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John Capra

Title(s)Assoc Professor in Residence, Computational Health Scienc
SchoolSchool of Medicine
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    The Evolution of Gene Regulation and Human Disease
    NIH/NIGMS R35GM127087Apr 1, 2018 - Mar 31, 2023
    Role: Principal Investigator
    Modeling the Dynamics of Genome-Scale Data Across Trees
    NIH/NIGMS R01GM115836Aug 1, 2015 - Jun 30, 2018
    Role: Co-Principal Investigator

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    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. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nat Commun. 2020 Jul 24; 11(1):3731. LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. PMID: 32709900.
      View in: PubMed   Mentions:    Fields:    
    2. 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.
      View in: PubMed   Mentions:
    3. 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 Jun 18. 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. PMID: 32565236.
      View in: PubMed   Mentions:    Fields:    
    4. High-Throughput Reclassification of SCN5A Variants. Am J Hum Genet. 2020 Jul 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.
      View in: PubMed   Mentions: 1     Fields:    
    5. Functional annotation of rare structural variation in the human brain. Nat Commun. 2020 Jun 12; 11(1):2990. Han L, Zhao X, Benton ML, Perumal T, Collins RL, Hoffman GE, Johnson JS, Sloofman L, Wang HZ, Stone MR, Brennand KJ, Brand H, Sieberts SK, Marenco S, Peters MA, Lipska BK, Roussos P, Capra JA, Talkowski M, Ruderfer DM. PMID: 32533064.
      View in: PubMed   Mentions:    Fields:    
    6. 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.
      View in: PubMed   Mentions: 1     Fields:    
    7. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    8. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    9. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    10. 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: 1     Fields:    Translation:HumansAnimalsCells
    11. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    12. 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.
      View in: PubMed   Mentions:
    13. 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. PMID: 30993913.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. 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.
      View in: PubMed   Mentions:
    15. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    16. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    17. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    18. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    19. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    20. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    21. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    22. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    23. Local ancestry transitions modify snp-trait associations. Pac Symp Biocomput. 2018; 23:424-435. Fish AE, Crawford DC, Capra JA, Bush WS. PMID: 29218902.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    24. 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.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    25. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    26. What is a placental mammal anyway? Elife. 2017 09 12; 6. Abbot P, Capra JA. PMID: 28895533.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    27. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    28. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    29. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    30. 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: 3     Fields:    Translation:Humans
    31. 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.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    32. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    33. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    34. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    35. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    36. 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.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimals
    37. 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.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimals
    38. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    39. The evolution of the human genome. Curr Opin Genet Dev. 2015 Dec; 35:9-15. Simonti CN, Capra JA. PMID: 26338498.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    40. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    41. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    42. 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.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    43. Log-odds sequence logos. Bioinformatics. 2015 Feb 01; 31(3):324-31. Yu YK, Capra JA, Stojmirovic A, Landsman D, Altschul SF. PMID: 25294922.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    44. Modeling DNA methylation dynamics with approaches from phylogenetics. Bioinformatics. 2014 Sep 01; 30(17):i408-14. Capra JA, Kostka D. PMID: 25161227.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    45. 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.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    46. 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.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    47. 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.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    48. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    49. How old is my gene? Trends Genet. 2013 Nov; 29(11):659-68. Capra JA, Stolzer M, Durand D, Pollard KS. PMID: 23915718.
      View in: PubMed   Mentions: 17     Fields:    
    50. 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.
      View in: PubMed   Mentions: 245     Fields:    Translation:HumansAnimalsCells
    51. 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.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimals
    52. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    53. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol. 2011; 3:516-27. Capra JA, Pollard KS. PMID: 21670083.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    54. 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.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    55. 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.
      View in: PubMed   Mentions: 199     Fields:    Translation:AnimalsCells
    56. 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.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    57. 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.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    58. Genomics through the lens of next-generation sequencing. Genome Biol. 2010; 11(6):306. Capra JA, Carbone L, Riesenfeld SJ, Wall JD. PMID: 20587080.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    59. 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.
      View in: PubMed   Mentions: 119     Fields:    Translation:Cells
    60. Characterization and prediction of residues determining protein functional specificity. Bioinformatics. 2008 Jul 01; 24(13):1473-80. Capra JA, Singh M. PMID: 18450811.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    61. 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: 168     Fields:    Translation:Cells
    62. 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: 25     Fields:    Translation:Animals
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