Tony Capra, PhD
Professor
Bioengineering
School of Pharmacy

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

Education & Training

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• N/A Diversity, Equity, and Inclusion Champion Training UCSF 2021
• Postdoc Comparative Genomics UCSF/Gladstone Institutes 02/2013
• PhD Computer Science Princeton University 05/2009
• BA Mathematics, Computer Science Columbia University 05/2004

Interests

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• protein structure
• electronic health records
• gene regulation
• machine learning
• evolution
• human genetics

Websites

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• Capra Lab (capralab.org)
• Posts on X capra_lab (X.com)

Grants and Projects

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• The Evolution of Gene Regulation and Human Disease, NIH, 2018-2029
• Allele Prospector: Leveraging human genetic variation to enable therapeutic genome editing in hundreds of disease genes, CIRM, 2026-2029
• Personalized Structural Biology: Enabling Exome Interpretation in Undiagnosed Diseases, NIH, 2021-2025
• Integrating ’Omics and EHRs to Elucidate the Genetic Architecture of Preterm Birth, Burroughs Wellcome Fund, 2017-2021
• Modeling the Dynamics of Genome-Scale Data Across Trees, NIH, 2015-2019

Publications (142)

Top publication keywords:
DiseaseMachine LearningGenetic VariationEnhancer Elements, GeneticMultifactorial InheritanceGenome, HumanEvolution, MolecularConserved SequenceHominidaePan troglodytesModels, GeneticDNA, AncientRegulatory Sequences, Nucleic AcidGenomicsNeanderthals

• Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations.
  Nature ecology & evolution 2020 Rinker DC, Simonti CN, McArthur E, Shaw D, Hodges E, Capra JA
• Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci.
  Nature communications 2020 LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA
• Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.
  Nature ecology & evolution 2019 Colbran LL, Gamazon ER, Zhou D, Evans P, Cox NJ, Capra JA
• Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function.
  BMC genomics 2019 Benton ML, Talipineni SC, Kostka D, Capra JA
• Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.
  PLoS computational biology 2018 Chen L, Fish AE, Capra JA
• Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures.
  American journal of human genetics 2018 Sivley RM, Dou X, Meiler J, Bush WS, Capra JA
• Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?
  American journal of human genetics 2016 Fish AE, Capra JA, Bush WS
• The phenotypic legacy of admixture between modern humans and Neandertals.
  Science (New York, N.Y.) 2016 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, …

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• AncientProxy: A catalog of ancient proxies for modern genetic variants.
  American journal of human genetics 2026 Brand CM, Capra JA
• Discovering latent subtypes of preterm birth and genetic risk using tensor decomposition on electronic health records.
  medRxiv : the preprint server for health sciences 2025 Abraham A, Bejan C, Takasuka H, Sirota M, Capra JA
• Haplotype editing with CRISPR-Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL.
  Molecular therapy : the journal of the American Society of Gene Therapy 2025 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
• Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity.
  bioRxiv : the preprint server for biology 2025 Chen Y, Velazquez-Arcelay K, Capra JA
• Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.
  bioRxiv : the preprint server for biology 2025 McArthur E, Rinker DC, Cheng Y, Wang Q, Wang J, Gilbertson EN, Fudenberg G, Pittman M, Keough K, Yue F, Pollard KS, Capra JA
• Strategies for Creating Robust Patient Groups to Study Diverse Conditions with Electronic Health Records.
  Annual review of biomedical data science 2025 Ramey GD, Takasuka H, Capra JA
• VUStruct: a compute pipeline for high throughput and personalized structural biology.
  bioRxiv : the preprint server for biology 2025 Moth CW, Sheehan JH, Mamun AA, Sivley RM, Gulsevin A, Rinker D, Undiagnosed Diseases Network, Capra JA, Meiler J
• Comparing chromatin contact maps at scale: methods and insights.
  Nature methods 2025 Gjoni K, Gunsalus LM, Kuang S, McArthur E, Pittman M, Capra JA, Pollard KS
• Identifying deleterious noncoding variation through gain and loss of CTCF binding activity.
  American journal of human genetics 2025 Tubbs C, Benton ML, McArthur E, Capra JA, Ruderfer DM
• Exposure to autoimmune disorders is associated with increased Alzheimer's disease risk in a multi-site electronic health record analysis.
  Cell reports. Medicine 2025 Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M
• Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning.
  eLife 2025 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
• Pre-conception clinical risk factors differ between spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.
  BMC pregnancy and childbirth 2025 Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA
• Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL.
  bioRxiv : the preprint server for biology 2024 Dua PH, Simon BMJ, Marley CBE, Feliciano CM, Watry HL, Steury D, Abraham A, Gilbertson EN, Ramey GD, Capra JA, Conklin BR, Judge LM
• Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning.
  bioRxiv : the preprint server for biology 2024 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
• Inferring human phenotypes using ancient DNA: from molecules to populations.
  Current opinion in genetics & development 2024 Ferrando-Bernal M, Brand CM, Capra JA
• Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.
  Genome biology and evolution 2024 Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA
• Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals.
  bioRxiv : the preprint server for biology 2024 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
• Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns.
  Molecular biology and evolution 2024 Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA
• Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale.
  PLoS biology 2024 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
• Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.
  ACR open rheumatology 2024 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
• High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology.
  Genome medicine 2024 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
• Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates.
  Nature communications 2024 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…
• Disease-specific prioritization of non-coding GWAS variants based on chromatin accessibility.
  HGG advances 2024 Liang Q, Abraham A, Capra JA, Kostka D
• Exposure to autoimmune disorders increases Alzheimer's disease risk in a multi-site electronic health record analysis.
  medRxiv : the preprint server for health sciences 2024 Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M
• Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans.
  Cell genomics 2024 Hansen TJ, Fong SL, Day JK, Capra JA, Hodges E
• Machine learning reveals the diversity of human 3D chromatin contact patterns.
  bioRxiv : the preprint server for biology 2023 Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA
• Archaic Introgression Shaped Human Circadian Traits.
  Genome biology and evolution 2023 Velazquez-Arcelay K, Colbran LL, McArthur E, Brand CM, Rinker DC, Siemann JK, McMahon DG, Capra JA
• Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.
  medRxiv : the preprint server for health sciences 2023 Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA
• Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.
  bioRxiv : the preprint server for biology 2023 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
• Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.
  bioRxiv : the preprint server for biology 2023 Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA
• Archaic Introgression Shaped Human Circadian Traits.
  bioRxiv : the preprint server for biology 2023 Velazquez-Arcelay K, Colbran LL, McArthur E, Brand C, Rinker D, Siemann J, McMahon D, Capra JA
• Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.
  Research square 2023 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, …
• Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.
  bioRxiv : the preprint server for biology 2023 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, …
• Cis-regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression.
  Genome biology and evolution 2023 Benton ML, Ruderfer DM, Capra JA
• Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight.
  Nature genetics 2023 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, …
• Comparing chromatin contact maps at scale: methods and insights.
  Research square 2023 Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS
• Resurrecting the alternative splicing landscape of archaic hominins using machine learning.
  Nature ecology & evolution 2023 Brand CM, Colbran LL, Capra JA
• High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology.
  bioRxiv : the preprint server for biology 2023 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
• Comparing chromatin contact maps at scale: methods and insights.
  bioRxiv : the preprint server for biology 2023 Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS
• Genetic effects on the timing of parturition and links to fetal birth weight.
  Nature genetics 2023 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, …
• Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes.
  JAMIA open 2023 McArthur E, Bastarache L, Capra JA
• Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans.
  bioRxiv : the preprint server for biology 2023 Hansen T, Fong S, Capra JA, Hodges E
• GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions.
  Bioinformatics (Oxford, England) 2023 Abraham A, Labella AL, Benton ML, Rokas A, Capra JA
• Integrating Computational Approaches to Predict the Effect of Genetic Variants on Protein Stability in Retinal Degenerative Disease.
  Advances in experimental medicine and biology 2023 Grunin M, Palmer E, de Jong S, Jin B, Rinker D, Moth C, Capra JA, Haines JL, Bush WS, den Hollander AI
• Clinical characteristics and electrophysiologic properties of SCN5A variants in fever-induced Brugada syndrome.
  EBioMedicine 2022 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…
• Nucleoporins facilitate ORC loading onto chromatin.
  Cell reports 2022 Richards L, Lord CL, Benton ML, Capra JA, Nordman JT
• Mosaic patterns of selection in genomic regions associated with diverse human traits.
  PLoS genetics 2022 Abraham A, LaBella AL, Capra JA, Rokas A
• Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins.
  Genome biology and evolution 2022 Fong SL, Capra JA
• Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth.
  BMC medicine 2022 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
• The immune deficiency and c-Jun N-terminal kinase pathways drive the functional integration of the immune and circulatory systems of mosquitoes.
  Open biology 2022 Yan Y, Sigle LT, Rinker DC, Estévez-Lao TY, Capra JA, Hillyer JF
• An Active Learning Framework Improves Tumor Variant Interpretation.
  Cancer research 2022 Blee AM, Li B, Pecen T, Meiler J, Nagel ZD, Capra JA, Chazin WJ
• Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants.
  HGG advances 2022 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…
• Machine Learning Models to Predict 24 Hour Urinary Abnormalities for Kidney Stone Disease.
  Urology 2022 Kavoussi NL, Floyd C, Abraham A, Sui W, Bejan C, Capra JA, Hsi R
• Microbiome-associated human genetic variants impact phenome-wide disease risk.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Markowitz RHG, LaBella AL, Shi M, Rokas A, Capra JA, Ferguson JF, Mosley JD, Bordenstein SR
• Genome-wide association study of musical beat synchronization demonstrates high polygenicity.
  Nature human behaviour 2022 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, …
• The 3D mutational constraint on amino acid sites in the human proteome.
  Nature communications 2022 Li B, Roden DM, Capra JA
• Diverse functions associate with non-coding polymorphisms shared between humans and chimpanzees.
  BMC ecology and evolution 2022 Velazquez-Arcelay K, Benton ML, Capra JA
• R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures.
  Journal of molecular biology 2022 Munden A, Benton ML, Capra JA, Nordman JT
• Integration of Protein Structure and Population-Scale DNA Sequence Data for Disease Gene Discovery and Variant Interpretation.
  Annual review of biomedical data science 2022 Li B, Jin B, Capra JA, Bush WS
• Predicting Archaic Hominin Phenotypes from Genomic Data.
  Annual review of genomics and human genetics 2022 Brand CM, Colbran LL, Capra JA
• An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns.
  Genome research 2022 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, …
• Vascular alterations impede fragile tolerance to pregnancy in type 1 diabetes.
  F&S science 2022 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
• Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features.
  Journal of endourology 2022 Abraham A, Kavoussi NL, Sui W, Bejan C, Capra JA, Hsi R
• Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment.
  Genome biology and evolution 2021 Colbran LL, Johnson MR, Mathieson I, Capra JA
• Distinct Features of Probands With Early Repolarization and Brugada Syndromes Carrying SCN5A Pathogenic Variants.
  Journal of the American College of Cardiology 2021 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
• Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network.
  American journal of human genetics 2021 Mukherjee S, Cogan JD, Newman JH, Phillips JA, Hamid R, Undiagnosed Diseases Network, Meiler J, Capra JA
• Modeling the Evolutionary Architectures of Transcribed Human Enhancer Sequences Reveals Distinct Origins, Functions, and Associations with Human Trait Variation.
  Molecular biology and evolution 2021 Fong SL, Capra JA
• Quantifying the contribution of Neanderthal introgression to the heritability of complex traits.
  Nature communications 2021 McArthur E, Rinker DC, Capra JA
• A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins.
  Journal of proteome research 2021 Li B, Mendenhall J, Capra JA, Meiler J
• Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants.
  Neurology 2021 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
• Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks.
  Genetics 2021 Kasimatis KR, Abraham A, Ralph PL, Kern AD, Capra JA, Phillips PC
• Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability.
  American journal of human genetics 2021 McArthur E, Capra JA
• Genetics of agenesis/hypoplasia of the uterus and vagina: narrowing down the number of candidate genes for Mayer-Rokitansky-Küster-Hauser Syndrome.
  Human genetics 2021 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
• The influence of evolutionary history on human health and disease.
  Nature reviews. Genetics 2021 Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA
• Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
  PLoS computational biology 2020 Li B, Yang YT, Capra JA, Gerstein MB
• Learning and interpreting the gene regulatory grammar in a deep learning framework.
  PLoS computational biology 2020 Chen L, Capra JA
• Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species.
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2020 Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS
• PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection.
  Genome biology 2020 Tang ZZ, Sliwoski GR, Chen G, Jin B, Bush WS, Li B, Capra JA
• Which animals are at risk? Predicting species susceptibility to Covid-19.
  bioRxiv : the preprint server for biology 2020 Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS
• Phenotypic Profiling in Subjects Heterozygous for 1 of 2 Rare Variants in the Hypophosphatasia Gene (ALPL).
  Journal of the Endocrine Society 2020 Tilden DR, Sheehan JH, Newman JH, Meiler J, Capra JA, Ramirez A, Simmons J, Dahir K
• Advancing human health in the decade ahead: pregnancy as a key window for discovery: A Burroughs Wellcome Fund Pregnancy Think Tank.
  American journal of obstetrics and gynecology 2020 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, …
• Functional annotation of rare structural variation in the human brain.
  Nature communications 2020 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, …
• High-Throughput Reclassification of SCN5A Variants.
  American journal of human genetics 2020 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
• Integrating structural and evolutionary data to interpret variation and pathogenicity in adapter protein complex 4.
  Protein science : a publication of the Protein Society 2020 Gadbery JE, Abraham A, Needle CD, Moth C, Sheehan J, Capra JA, Jackson LP
• The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins.
  Genome biology and evolution 2019 Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A
• Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues.
  G3 (Bethesda, Md.) 2019 Moon JM, Capra JA, Abbot P, Rokas A
• Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation.
  BioEssays : news and reviews in molecular, cellular and developmental biology 2019 Moon JM, Capra JA, Abbot P, Rokas A
• Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication.
  Evolution, medicine, and public health 2019 Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A
• IgG4-related disease: Association with a rare gene variant expressed in cytotoxic T cells.
  Molecular genetics & genomic medicine 2019 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,…
• Protein structure aids predicting functional perturbation of missense variants in SCN5A and KCNQ1.
  Computational and structural biotechnology journal 2019 Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM
• Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity.
  Genetics 2019 Colbran LL, Chen L, Capra JA
• Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis.
  Chemical reviews 2019 Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR
• Genome-wide maps of distal gene regulatory enhancers active in the human placenta.
  PloS one 2018 Zhang J, Simonti CN, Capra JA
• integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth.
  BMC medical genomics 2018 Eidem HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, Rokas A
• Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology.
  G3 (Bethesda, Md.) 2018 Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A
• Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia.
  BMC bioinformatics 2018 Sivley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J, Capra JA
• Local ancestry transitions modify snp-trait associations.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2018 Fish AE, Crawford DC, Capra JA, Bush WS
• Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints.
  Molecular biology and evolution 2017 Simonti CN, Pavlicev M, Capra JA
• Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity.
  Genome biology and evolution 2017 Fish A, Chen L, Capra JA
• What is a placental mammal anyway?
  eLife 2017 Abbot P, Capra JA
• Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs.
  BMC genomics 2017 Patel VD, Capra JA
• Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability.
  Nucleic acids research 2017 Wanzek K, Schwindt E, Capra JA, Paeschke K
• Short DNA sequence patterns accurately identify broadly active human enhancers.
  BMC genomics 2017 Colbran LL, Chen L, Capra JA
• The transformative potential of an integrative approach to pregnancy.
  Placenta 2017 Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A
• SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.
  Cell metabolism 2017 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,…
• Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity.
  PLoS genetics 2016 McDonald KR, Guise AJ, Pourbozorgi-Langroudi P, Cristea IM, Zakian VA, Capra JA, Sabouri N
• Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk.
  Genetics 2016 Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y
• XPA: A key scaffold for human nucleotide excision repair.
  DNA repair 2016 Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ
• Joint mouse-human phenome-wide association to test gene function and disease risk.
  Nature communications 2016 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,…
• 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 research 2015 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
• The evolution of the human genome.
  Current opinion in genetics & development 2015 Simonti CN, Capra JA
• Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.
  BMC evolutionary biology 2015 Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA
• Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study.
  BMC genomics 2015 Capra JA
• The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage.
  BMC biology 2014 Sabouri N, Capra JA, Zakian VA
• Log-odds sequence logos.
  Bioinformatics (Oxford, England) 2014 Yu YK, Capra JA, Stojmirovic A, Landsman D, Altschul SF
• Modeling DNA methylation dynamics with approaches from phylogenetics.
  Bioinformatics (Oxford, England) 2014 Capra JA, Kostka D
• Integrating diverse datasets improves developmental enhancer prediction.
  PLoS computational biology 2014 Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA
• Many human accelerated regions are developmental enhancers.
  Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013 Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS
• Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.
  Molecular cell 2013 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
• A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.
  PLoS genetics 2013 Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A
• How old is my gene?
  Trends in genetics : TIG 2013 Capra JA, Stolzer M, Durand D, Pollard KS
• Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.
  Cell 2012 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, …
• ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
  PLoS computational biology 2012 Capra JA, Williams AG, Pollard KS
• Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.
  Genome biology and evolution 2011 Katzman S, Capra JA, Haussler D, Pollard KS
• Substitution patterns are GC-biased in divergent sequences across the metazoans.
  Genome biology and evolution 2011 Capra JA, Pollard KS
• SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.
  Aging 2011 Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E
• DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase.
  Cell 2011 Paeschke K, Capra JA, Zakian VA
• Novel genes exhibit distinct patterns of function acquisition and network integration.
  Genome biology 2010 Capra JA, Pollard KS, Singh M
• G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.
  PLoS computational biology 2010 Capra JA, Paeschke K, Singh M, Zakian VA
• Genomics through the lens of next-generation sequencing.
  Genome biology 2010 Capra JA, Carbone L, Riesenfeld SJ, Wall JD
• Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
  PLoS computational biology 2009 Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA
• Characterization and prediction of residues determining protein functional specificity.
  Bioinformatics (Oxford, England) 2008 Capra JA, Singh M
• Predicting functionally important residues from sequence conservation.
  Bioinformatics (Oxford, England) 2007 Capra JA, Singh M
• Informatics center for mouse genomics: the dissection of complex traits of the nervous system.
  Neuroinformatics 2003 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