN, McMillan BR. PMID: 23305800.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    757. Advancing our understanding of the human microbiome using QIIME. Methods Enzymol. 2013; 531:371-444. Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R. PMID: 24060131; PMCID: PMC4517945.
      View in: PubMed   Mentions: 320     Fields:    Translation:HumansAnimalsCells
    758. Global biogeography of highly diverse protistan communities in soil. ISME J. 2013 Mar; 7(3):652-9. Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, Fierer N. PMID: 23235291; PMCID: PMC3578557.
      View in: PubMed   Mentions: 126     Fields:    Translation:AnimalsPHPublic Health
    759. Insights from characterizing extinct human gut microbiomes. PLoS One. 2012; 7(12):e51146. Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM. PMID: 23251439; PMCID: PMC3521025.
      View in: PubMed   Mentions: 84     Fields:    Translation:Humans
    760. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013 Jan; 10(1):57-9. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. PMID: 23202435; PMCID: PMC3531572.
      View in: PubMed   Mentions: 1842     Fields:    Translation:Humans
    761. Diversity, distribution and sources of bacteria in residential kitchens. Environ Microbiol. 2013 Feb; 15(2):588-96. Flores GE, Bates ST, Caporaso JG, Lauber CL, Leff JW, Knight R, Fierer N. PMID: 23171378; PMCID: PMC5100818.
      View in: PubMed   Mentions: 97     Fields:    Translation:CellsPHPublic Health
    762. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Microbiol. 2012 Nov; Chapter 1:Unit 1E.5.. Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R. PMID: 23184592; PMCID: PMC4477843.
      View in: PubMed   Mentions: 258     Fields:    Translation:Cells
    763. Collaborative cloud-enabled tools allow rapid, reproducible biological insights. ISME J. 2013 Mar; 7(3):461-4. Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG. PMID: 23096404; PMCID: PMC3578576.
      View in: PubMed   Mentions: 13     Fields:    
    764. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res. 2012 Nov; 22(11):2146-52. Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS. PMID: 23064750; PMCID: PMC3483544.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    765. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. ISME J. 2013 Jan; 7(1):85-95. Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R. PMID: 22895161; PMCID: PMC3526177.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    766. Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome. PLoS One. 2012; 7(8):e43052. Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM. PMID: 22905200; PMCID: PMC3419686.
      View in: PubMed   Mentions: 113     Fields:    Translation:Humans
    767. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012 Aug 03; 150(3):470-80. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Bäckhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Bäckhed F, Isolauri E, Salminen S, Ley RE. PMID: 22863002; PMCID: PMC3505857.
      View in: PubMed   Mentions: 1033     Fields:    Translation:HumansAnimalsCells
    768. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe. 2012 Aug 16; 12(2):139-52. Carvalho FA, Koren O, Goodrich JK, Johansson ME, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, González A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, Gewirtz AT. PMID: 22863420; PMCID: PMC4310462.
      View in: PubMed   Mentions: 291     Fields:    Translation:HumansAnimalsCells
    769. Defining the human microbiome. Nutr Rev. 2012 Aug; 70 Suppl 1:S38-44. Ursell LK, Metcalf JL, Parfrey LW, Knight R. PMID: 22861806; PMCID: PMC3426293.
      View in: PubMed   Mentions: 526     Fields:    Translation:HumansCells
    770. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 2013 Jan; 7(1):50-60. Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR. PMID: 22832344; PMCID: PMC3526174.
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    771. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2012 Jul 12; 1(1):7. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG. PMID: 23587224; PMCID: PMC3626512.
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    772. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J. 2012 Dec; 6(12):2153-67. Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK, Lottig NR, Roden EE, Stanley EH, Stombaugh J, Whitaker RJ, Wu CH, McMahon KD. PMID: 22739495; PMCID: PMC3504957.
      View in: PubMed   Mentions: 88     Fields:    Translation:CellsPHPublic Health
    773. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012 Jun 07; 30(6):513-20. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA. PMID: 22678395; PMCID: PMC4902277.
      View in: PubMed   Mentions: 112     Fields:    Translation:HumansAnimals
    774. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res. 2012 Oct; 22(10):1974-84. Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. PMID: 22665442; PMCID: PMC3460192.
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    775. RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA. 2012 Jul; 18(7):1319-27. Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R. PMID: 22645380; PMCID: PMC3383963.
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    776. Human gut microbiome viewed across age and geography. Nature. 2012 May 09; 486(7402):222-7. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. PMID: 22699611; PMCID: PMC3376388.
      View in: PubMed   Mentions: 3941     Fields:    Translation:HumansCells
    777. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol. 2012 May; 129(5):1204-8. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. PMID: 22541361; PMCID: PMC3342686.
      View in: PubMed   Mentions: 148     Fields:    Translation:Humans
    778. The impact of the gut microbiota on human health: an integrative view. Cell. 2012 Mar 16; 148(6):1258-70. Clemente JC, Ursell LK, Parfrey LW, Knight R. PMID: 22424233; PMCID: PMC5050011.
      View in: PubMed   Mentions: 1707     Fields:    Translation:HumansAnimalsCells
    779. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012 Aug; 6(8):1621-4. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. PMID: 22402401; PMCID: PMC3400413.
      View in: PubMed   Mentions: 3804     Fields:    Translation:CellsPHPublic Health
    780. Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension. AIDS Res Hum Retroviruses. 2012 Jun; 28(6):607-18. Almodovar S, Knight R, Allshouse AA, Roemer S, Lozupone C, McDonald D, Widmann J, Voelkel NF, Shelton RJ, Suarez EB, Hammer KW, Goujard C, Petrosillo N, Simonneau G, Hsue PY, Humbert M, Flores SC. PMID: 22066947; PMCID: PMC3358101.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    781. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012 Jul; 6(7):1440-4. Soergel DA, Dey N, Knight R, Brenner SE. PMID: 22237546; PMCID: PMC3379642.
      View in: PubMed   Mentions: 177     Fields:    Translation:Humans
    782. Detecting event-related changes of multivariate phase coupling in dynamic brain networks. J Neurophysiol. 2012 Apr; 107(7):2020-31. Canolty RT, Cadieu CF, Koepsell K, Ganguly K, Knight RT, Carmena JM. PMID: 22236706; PMCID: PMC3331660.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    783. Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol. 2012 Apr; 27(4):233-43. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. PMID: 22244672; PMCID: PMC3311718.
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    784. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2011 Dec 16; 13(1):47-58. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R. PMID: 22179717; PMCID: PMC5119550.
      View in: PubMed   Mentions: 334     Fields:    Translation:Humans
    785. Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. ISME J. 2012 Jul; 6(7):1277-80. Wang X, Cai Y, Sun Y, Knight R, Mai V. PMID: 22170430; PMCID: PMC3379628.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    786. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J. 2012 Jul; 6(7):1273-6. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. PMID: 22170427; PMCID: PMC3379627.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    787. Advancing analytical algorithms and pipelines for billions of microbial sequences. Curr Opin Biotechnol. 2012 Feb; 23(1):64-71. Gonzalez A, Knight R. PMID: 22172529; PMCID: PMC3273654.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    788. SitePainter: a tool for exploring biogeographical patterns. Bioinformatics. 2012 Feb 01; 28(3):436-8. Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R. PMID: 22171330; PMCID: PMC3268248.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    789. Characterizing microbial communities through space and time. Curr Opin Biotechnol. 2012 Jun; 23(3):431-6. Gonzalez A, King A, Robeson MS, Song S, Shade A, Metcalf JL, Knight R. PMID: 22154467; PMCID: PMC3311466.
      View in: PubMed   Mentions: 51     Fields:    Translation:CellsPHPublic Health
    790. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012 May; 6(5):1007-17. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. PMID: 22134642; PMCID: PMC3329107.
      View in: PubMed   Mentions: 488     Fields:    Translation:CellsPHPublic Health
    791. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012 Mar; 6(3):610-8. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. PMID: 22134646; PMCID: PMC3280142.
      View in: PubMed   Mentions: 2443     Fields:    Translation:Cells
    792. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics. 2011 Dec; Chapter 10:10.7.1-10.7.20. Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R. PMID: 22161565; PMCID: PMC3249058.
      View in: PubMed   Mentions: 306     Fields:    Translation:Cells
    793. The Western English Channel contains a persistent microbial seed bank. ISME J. 2012 Jun; 6(6):1089-93. Caporaso JG, Paszkiewicz K, Field D, Knight R, Gilbert JA. PMID: 22071345; PMCID: PMC3358019.
      View in: PubMed   Mentions: 93     Fields:    Translation:Cells
    794. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med. 2011 Oct 26; 3(106):106ra106. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. PMID: 22030749; PMCID: PMC3303609.
      View in: PubMed   Mentions: 258     Fields:    Translation:HumansAnimalsCells
    795. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe. 2011 Oct 20; 10(4):292-6. Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R. PMID: 22018228; PMCID: PMC3879110.
      View in: PubMed   Mentions: 77     Fields:    Translation:Humans
    796. Multivariate phase-amplitude cross-frequency coupling in neurophysiological signals. IEEE Trans Biomed Eng. 2012 Jan; 59(1):8-11. Canolty RT, Cadieu CF, Koepsell K, Knight RT, Carmena JM. PMID: 22020662; PMCID: PMC4090099.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    797. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations. ISME J. 2012 Mar; 6(3):588-96. McKenzie VJ, Bowers RM, Fierer N, Knight R, Lauber CL. PMID: 21955991; PMCID: PMC3280140.
      View in: PubMed   Mentions: 143     Fields:    Translation:AnimalsCells
    798. TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Bioinformatics. 2011 Nov 01; 27(21):3067-9. Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R. PMID: 21903626; PMCID: PMC3198578.
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    799. Defining seasonal marine microbial community dynamics. ISME J. 2012 Feb; 6(2):298-308. Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D. PMID: 21850055; PMCID: PMC3260500.
      View in: PubMed   Mentions: 416     Fields:    Translation:Cells
    800. Sources of bacteria in outdoor air across cities in the midwestern United States. Appl Environ Microbiol. 2011 Sep; 77(18):6350-6. Bowers RM, Sullivan AP, Costello EK, Collett JL, Knight R, Fierer N. PMID: 21803902; PMCID: PMC3187178.
      View in: PubMed   Mentions: 84     Fields:    Translation:AnimalsCellsPHPublic Health
    801. Bayesian community-wide culture-independent microbial source tracking. Nat Methods. 2011 Jul 17; 8(9):761-3. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. PMID: 21765408; PMCID: PMC3791591.
      View in: PubMed   Mentions: 755     Fields:    Translation:HumansPHPublic Health
    802. Our microbial selves: what ecology can teach us. EMBO Rep. 2011 Jul 01; 12(8):775-84. Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, Knight R. PMID: 21720391; PMCID: PMC3147266.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimals
    803. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem. 2011 Jul; 43(7):1450-1455. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N. PMID: 22267877; PMCID: PMC3260529.
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    804. Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J. 2012 Jan; 6(1):94-103. Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE. PMID: 21716311; PMCID: PMC3217155.
      View in: PubMed   Mentions: 255     Fields:    Translation:HumansAnimalsCells
    805. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011 May 20; 332(6032):970-4. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. PMID: 21596990; PMCID: PMC3303602.
      View in: PubMed   Mentions: 966     Fields:    Translation:HumansAnimalsCells
    806. Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Bioinformatics. 2011 Jun 15; 27(12):1706-7. Stombaugh J, Widmann J, McDonald D, Knight R. PMID: 21546392; PMCID: PMC3106197.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    807. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology. 2011 May; 140(6):1713-9. Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. PMID: 21530737; PMCID: PMC10924805.
      View in: PubMed   Mentions: 168     Fields:    Translation:HumansCells
    808. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 May; 29(5):415-20. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. PMID: 21552244; PMCID: PMC3367316.
      View in: PubMed   Mentions: 369     Fields:    Translation:Humans
    809. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Stand Genomic Sci. 2011 Apr 29; 4(2):252-6. Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A. PMID: 21677862; PMCID: PMC3111981.
      View in: PubMed   Mentions: 1  
    810. New insight into the diversity of life's building blocks: evenness, not variance. Astrobiology. 2011 Apr; 11(3):197-8. Caporaso JG, Knight R. PMID: 21417743.
      View in: PubMed   Mentions:
    811. Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PLoS One. 2011 Feb 24; 6(2):e16900. Caporaso JG, Knight R, Kelley ST. PMID: 21383980; PMCID: PMC3044705.
      View in: PubMed   Mentions:
    812. PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics. 2011 Apr 15; 27(8):1159-61. Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R. PMID: 21349862; PMCID: PMC3072552.
      View in: PubMed   Mentions: 209     Fields:    Translation:HumansCells
    813. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A. 2011 Mar 15; 108 Suppl 1:4599-606. Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI. PMID: 21317366; PMCID: PMC3063581.
      View in: PubMed   Mentions: 141     Fields:    Translation:HumansCells
    814. Global patterns in the biogeography of bacterial taxa. Environ Microbiol. 2011 Jan; 13(1):135-144. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R. PMID: 21199253; PMCID: PMC5834236.
      View in: PubMed   Mentions: 158     Fields:    Translation:CellsPHPublic Health
    815. The mind-body-microbial continuum. Dialogues Clin Neurosci. 2011; 13(1):55-62. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. PMID: 21485746; PMCID: PMC3139398.
      View in: PubMed   Mentions: 55     Fields:    Translation:Humans
    816. Moving pictures of the human microbiome. Genome Biol. 2011; 12(5):R50. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. PMID: 21624126; PMCID: PMC3271711.
      View in: PubMed   Mentions: 585     Fields:    Translation:HumansCells
    817. Bacterial communities associated with the lichen symbiosis. Appl Environ Microbiol. 2011 Feb; 77(4):1309-14. Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N. PMID: 21169444; PMCID: PMC3067232.
      View in: PubMed   Mentions: 120     Fields:    Translation:AnimalsCells
    818. Examining the global distribution of dominant archaeal populations in soil. ISME J. 2011 May; 5(5):908-17. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. PMID: 21085198; PMCID: PMC3105767.
      View in: PubMed   Mentions: 382     Fields:    Translation:CellsPHPublic Health
    819. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol. 2010 Nov; 12(11):2998-3006. Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. PMID: 20561020.
      View in: PubMed   Mentions: 187     Fields:    Translation:CellsPHPublic Health
    820. Supervised classification of microbiota mitigates mislabeling errors. ISME J. 2011 Apr; 5(4):570-3. Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ, Kelley ST. PMID: 20927137; PMCID: PMC3105748.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    821. Supervised classification of human microbiota. FEMS Microbiol Rev. 2011 Mar; 35(2):343-59. Knights D, Costello EK, Knight R. PMID: 21039646.
      View in: PubMed   Mentions: 217     Fields:    Translation:HumansCells
    822. The bacterial microbiota in the oral mucosa of rural Amerindians. Microbiology (Reading). 2010 Nov; 156(Pt 11):3282-3287. Contreras M, Costello EK, Hidalgo G, Magris M, Knight R, Dominguez-Bello MG. PMID: 20847007.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    823. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods. 2010 Oct; 7(10):813-9. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R. PMID: 20818378; PMCID: PMC2948603.
      View in: PubMed   Mentions: 138     Fields:    Translation:CellsPHPublic Health
    824. Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA. RNA. 2010 Oct; 16(10):1915-24. Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, Iyer M, Illangasekare M, Yarus M, Knight R. PMID: 20699302; PMCID: PMC2941100.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    825. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 2010 Jul 30; 10:206. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. PMID: 20673359; PMCID: PMC2921404.
      View in: PubMed   Mentions: 216     Fields:    Translation:HumansCells
    826. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010 Jun 29; 107(26):11971-5. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. PMID: 20566857; PMCID: PMC2900693.
      View in: PubMed   Mentions: 2160     Fields:    Translation:HumansCells
    827. Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J. 2010 Nov; 4(11):1375-85. Costello EK, Gordon JI, Secor SM, Knight R. PMID: 20520652; PMCID: PMC3923499.
      View in: PubMed   Mentions: 139     Fields:    Translation:AnimalsCells
    828. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011 Mar 15; 108 Suppl 1:4516-22. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. PMID: 20534432; PMCID: PMC3063599.
      View in: PubMed   Mentions: 3949     Fields:    Translation:Cells
    829. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010 Oct; 4(10):1340-51. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. PMID: 20445636.
      View in: PubMed   Mentions:
    830. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol. 2010; 11(5):210. Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R. PMID: 20441597; PMCID: PMC2898070.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansCells
    831. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May; 7(5):335-6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. PMID: 20383131; PMCID: PMC3156573.
      View in: PubMed   Mentions: 15156     Fields:    Translation:HumansAnimals
    832. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett. 2010 Jun; 307(1):80-6. Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. PMID: 20412303; PMCID: PMC3148093.
      View in: PubMed   Mentions: 201     Fields:    Translation:HumansPHPublic Health
    833. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A. 2010 Apr 06; 107(14):6477-81. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. PMID: 20231444; PMCID: PMC2852011.
      View in: PubMed   Mentions: 252     Fields:    Translation:Humans
    834. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010 Jan 15; 26(2):266-7. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PMID: 19914921; PMCID: PMC2804299.
      View in: PubMed   Mentions: 1658     Fields:    
    835. Bacterial community variation in human body habitats across space and time. Science. 2009 Dec 18; 326(5960):1694-7. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. PMID: 19892944; PMCID: PMC3602444.
      View in: PubMed   Mentions: 1569     Fields:    Translation:HumansCells
    836. The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework. Int J Mol Sci. 2009 Nov 03; 10(11):4723-4741. Faith DP, Lozupone CA, Nipperess D, Knight R. PMID: 20087461; PMCID: PMC2808007.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    837. Bacterial communities of disease vectors sampled across time, space, and species. ISME J. 2010 Feb; 4(2):223-31. Jones RT, Knight R, Martin AP. PMID: 19865184.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCellsPHPublic Health
    838. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe. 2009 Sep 17; 6(3):279-89. Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI. PMID: 19748469; PMCID: PMC2895552.
      View in: PubMed   Mentions: 437     Fields:    Translation:HumansAnimalsCells
    839. Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci U S A. 2009 Jul 07; 106(27):11276-81. Crawford PA, Crowley JR, Sambandam N, Muegge BD, Costello EK, Hamady M, Knight R, Gordon JI. PMID: 19549860; PMCID: PMC2700149.
      View in: PubMed   Mentions: 144     Fields:    Translation:AnimalsCells
    840. Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei. Appl Environ Microbiol. 2009 Aug; 75(15):5121-30. Bowers RM, Lauber CL, Wiedinmyer C, Hamady M, Hallar AG, Fall R, Knight R, Fierer N. PMID: 19502432; PMCID: PMC2725505.
      View in: PubMed   Mentions: 74     Fields:    Translation:AnimalsCellsPHPublic Health
    841. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol. 2009 Aug; 75(15):5111-20. Lauber CL, Hamady M, Knight R, Fierer N. PMID: 19502440; PMCID: PMC2725504.
      View in: PubMed   Mentions: 1110     Fields:    Translation:CellsPHPublic Health
    842. Activating and inhibiting connections in biological network dynamics. Biol Direct. 2008 Dec 04; 3:49. McDonald D, Waterbury L, Knight R, Betterton MD. PMID: 19055800; PMCID: PMC2651858.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    843. Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics. BMC Evol Biol. 2008 Dec 03; 8:327. Caporaso JG, Smit S, Easton BC, Hunter L, Huttley GA, Knight R. PMID: 19055758; PMCID: PMC2637866.
      View in: PubMed   Mentions:
    844. Comparison of methods for estimating the nucleotide substitution matrix. BMC Bioinformatics. 2008 Dec 01; 9:511. Oscamou M, McDonald D, Yap VB, Huttley GA, Lladser ME, Knight R. PMID: 19046431; PMCID: PMC2655096.
      View in: PubMed   Mentions: 5     Fields:    
    845. A core gut microbiome in obese and lean twins. Nature. 2009 Jan 22; 457(7228):480-4. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. PMID: 19043404; PMCID: PMC2677729.
      View in: PubMed   Mentions: 3750     Fields:    Translation:Humans
    846. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008 10; 6(10):776-88. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. PMID: 18794915; PMCID: PMC2664199.
      View in: PubMed   Mentions: 774     Fields:    Translation:HumansAnimalsCells
    847. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008 Oct; 36(18):e120. Liu Z, DeSantis TZ, Andersen GL, Knight R. PMID: 18723574; PMCID: PMC2566877.
      View in: PubMed   Mentions: 256     Fields:    Translation:HumansAnimalsCells
    848. Localization of neurosurgically implanted electrodes via photograph-MRI-radiograph coregistration. J Neurosci Methods. 2008 Sep 15; 174(1):106-15. Dalal SS, Edwards E, Kirsch HE, Barbaro NM, Knight RT, Nagarajan SS. PMID: 18657573; PMCID: PMC2695765.
      View in: PubMed   Mentions: 57     Fields:    Translation:Humans
    849. Evolution of mammals and their gut microbes. Science. 2008 Jun 20; 320(5883):1647-51. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. PMID: 18497261; PMCID: PMC2649005.
      View in: PubMed   Mentions: 1750     Fields:    Translation:HumansAnimalsCells
    850. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods. 2008 Mar; 5(3):235-7. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. PMID: 18264105; PMCID: PMC3439997.
      View in: PubMed   Mentions: 592     Fields:    
    851. Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiology (Reading). 2008 Jan; 154(Pt 1):1-15. Zaneveld JR, Nemergut DR, Knight R. PMID: 18174121.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    852. Short-term temporal variability in airborne bacterial and fungal populations. Appl Environ Microbiol. 2008 Jan; 74(1):200-7. Fierer N, Liu Z, Rodríguez-Hernández M, Knight R, Henn M, Hernandez MT. PMID: 17981945; PMCID: PMC2223228.
      View in: PubMed   Mentions: 75     Fields:    Translation:AnimalsCellsPHPublic Health
    853. The human microbiome project. Nature. 2007 Oct 18; 449(7164):804-10. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. PMID: 17943116; PMCID: PMC3709439.
      View in: PubMed   Mentions: 2567     Fields:    Translation:HumansAnimals
    854. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol. 2007 Nov; 73(21):7059-66. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB. PMID: 17827313; PMCID: PMC2074941.
      View in: PubMed   Mentions: 172     Fields:    Translation:CellsPHPublic Health
    855. Multiple pattern matching: a Markov chain approach. J Math Biol. 2008 Jan; 56(1-2):51-92. Lladser ME, Betterton MD, Knight R. PMID: 17668213.
      View in: PubMed   Mentions:
    856. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A. 2007 Jul 03; 104(27):11436-40. Lozupone CA, Knight R. PMID: 17592124; PMCID: PMC2040916.
      View in: PubMed   Mentions: 608     Fields:    Translation:CellsPHPublic Health
    857. PyCogent: a toolkit for making sense from sequence. Genome Biol. 2007; 8(8):R171. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. PMID: 17708774; PMCID: PMC2375001.
      View in: PubMed   Mentions: 121     Fields:    Translation:HumansAnimalsCells
    858. Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code. J Mol Evol. 2005 Nov; 61(5):597-607. Caporaso JG, Yarus M, Knight R. PMID: 16211428.
      View in: PubMed   Mentions:
    859. Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem. 2005; 74:179-98. Yarus M, Caporaso JG, Knight R. PMID: 15952885.
      View in: PubMed   Mentions:
    860. Hemispheric asymmetries for kinematic and positional aspects of reaching. Brain. 2004 May; 127(Pt 5):1145-58. Haaland KY, Prestopnik JL, Knight RT, Lee RR. PMID: 15033898.
      View in: PubMed   Mentions: 76     Fields:    Translation:Humans
    861. Dissociable neural correlates for familiarity and recollection during the encoding and retrieval of pictures. Brain Res Cogn Brain Res. 2004 Feb; 18(3):255-72. Duarte A, Ranganath C, Winward L, Hayward D, Knight RT. PMID: 14741312.
      View in: PubMed   Mentions: 70     Fields:    Translation:Humans
    862. Voxel-based lesion-symptom mapping. Nat Neurosci. 2003 May; 6(5):448-50. Bates E, Wilson SM, Saygin AP, Dick F, Sereno MI, Knight RT, Dronkers NF. PMID: 12704393.
      View in: PubMed   Mentions: 650     Fields:    Translation:Humans
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