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Tony Capra, PhD

Photo of Tony Capra, PhD
Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address600 16th Street, #N472D
San Francisco CA 94158
PronounsHe/Him/His
ORCID ORCID Icon0000-0001-9743-1795 Additional info
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    Collapse Biography 
    Collapse education and training
    UCSFN/A2021Diversity, Equity, and Inclusion Champion Training
    UCSF/Gladstone InstitutesPostdoc02/2013Comparative Genomics
    Princeton UniversityPhD05/2009Computer Science
    Columbia UniversityBA05/2004Mathematics, Computer Science

    Collapse Overview 
    Collapse overview
    The Capra Lab uses the tools of computer science and statistics to address problems in genetics, evolution, and biomedicine.

    Collapse Research 
    Collapse research activities and funding
    Allele Prospector: Leveraging human genetic variation to enable therapeutic genome editing in hundreds of disease genes
    CIRM DISC0-17363Feb 2, 2026 - Feb 1, 2029
    Role: Co-Principal Investigator
    Personalized Structural Biology: Enabling Exome Interpretation in Undiagnosed Diseases
    NIH R01LM013434Aug 5, 2021 - May 31, 2025
    Role: Co-Principal Investigator
    The Evolution of Gene Regulation and Human Disease
    NIH R35GM127087Apr 1, 2018 - Mar 31, 2029
    Role: Principal Investigator
    Integrating ’Omics and EHRs to Elucidate the Genetic Architecture of Preterm Birth
    Burroughs Wellcome Fund Jun 1, 2017 - Mar 31, 2021
    Role: Principal Investigator
    Modeling the Dynamics of Genome-Scale Data Across Trees
    NIH R01GM115836Aug 1, 2015 - Jun 30, 2019
    Role: Co-Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. AncientProxy: A catalog of ancient proxies for modern genetic variants. Am J Hum Genet. 2026 Feb 05; 113(2):247-259. Brand CM, Capra JA. PMID: 41605204.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Discovering latent subtypes of preterm birth and genetic risk using tensor decomposition on electronic health records. medRxiv. 2025 Nov 19. Abraham A, Bejan C, Takasuka H, Sirota M, Capra JA. PMID: 41332802; PMCID: PMC12668106.
      View in: PubMed   Mentions:
    3. Haplotype editing with CRISPR-Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL. Mol Ther. 2026 Mar 04; 34(3):1633-1651. Dua PH, Simon BMJ, Marley CBE, Feliciano CM, Watry HL, Cowan QT, Steury D, Abraham A, Gilbertson EN, Ramey GD, Capra JA, Conklin BR, Judge LM. PMID: 41267399; PMCID: PMC12974165.
      View in: PubMed   Mentions:
    4. Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity. bioRxiv. 2025 Sep 24. Chen Y, Velazquez-Arcelay K, Capra JA. PMID: 41040238; PMCID: PMC12485899.
      View in: PubMed   Mentions:
    5. Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence. bioRxiv. 2025 Sep 02. McArthur E, Rinker DC, Cheng Y, Wang Q, Wang J, Gilbertson EN, Fudenberg G, Pittman M, Keough K, Yue F, Pollard KS, Capra JA. PMID: 40949959; PMCID: PMC12424642.
      View in: PubMed   Mentions:
    6. Strategies for Creating Robust Patient Groups to Study Diverse Conditions with Electronic Health Records. Annu Rev Biomed Data Sci. 2025 Aug; 8(1):317-340. Ramey GD, Takasuka H, Capra JA. PMID: 40198843.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    7. VUStruct: a compute pipeline for high throughput and personalized structural biology. bioRxiv. 2025 Mar 26. Moth CW, Sheehan JH, Mamun AA, Sivley RM, Gulsevin A, Rinker D, Undiagnosed Diseases Network, Capra JA, Meiler J. PMID: 39149406; PMCID: PMC11326201.
      View in: PubMed   Mentions:
    8. Comparing chromatin contact maps at scale: methods and insights. Nat Methods. 2025 Apr; 22(4):824-833. Gjoni K, Gunsalus LM, Kuang S, McArthur E, Pittman M, Capra JA, Pollard KS. PMID: 40108448; PMCID: PMC11978506.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    9. Identifying deleterious noncoding variation through gain and loss of CTCF binding activity. Am J Hum Genet. 2025 Apr 03; 112(4):892-902. Tubbs C, Benton ML, McArthur E, Capra JA, Ruderfer DM. PMID: 40049170; PMCID: PMC12081274.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    10. Exposure to autoimmune disorders is associated with increased Alzheimer's disease risk in a multi-site electronic health record analysis. Cell Rep Med. 2025 Mar 18; 6(3):101980. Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M. PMID: 39999839; PMCID: PMC11970322.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    11. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. Elife. 2025 Feb 17; 13. Estevam GO, Linossi E, Rao J, Macdonald CB, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS. PMID: 39960754; PMCID: PMC11832172.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    12. Pre-conception clinical risk factors differ between spontaneous and indicated preterm birth in a densely phenotyped EHR cohort. BMC Pregnancy Childbirth. 2025 Feb 12; 25(1):149. Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA. PMID: 39939846; PMCID: PMC11817080.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    13. Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL. bioRxiv. 2024 Dec 22. Dua PH, Simon BMJ, Marley CBE, Feliciano CM, Watry HL, Steury D, Abraham A, Gilbertson EN, Ramey GD, Capra JA, Conklin BR, Judge LM. PMID: 39763989; PMCID: PMC11702708.
      View in: PubMed   Mentions:
    14. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv. 2024 Dec 05. Estevam GO, Linossi EM, Rao J, Macdonald CB, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS. PMID: 39071407; PMCID: PMC11275805.
      View in: PubMed   Mentions:
    15. Inferring human phenotypes using ancient DNA: from molecules to populations. Curr Opin Genet Dev. 2025 Feb; 90:102283. Ferrando-Bernal M, Brand CM, Capra JA. PMID: 39612613.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    16. Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees. Genome Biol Evol. 2024 Nov 01; 16(11). Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. PMID: 39382451; PMCID: PMC11579661.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    17. Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals. bioRxiv. 2024 Oct 18. Cruz-González S, Gu E, Gomez L, Mews M, Vance JM, Cuccaro ML, Cornejo-Olivas MR, Feliciano-Astacio BE, Byrd GS, Haines JL, Pericak-Vance MA, Griswold AJ, Bush WS, Capra JA. PMID: 39464059; PMCID: PMC11507840.
      View in: PubMed   Mentions: 1  
    18. Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns. Mol Biol Evol. 2024 Oct 04; 41(10). Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA. PMID: 39404010; PMCID: PMC11523124.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    19. Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale. PLoS Biol. 2024 Sep; 22(9):e3002782. Hoang N, Sardaripour N, Ramey GD, Schilling K, Liao E, Chen Y, Park JH, Bledsoe X, Landman BA, Gamazon ER, Benton ML, Capra JA, Rubinov M. PMID: 39269986; PMCID: PMC11424006.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    20. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatol. 2024 Nov; 6(11):769-779. Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. PMID: 39143499; PMCID: PMC11557995.
      View in: PubMed   Mentions: 3  
    21. High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology. Genome Med. 2024 05 30; 16(1):73. Muhammad A, Calandranis ME, Li B, Yang T, Blackwell DJ, Harvey ML, Smith JE, Daniel ZA, Chew AE, Capra JA, Matreyek KA, Fowler DM, Roden DM, Glazer AM. PMID: 38816749; PMCID: PMC11138074.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    22. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nat Commun. 2024 May 23; 15(1):4380. Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. PMID: 38782905; PMCID: PMC11116522.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    23. Disease-specific prioritization of non-coding GWAS variants based on chromatin accessibility. HGG Adv. 2024 Jul 18; 5(3):100310. Liang Q, Abraham A, Capra JA, Kostka D. PMID: 38773771; PMCID: PMC11259938.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    24. Exposure to autoimmune disorders increases Alzheimer's disease risk in a multi-site electronic health record analysis. medRxiv. 2024 May 04. Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M. PMID: 38746318; PMCID: PMC11092711.
      View in: PubMed   Mentions:
    25. Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans. Cell Genom. 2024 Apr 10; 4(4):100536. Hansen TJ, Fong SL, Day JK, Capra JA, Hodges E. PMID: 38604126; PMCID: PMC11019363.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    26. Machine learning reveals the diversity of human 3D chromatin contact patterns. bioRxiv. 2023 Dec 23. Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA. PMID: 38187606; PMCID: PMC10769343.
      View in: PubMed   Mentions:
    27. Archaic Introgression Shaped Human Circadian Traits. Genome Biol Evol. 2023 12 01; 15(12). Velazquez-Arcelay K, Colbran LL, McArthur E, Brand CM, Rinker DC, Siemann JK, McMahon DG, Capra JA. PMID: 38095367; PMCID: PMC10719892.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    28. Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort. medRxiv. 2023 Nov 30. Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA. PMID: 38077057; PMCID: PMC10705634.
      View in: PubMed   Mentions:
    29. Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. bioRxiv. 2023 Nov 28. Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. PMID: 38076936; PMCID: PMC10705239.
      View in: PubMed   Mentions:
    30. Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees. bioRxiv. 2023 Oct 26. Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. PMID: 37961120; PMCID: PMC10634871.
      View in: PubMed   Mentions:
    31. Archaic Introgression Shaped Human Circadian Traits. bioRxiv. 2023 Sep 17. Velazquez-Arcelay K, Colbran LL, McArthur E, Brand C, Rinker D, Siemann J, McMahon D, Capra JA. PMID: 36778254; PMCID: PMC9915721.
      View in: PubMed   Mentions:
    32. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. Res Sq. 2023 Sep 14. Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. PMID: 37790518; PMCID: PMC10543398.
      View in: PubMed   Mentions:
    33. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. bioRxiv. 2023 Aug 12. Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. PMID: 37609337; PMCID: PMC10441401.
      View in: PubMed   Mentions:
    34. Cis-regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression. Genome Biol Evol. 2023 07 03; 15(7). Benton ML, Ruderfer DM, Capra JA. PMID: 37410590; PMCID: PMC10351668.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    35. Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight. Nat Genet. 2023 Jul; 55(7):1250. Solé-Navais P, Flatley C, Steinthorsdottir V, Vaudel M, Juodakis J, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, Wielscher M, Lin F, Briggs C, Wang CA, Moen GH, Beaumont RN, Bradfield JP, Abraham A, Thorleifsson G, Gabrielsen ME, Ostrowski SR, Modzelewska D, Nohr EA, Hypponen E, Srivastava A, Talbot O, Allard C, Williams SM, Menon R, Shields BM, Sveinbjornsson G, Xu H, Melbye M, Lowe W, Bouchard L, Oken E, Pedersen OB, Gudbjartsson DF, Erikstrup C, Sørensen E, Early Growth Genetics Consortium, Estonian Biobank Research Team, Danish Blood Donor Study Genomic Consortium, Lie RT, Teramo K, Hallman M, Juliusdottir T, Hakonarson H, Ullum H, Hattersley AT, Sletner L, Merialdi M, Rifas-Shiman SL, Steingrimsdottir T, Scholtens D, Power C, West J, Nyegaard M, Capra JA, Skogholt AH, Magnus P, Andreassen OA, Thorsteinsdottir U, Grant SFA, Qvigstad E, Pennell CE, Hivert MF, Hayes GM, Jarvelin MR, McCarthy MI, Lawlor DA, Nielsen HS, Mägi R, Rokas A, Hveem K, Stefansson K, Feenstra B, Njolstad P, Muglia LJ, Freathy RM, Johansson S, Zhang G, Jacobsson B. PMID: 37165137; PMCID: PMC10335921.
      View in: PubMed   Mentions:    Fields:    
    36. Comparing chromatin contact maps at scale: methods and insights. Res Sq. 2023 May 23. Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. PMID: 37292728; PMCID: PMC10246266.
      View in: PubMed   Mentions: 1  
    37. Resurrecting the alternative splicing landscape of archaic hominins using machine learning. Nat Ecol Evol. 2023 06; 7(6):939-953. Brand CM, Colbran LL, Capra JA. PMID: 37142741; PMCID: PMC11440953.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    38. High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology. bioRxiv. 2023 Apr 29. Muhammad A, Calandranis ME, Li B, Yang T, Blackwell DJ, Harvey ML, Smith JE, Chew AE, Capra JA, Matreyek KA, Fowler DM, Roden DM, Glazer AM. PMID: 37162834; PMCID: PMC10168370.
      View in: PubMed   Mentions:
    39. Comparing chromatin contact maps at scale: methods and insights. bioRxiv. 2023 Apr 04. Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. PMID: 37066196; PMCID: PMC10104037.
      View in: PubMed   Mentions: 1  
    40. Genetic effects on the timing of parturition and links to fetal birth weight. Nat Genet. 2023 04; 55(4):559-567. Solé-Navais P, Flatley C, Steinthorsdottir V, Vaudel M, Juodakis J, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, Wielscher M, Lin F, Briggs C, Wang CA, Moen GH, Beaumont RN, Bradfield JP, Abraham A, Thorleifsson G, Gabrielsen ME, Ostrowski SR, Modzelewska D, Nohr EA, Hypponen E, Srivastava A, Talbot O, Allard C, Williams SM, Menon R, Shields BM, Sveinbjornsson G, Xu H, Melbye M, Lowe W, Bouchard L, Oken E, Pedersen OB, Gudbjartsson DF, Erikstrup C, Sørensen E, Early Growth Genetics Consortium, Estonian Biobank Research Team, Danish Blood Donor Study Genomic Consortium, Lie RT, Teramo K, Hallman M, Juliusdottir T, Hakonarson H, Ullum H, Hattersley AT, Sletner L, Merialdi M, Rifas-Shiman SL, Steingrimsdottir T, Scholtens D, Power C, West J, Nyegaard M, Capra JA, Skogholt AH, Magnus P, Andreassen OA, Thorsteinsdottir U, Grant SFA, Qvigstad E, Pennell CE, Hivert MF, Hayes GM, Jarvelin MR, McCarthy MI, Lawlor DA, Nielsen HS, Mägi R, Rokas A, Hveem K, Stefansson K, Feenstra B, Njolstad P, Muglia LJ, Freathy RM, Johansson S, Zhang G, Jacobsson B. PMID: 37012456; PMCID: PMC10101852.
      View in: PubMed   Mentions: 48     Fields:    Translation:Humans
    41. Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes. JAMIA Open. 2023 Apr; 6(1):ooad007. McArthur E, Bastarache L, Capra JA. PMID: 36875690; PMCID: PMC9976874.
      View in: PubMed   Mentions: 9  
    42. Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans. bioRxiv. 2023 Feb 15. Hansen T, Fong S, Capra JA, Hodges E. PMID: 36824965; PMCID: PMC9949080.
      View in: PubMed   Mentions:
    43. GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics. 2023 01 01; 39(1). Abraham A, Labella AL, Benton ML, Rokas A, Capra JA. PMID: 36655767; PMCID: PMC9879724.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    44. Integrating Computational Approaches to Predict the Effect of Genetic Variants on Protein Stability in Retinal Degenerative Disease. Adv Exp Med Biol. 2023; 1415:157-163. Grunin M, Palmer E, de Jong S, Jin B, Rinker D, Moth C, Capra JA, Haines JL, Bush WS, den Hollander AI. PMID: 37440029.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    45. Clinical characteristics and electrophysiologic properties of SCN5A variants in fever-induced Brugada syndrome. EBioMedicine. 2023 Jan; 87:104388. Chen GX, Barajas-Martínez H, Ciconte G, Wu CI, Monasky MM, Xia H, Li B, Capra JA, Guo K, Zhang ZH, Chen X, Yang B, Jiang H, Tse G, Mak CM, Aizawa Y, Gollob MH, Antzelevitch C, Wilde AAM, Pappone C, Hu D. PMID: 36516610; PMCID: PMC9768239.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    46. Nucleoporins facilitate ORC loading onto chromatin. Cell Rep. 2022 11 08; 41(6):111590. Richards L, Lord CL, Benton ML, Capra JA, Nordman JT. PMID: 36351393; PMCID: PMC10040217.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    47. Mosaic patterns of selection in genomic regions associated with diverse human traits. PLoS Genet. 2022 11; 18(11):e1010494. Abraham A, LaBella AL, Capra JA, Rokas A. PMID: 36342969; PMCID: PMC9671423.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    48. Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins. Genome Biol Evol. 2022 11 04; 14(11). Fong SL, Capra JA. PMID: 36314566; PMCID: PMC9673499.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    49. Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth. BMC Med. 2022 09 28; 20(1):333. Abraham A, Le B, Kosti I, Straub P, Velez-Edwards DR, Davis LK, Newton JM, Muglia LJ, Rokas A, Bejan CA, Sirota M, Capra JA. PMID: 36167547; PMCID: PMC9516830.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    50. The immune deficiency and c-Jun N-terminal kinase pathways drive the functional integration of the immune and circulatory systems of mosquitoes. Open Biol. 2022 09; 12(9):220111. Yan Y, Sigle LT, Rinker DC, Estévez-Lao TY, Capra JA, Hillyer JF. PMID: 36069078; PMCID: PMC9449813.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    51. An Active Learning Framework Improves Tumor Variant Interpretation. Cancer Res. 2022 08 03; 82(15):2704-2715. Blee AM, Li B, Pecen T, Meiler J, Nagel ZD, Capra JA, Chazin WJ. PMID: 35687855; PMCID: PMC9357215.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    52. Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants. HGG Adv. 2022 Oct 13; 3(4):100131. Mukherjee S, Cassini TA, Hu N, Yang T, Li B, Shen W, Moth CW, Rinker DC, Sheehan JH, Cogan JD, Undiagnosed Diseases Network, Newman JH, Hamid R, Macdonald RL, Roden DM, Meiler J, Kuenze G, Phillips JA, Capra JA. PMID: 36035247; PMCID: PMC9399384.
      View in: PubMed   Mentions: 6     Fields:    
    53. Machine Learning Models to Predict 24 Hour Urinary Abnormalities for Kidney Stone Disease. Urology. 2022 11; 169:52-57. Kavoussi NL, Floyd C, Abraham A, Sui W, Bejan C, Capra JA, Hsi R. PMID: 35853510.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    54. Microbiome-associated human genetic variants impact phenome-wide disease risk. Proc Natl Acad Sci U S A. 2022 06 28; 119(26):e2200551119. Markowitz RHG, LaBella AL, Shi M, Rokas A, Capra JA, Ferguson JF, Mosley JD, Bordenstein SR. PMID: 35749358; PMCID: PMC9245617.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    55. Genome-wide association study of musical beat synchronization demonstrates high polygenicity. Nat Hum Behav. 2022 09; 6(9):1292-1309. Niarchou M, Gustavson DE, Sathirapongsasuti JF, Anglada-Tort M, Eising E, Bell E, McArthur E, Straub P, 23andMe Research Team, McAuley JD, Capra JA, Ullén F, Creanza N, Mosing MA, Hinds DA, Davis LK, Jacoby N, Gordon RL. PMID: 35710621; PMCID: PMC9489530.
      View in: PubMed   Mentions: 41     Fields:    Translation:Humans
    56. The 3D mutational constraint on amino acid sites in the human proteome. Nat Commun. 2022 06 07; 13(1):3273. Li B, Roden DM, Capra JA. PMID: 35672414; PMCID: PMC9174330.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    57. Diverse functions associate with non-coding polymorphisms shared between humans and chimpanzees. BMC Ecol Evol. 2022 05 23; 22(1):68. Velazquez-Arcelay K, Benton ML, Capra JA. PMID: 35606693; PMCID: PMC9125839.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    58. R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. J Mol Biol. 2022 07 15; 434(13):167645. Munden A, Benton ML, Capra JA, Nordman JT. PMID: 35609632; PMCID: PMC9254486.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    59. Integration of Protein Structure and Population-Scale DNA Sequence Data for Disease Gene Discovery and Variant Interpretation. Annu Rev Biomed Data Sci. 2022 08 10; 5:141-161. Li B, Jin B, Capra JA, Bush WS. PMID: 35508071.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    60. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet. 2022 08 31; 23:591-612. Brand CM, Colbran LL, Capra JA. PMID: 35440148; PMCID: PMC10250142.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    61. An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns. Genome Res. 2022 04; 32(4):778-790. Jin B, Capra JA, Benchek P, Wheeler N, Naj AC, Hamilton-Nelson KL, Farrell JJ, Leung YY, Kunkle B, Vadarajan B, Schellenberg GD, Mayeux R, Wang LS, Farrer LA, Pericak-Vance MA, Martin ER, Haines JL, Crawford DC, Bush WS. PMID: 35210353; PMCID: PMC8997344.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    62. Vascular alterations impede fragile tolerance to pregnancy in type 1 diabetes. F S Sci. 2022 05; 3(2):148-158. McNew KL, Abraham A, Sack DE, Smart CD, Pettway YD, Falk AC, Lister RL, Faucon AB, Bejan CA, Capra JA, Aronoff DM, Boyd KL, Moore DJ. PMID: 35560012; PMCID: PMC9850286.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    63. Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features. J Endourol. 2022 02; 36(2):243-250. Abraham A, Kavoussi NL, Sui W, Bejan C, Capra JA, Hsi R. PMID: 34314237; PMCID: PMC8861926.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    64. Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment. Genome Biol Evol. 2021 11 05; 13(11). Colbran LL, Johnson MR, Mathieson I, Capra JA. PMID: 34718543; PMCID: PMC8576593.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    65. Distinct Features of Probands With Early Repolarization and Brugada Syndromes Carrying SCN5A Pathogenic Variants. J Am Coll Cardiol. 2021 10 19; 78(16):1603-1617. Zhang ZH, Barajas-Martínez H, Xia H, Li B, Capra JA, Clatot J, Chen GX, Chen X, Yang B, Jiang H, Tse G, Aizawa Y, Gollob MH, Scheinman M, Antzelevitch C, Hu D. PMID: 34649698; PMCID: PMC9272763.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    66. Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. Am J Hum Genet. 2021 10 07; 108(10):1946-1963. Mukherjee S, Cogan JD, Newman JH, Phillips JA, Hamid R, Undiagnosed Diseases Network, Meiler J, Capra JA. PMID: 34529933; PMCID: PMC8546038.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    67. Modeling the Evolutionary Architectures of Transcribed Human Enhancer Sequences Reveals Distinct Origins, Functions, and Associations with Human Trait Variation. Mol Biol Evol. 2021 08 23; 38(9):3681-3696. Fong SL, Capra JA. PMID: 33973014; PMCID: PMC8382917.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    68. Quantifying the contribution of Neanderthal introgression to the heritability of complex traits. Nat Commun. 2021 07 22; 12(1):4481. McArthur E, Rinker DC, Capra JA. PMID: 34294692; PMCID: PMC8298587.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimals
    69. A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins. J Proteome Res. 2021 08 06; 20(8):4089-4100. Li B, Mendenhall J, Capra JA, Meiler J. PMID: 34236204; PMCID: PMC8650144.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    70. Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants. Neurology. 2021 07 13; 97(2):e145-e155. Shibao CA, Joos K, Phillips JA, Cogan J, Newman JH, Hamid R, Meiler J, Capra J, Sheehan J, Vetrini F, Yang Y, Black B, Diedrich A, Roberston D, Biaggioni I. PMID: 33947782; PMCID: PMC8279568.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCTClinical Trials
    71. Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks. Genetics. 2021 03 03; 217(1):1-10. Kasimatis KR, Abraham A, Ralph PL, Kern AD, Capra JA, Phillips PC. PMID: 33683357; PMCID: PMC8045711.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    72. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet. 2021 02 04; 108(2):269-283. McArthur E, Capra JA. PMID: 33545030; PMCID: PMC7895846.
      View in: PubMed   Mentions: 115     Fields:    Translation:HumansCells
    73. Genetics of agenesis/hypoplasia of the uterus and vagina: narrowing down the number of candidate genes for Mayer-Rokitansky-Küster-Hauser Syndrome. Hum Genet. 2021 Apr; 140(4):667-680. Mikhael S, Dugar S, Morton M, Chorich LP, Tam KB, Lossie AC, Kim HG, Knight J, Taylor HS, Mukherjee S, Capra JA, Phillips JA, Friez M, Layman LC. PMID: 33469725; PMCID: PMC9211441.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimals
    74. The influence of evolutionary history on human health and disease. Nat Rev Genet. 2021 05; 22(5):269-283. Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. PMID: 33408383; PMCID: PMC7787134.
      View in: PubMed   Mentions: 126     Fields:    Translation:Humans
    75. Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS Comput Biol. 2020 11; 16(11):e1008291. Li B, Yang YT, Capra JA, Gerstein MB. PMID: 33253214; PMCID: PMC7728386.
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    76. Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput Biol. 2020 11; 16(11):e1008334. Chen L, Capra JA. PMID: 33137083; PMCID: PMC7660921.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    77. Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species. FASEB J. 2020 12; 34(12):15946-15960. Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. PMID: 33015868; PMCID: PMC7675292.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    78. PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. Genome Biol. 2020 08 26; 21(1):217. Tang ZZ, Sliwoski GR, Chen G, Jin B, Bush WS, Li B, Capra JA. PMID: 32847609; PMCID: PMC7448521.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    79. Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations. Nat Ecol Evol. 2020 10; 4(10):1332-1341. Rinker DC, Simonti CN, McArthur E, Shaw D, Hodges E, Capra JA. PMID: 32719451; PMCID: PMC7529911.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    80. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nat Commun. 2020 07 24; 11(1):3731. LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. PMID: 32709900; PMCID: PMC7382462.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    81. Which animals are at risk? Predicting species susceptibility to Covid-19. bioRxiv. 2020 Jul 10. Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. PMID: 32676592; PMCID: PMC7359514.
      View in: PubMed   Mentions: 2  
    82. Phenotypic Profiling in Subjects Heterozygous for 1 of 2 Rare Variants in the Hypophosphatasia Gene (ALPL). J Endocr Soc. 2020 Aug 01; 4(8):bvaa084. Tilden DR, Sheehan JH, Newman JH, Meiler J, Capra JA, Ramirez A, Simmons J, Dahir K. PMID: 32803091; PMCID: PMC7417882.
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    83. Advancing human health in the decade ahead: pregnancy as a key window for discovery: A Burroughs Wellcome Fund Pregnancy Think Tank. Am J Obstet Gynecol. 2020 09; 223(3):312-321. Sadovsky Y, Mesiano S, Burton GJ, Lampl M, Murray JC, Freathy RM, Mahadevan-Jansen A, Moffett A, Price ND, Wise PH, Wildman DE, Snyderman R, Paneth N, Capra JA, Nobrega MA, Barak Y, Muglia LJ, Burroughs Wellcome Fund Pregnancy Think Tank Working Group. PMID: 32565236; PMCID: PMC7303037.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    84. High-Throughput Reclassification of SCN5A Variants. Am J Hum Genet. 2020 07 02; 107(1):111-123. Glazer AM, Wada Y, Li B, Muhammad A, Kalash OR, O'Neill MJ, Shields T, Hall L, Short L, Blair MA, Kroncke BM, Capra JA, Roden DM. PMID: 32533946; PMCID: PMC7332654.
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    85. Functional annotation of rare structural variation in the human brain. Nat Commun. 2020 06 12; 11(1):2990. Han L, Zhao X, Benton ML, Perumal T, Collins RL, Hoffman GE, Johnson JS, Sloofman L, Wang HZ, Stone MR, CommonMind Consortium, Brennand KJ, Brand H, Sieberts SK, Marenco S, Peters MA, Lipska BK, Roussos P, Capra JA, Talkowski M, Ruderfer DM. PMID: 32533064; PMCID: PMC7293301.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    86. Integrating structural and evolutionary data to interpret variation and pathogenicity in adapter protein complex 4. Protein Sci. 2020 06; 29(6):1535-1549. Gadbery JE, Abraham A, Needle CD, Moth C, Sheehan J, Capra JA, Jackson LP. PMID: 32285480; PMCID: PMC7255511.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    87. Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Nat Ecol Evol. 2019 11; 3(11):1598-1606. Colbran LL, Gamazon ER, Zhou D, Evans P, Cox NJ, Capra JA. PMID: 31591491; PMCID: PMC7046098.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimals
    88. The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins. Genome Biol Evol. 2019 09 01; 11(9):2574-2592. Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A. PMID: 31504490; PMCID: PMC6751361.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    89. Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. G3 (Bethesda). 2019 08 08; 9(8):2761-2774. Moon JM, Capra JA, Abbot P, Rokas A. PMID: 31213516; PMCID: PMC6686946.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    90. Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation. Bioessays. 2019 09; 41(9):e1900072. Moon JM, Capra JA, Abbot P, Rokas A. PMID: 31373044.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    91. Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function. BMC Genomics. 2019 Jun 20; 20(1):511. Benton ML, Talipineni SC, Kostka D, Capra JA. PMID: 31221079; PMCID: PMC6585034.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    92. Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Evol Med Public Health. 2019; 2019(1):93-103. Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A. PMID: 31263560; PMCID: PMC6592264.
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    93. IgG4-related disease: Association with a rare gene variant expressed in cytotoxic T cells. Mol Genet Genomic Med. 2019 06; 7(6):e686. Newman JH, Shaver A, Sheehan JH, Mallal S, Stone JH, Pillai S, Bastarache L, Riebau D, Allard-Chamard H, Stone WM, Perugino C, Pilkinton M, Smith SA, McDonnell WJ, Capra JA, Meiler J, Cogan J, Xing K, Mahajan VS, Mattoo H, Hamid R, Phillips JA, Undiagnosed Disease Network. PMID: 30993913; PMCID: PMC6565556.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    94. Protein structure aids predicting functional perturbation of missense variants in SCN5A and KCNQ1. Comput Struct Biotechnol J. 2019; 17:206-214. Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM. PMID: 30828412; PMCID: PMC6383132.
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    95. Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. Genetics. 2019 04; 211(4):1205-1217. Colbran LL, Chen L, Capra JA. PMID: 30696717; PMCID: PMC6456323.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    96. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev. 2019 05 08; 119(9):5537-5606. Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. PMID: 30608666; PMCID: PMC6506414.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansCells
    97. Genome-wide maps of distal gene regulatory enhancers active in the human placenta. PLoS One. 2018; 13(12):e0209611. Zhang J, Simonti CN, Capra JA. PMID: 30589856; PMCID: PMC6320013.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    98. integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth. BMC Med Genomics. 2018 Nov 19; 11(1):107. Eidem HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, Rokas A. PMID: 30453955; PMCID: PMC6245874.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    99. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput Biol. 2018 10; 14(10):e1006484. Chen L, Fish AE, Capra JA. PMID: 30286077; PMCID: PMC6191148.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    100. Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology. G3 (Bethesda). 2018 03 28; 8(4):1315-1325. Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A. PMID: 29467190; PMCID: PMC5873920.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    101. Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures. Am J Hum Genet. 2018 03 01; 102(3):415-426. Sivley RM, Dou X, Meiler J, Bush WS, Capra JA. PMID: 29455857; PMCID: PMC5985282.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    102. Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. BMC Bioinformatics. 2018 01 23; 19(1):18. Sivley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J, Capra JA. PMID: 29361909; PMCID: PMC5781290.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    103. Local ancestry transitions modify snp-trait associations. Pac Symp Biocomput. 2018; 23:424-435. Fish AE, Crawford DC, Capra JA, Bush WS. PMID: 29218902; PMCID: PMC5728664.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    104. Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints. Mol Biol Evol. 2017 Nov 01; 34(11):2856-2869. Simonti CN, Pavlicev M, Capra JA. PMID: 28961735; PMCID: PMC5850124.
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    105. Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity. Genome Biol Evol. 2017 10 01; 9(10):2615-2625. Fish A, Chen L, Capra JA. PMID: 28985297; PMCID: PMC5737616.
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    106. What is a placental mammal anyway? Elife. 2017 09 12; 6. Abbot P, Capra JA. PMID: 28895533; PMCID: PMC5595430.
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    107. Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs. BMC Genomics. 2017 Aug 31; 18(1):672. Patel VD, Capra JA. PMID: 28859623; PMCID: PMC5579935.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    108. Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability. Nucleic Acids Res. 2017 Jul 27; 45(13):7796-7806. Wanzek K, Schwindt E, Capra JA, Paeschke K. PMID: 28535251; PMCID: PMC5570088.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    109. Short DNA sequence patterns accurately identify broadly active human enhancers. BMC Genomics. 2017 07 17; 18(1):536. Colbran LL, Chen L, Capra JA. PMID: 28716036; PMCID: PMC5512948.
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    110. The transformative potential of an integrative approach to pregnancy. Placenta. 2017 Sep; 57:204-215. Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A. PMID: 28864013.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    111. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. Cell Metab. 2017 Apr 04; 25(4):838-855.e15. Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD. PMID: 28380376; PMCID: PMC5444661.
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    112. Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts? Am J Hum Genet. 2016 Oct 06; 99(4):817-830. Fish AE, Capra JA, Bush WS. PMID: 27640306; PMCID: PMC5065654.
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    113. Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity. PLoS Genet. 2016 09; 12(9):e1006238. McDonald KR, Guise AJ, Pourbozorgi-Langroudi P, Cristea IM, Zakian VA, Capra JA, Sabouri N. PMID: 27611590; PMCID: PMC5017727.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    114. Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Genetics. 2016 11; 204(3):893-904. Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y. PMID: 27585849; PMCID: PMC5105867.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    115. XPA: A key scaffold for human nucleotide excision repair. DNA Repair (Amst). 2016 08; 44:123-135. Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ. PMID: 27247238; PMCID: PMC4958585.
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    116. The phenotypic legacy of admixture between modern humans and Neandertals. Science. 2016 Feb 12; 351(6274):737-41. Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA. PMID: 26912863; PMCID: PMC4849557.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansAnimals
    117. Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun. 2016 Feb 02; 7:10464. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW. PMID: 26833085; PMCID: PMC4740880.
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    118. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. Nucleic Acids Res. 2016 Jan 04; 44(D1):D908-16. Kim M, Cooper BA, Venkat R, Phillips JB, Eidem HR, Hirbo J, Nutakki S, Williams SM, Muglia LJ, Capra JA, Petren K, Abbot P, Rokas A, McGary KL. PMID: 26567549; PMCID: PMC4702823.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    119. The evolution of the human genome. Curr Opin Genet Dev. 2015 Dec; 35:9-15. Simonti CN, Capra JA. PMID: 26338498; PMCID: PMC4695266.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    120. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. BMC Evol Biol. 2015 Mar 10; 15:35. Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. PMID: 25887984; PMCID: PMC4362643.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    121. Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study. BMC Genomics. 2015 Feb 21; 16:104. Capra JA. PMID: 25765133; PMCID: PMC4342796.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    122. The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage. BMC Biol. 2014 Dec 04; 12:101. Sabouri N, Capra JA, Zakian VA. PMID: 25471935; PMCID: PMC4275981.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    123. Log-odds sequence logos. Bioinformatics. 2015 Feb 01; 31(3):324-31. Yu YK, Capra JA, Stojmirovic A, Landsman D, Altschul SF. PMID: 25294922; PMCID: PMC4318935.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    124. Modeling DNA methylation dynamics with approaches from phylogenetics. Bioinformatics. 2014 Sep 01; 30(17):i408-14. Capra JA, Kostka D. PMID: 25161227; PMCID: PMC4147898.
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    125. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun; 10(6):e1003677. Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. PMID: 24967590; PMCID: PMC4072507.
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    126. Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19; 368(1632):20130025. Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. PMID: 24218637; PMCID: PMC3826498.
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    127. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 07; 52(3):314-24. Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. PMID: 24207025; PMCID: PMC3936344.
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    128. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 2013; 9(8):e1003684. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. PMID: 23966869; PMCID: PMC3744432.
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    129. How old is my gene? Trends Genet. 2013 Nov; 29(11):659-68. Capra JA, Stolzer M, Durand D, Pollard KS. PMID: 23915718; PMCID: PMC3812327.
      View in: PubMed   Mentions: 33     Fields:    
    130. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG. PMID: 22981692; PMCID: PMC3462286.
      View in: PubMed   Mentions: 382     Fields:    Translation:HumansAnimalsCells
    131. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput Biol. 2012; 8(6):e1002567. Capra JA, Williams AG, Pollard KS. PMID: 22761559; PMCID: PMC3386163.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansAnimals
    132. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 2011; 3:614-26. Katzman S, Capra JA, Haussler D, Pollard KS. PMID: 21697099; PMCID: PMC3157837.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    133. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol. 2011; 3:516-27. Capra JA, Pollard KS. PMID: 21670083; PMCID: PMC3138425.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    134. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Aging (Albany NY). 2011 Jun; 3(6):635-42. Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. PMID: 21701047; PMCID: PMC3164371.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansAnimalsCells
    135. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell. 2011 May 27; 145(5):678-91. Paeschke K, Capra JA, Zakian VA. PMID: 21620135; PMCID: PMC3129610.
      View in: PubMed   Mentions: 338     Fields:    Translation:AnimalsCells
    136. Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol. 2010; 11(12):R127. Capra JA, Pollard KS, Singh M. PMID: 21187012; PMCID: PMC3046487.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    137. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. PLoS Comput Biol. 2010 Jul 22; 6(7):e1000861. Capra JA, Paeschke K, Singh M, Zakian VA. PMID: 20676380; PMCID: PMC2908698.
      View in: PubMed   Mentions: 159     Fields:    Translation:AnimalsCells
    138. Genomics through the lens of next-generation sequencing. Genome Biol. 2010; 11(6):306. Capra JA, Carbone L, Riesenfeld SJ, Wall JD. PMID: 20587080; PMCID: PMC2911104.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    139. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol. 2009 Dec; 5(12):e1000585. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. PMID: 19997483; PMCID: PMC2777313.
      View in: PubMed   Mentions: 206     Fields:    Translation:Cells
    140. Characterization and prediction of residues determining protein functional specificity. Bioinformatics. 2008 Jul 01; 24(13):1473-80. Capra JA, Singh M. PMID: 18450811; PMCID: PMC2718669.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    141. Predicting functionally important residues from sequence conservation. Bioinformatics. 2007 Aug 01; 23(15):1875-82. Capra JA, Singh M. PMID: 17519246.
      View in: PubMed   Mentions: 360     Fields:    Translation:Cells
    142. Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics. 2003; 1(4):327-42. Rosen GD, La Porte NT, Diechtiareff B, Pung CJ, Nissanov J, Gustafson C, Bertrand L, Gefen S, Fan Y, Tretiak OJ, Manly KF, Park MR, Williams AG, Connolly MT, Capra JA, Williams RW. PMID: 15043219.
      View in: PubMed   Mentions: 27     Fields:    Translation:Animals
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