John A. Capra, Ph.D. - Publications

Affiliations: 
2009 Princeton University, Princeton, NJ 
Area:
Computational molecular biology, as well as its interface with machine learning and algorithms.

77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Mukherjee S, Cogan JD, Newman JH, Phillips JA, Hamid R, Meiler J, Capra JA. Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. American Journal of Human Genetics. PMID 34529933 DOI: 10.1016/j.ajhg.2021.08.010  1
2021 Abraham A, Kavoussi N, Sui W, Bejan C, Capra JA, Hsi R. Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features. Journal of Endourology. PMID 34314237 DOI: 10.1089/end.2021.0211  1
2021 McArthur E, Rinker DC, Capra JA. Quantifying the contribution of Neanderthal introgression to the heritability of complex traits. Nature Communications. 12: 4481. PMID 34294692 DOI: 10.1038/s41467-021-24582-y  1
2021 Fong SL, 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. PMID 33973014 DOI: 10.1093/molbev/msab138  1
2021 Kasimatis KR, Abraham A, Ralph PL, Kern AD, Capra JA, Phillips PC. Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks. Genetics. 217: 1-10. PMID 33683357 DOI: 10.1093/genetics/iyaa015  1
2021 McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. American Journal of Human Genetics. 108: 269-283. PMID 33545030 DOI: 10.1016/j.ajhg.2021.01.001  1
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. Genetics of agenesis/hypoplasia of the uterus and vagina: narrowing down the number of candidate genes for Mayer-Rokitansky-Küster-Hauser Syndrome. Human Genetics. PMID 33469725 DOI: 10.1007/s00439-020-02239-y  1
2021 Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nature Reviews. Genetics. PMID 33408383 DOI: 10.1038/s41576-020-00305-9  1
2020 Li B, Yang YT, Capra JA, Gerstein MB. Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. Plos Computational Biology. 16: e1008291. PMID 33253214 DOI: 10.1371/journal.pcbi.1008291  1
2020 Chen L, Capra JA. Learning and interpreting the gene regulatory grammar in a deep learning framework. Plos Computational Biology. 16: e1008334. PMID 33137083 DOI: 10.1371/journal.pcbi.1008334  1
2020 Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. 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. PMID 33015868 DOI: 10.1096/fj.202001808R  1
2020 Tang ZZ, Sliwoski GR, Chen G, Jin B, Bush WS, Li B, Capra JA. PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. Genome Biology. 21: 217. PMID 32847609 DOI: 10.1186/S13059-020-02121-0  1
2020 Tilden DR, Sheehan JH, Newman JH, Meiler J, Capra JA, Ramirez A, Simmons J, Dahir K. Phenotypic Profiling in Subjects Heterozygous for 1 of 2 Rare Variants in the Hypophosphatasia Gene (). Journal of the Endocrine Society. 4: bvaa084. PMID 32803091 DOI: 10.1210/Jendso/Bvaa084  1
2020 Rinker DC, Simonti CN, McArthur E, Shaw D, Hodges E, Capra JA. Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations. Nature Ecology & Evolution. PMID 32719451 DOI: 10.1038/S41559-020-1261-Z  1
2020 LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nature Communications. 11: 3731. PMID 32709900 DOI: 10.1038/S41467-020-17258-6  1
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, et al. 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. PMID 32565236 DOI: 10.1016/J.Ajog.2020.06.031  1
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. High-Throughput Reclassification of SCN5A Variants. American Journal of Human Genetics. PMID 32533946 DOI: 10.1016/J.Ajhg.2020.05.015  1
2020 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, ... ... Capra JA, et al. Functional annotation of rare structural variation in the human brain. Nature Communications. 11: 2990. PMID 32533064 DOI: 10.1038/S41467-020-16736-1  1
2020 Gadbery JE, Abraham A, Needle CD, Moth C, Sheehan J, Capra JA, Jackson LP. Integrating structural and evolutionary data to interpret variation and pathogenicity in Adapter Protein Complex 4 (AP-4). Protein Science : a Publication of the Protein Society. PMID 32285480 DOI: 10.1002/Pro.3870  1
2019 Colbran LL, Gamazon ER, Zhou D, Evans P, Cox NJ, Capra JA. Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Nature Ecology & Evolution. PMID 31591491 DOI: 10.1038/S41559-019-0996-X  1
2019 Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A. The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biology and Evolution. PMID 31504490 DOI: 10.1093/Gbe/Evz183  1
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. e1900072. PMID 31373044 DOI: 10.1002/Bies.201900072  1
2019 Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A. Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Evolution, Medicine, and Public Health. 2019: 93-103. PMID 31263560 DOI: 10.1093/Emph/Eoz015  1
2019 Benton ML, Talipineni SC, Kostka D, Capra JA. Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function. Bmc Genomics. 20: 511. PMID 31221079 DOI: 10.1186/S12864-019-5779-X  1
2019 Moon JM, Capra JA, Abbot P, Rokas A. Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. G3 (Bethesda, Md.). PMID 31213516 DOI: 10.1534/G3.119.400186  1
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, et al. IgG4-related disease: Association with a rare gene variant expressed in cytotoxic T cells. Molecular Genetics & Genomic Medicine. e686. PMID 30993913 DOI: 10.1002/Mgg3.686  1
2019 Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM. Protein structure aids predicting functional perturbation of missense variants in and . Computational and Structural Biotechnology Journal. 17: 206-214. PMID 30828412 DOI: 10.1016/J.Csbj.2019.01.008  1
2019 Colbran LL, Chen L, Capra JA. Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. Genetics. PMID 30696717 DOI: 10.1534/Genetics.118.301895  1
2019 Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chemical Reviews. PMID 30608666 DOI: 10.1021/Acs.Chemrev.8B00532  1
2019 Shibao CA, Phillips J, Cogan JD, Newman JH, Hamid R, Meiler J, Capra JA, Sheehan J, Yan Y, Vetrini F, Black B, Joos K, Robertson D, Biaggioni I. Abstract P176: Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants. Novel Genetic Cause of Neurogenic Orthostatic Hypotension Hypertension. 74. DOI: 10.1161/Hyp.74.Suppl_1.P176  1
2019 Han L, Zhao X, Benton ML, Perumal T, Collins R, Brand H, Hoffman G, Johnson J, Sloofman L, Brennand K, Sieberts S, Marenco S, Peters M, Lipska BK, Roussos P, ... Capra J, et al. 25 Functional Annotation Of Rare Structural Variation In The Human Brain European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2019.07.166  1
2018 Zhang J, Simonti CN, Capra JA. Genome-wide maps of distal gene regulatory enhancers active in the human placenta. Plos One. 13: e0209611. PMID 30589856 DOI: 10.1371/Journal.Pone.0209611  1
2018 Eidem HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, Rokas A. 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. 11: 107. PMID 30453955 DOI: 10.1186/S12920-018-0426-Y  1
2018 Chen L, Fish AE, Capra JA. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. Plos Computational Biology. 14: e1006484. PMID 30286077 DOI: 10.1371/Journal.Pcbi.1006484  1
2018 Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A. Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology. G3 (Bethesda, Md.). PMID 29467190 DOI: 10.1534/G3.118.200035  1
2018 Sivley RM, Dou X, Meiler J, Bush WS, Capra JA. Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures. American Journal of Human Genetics. PMID 29455857 DOI: 10.1016/J.Ajhg.2018.01.017  1
2018 Sivley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J, Capra JA. Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. Bmc Bioinformatics. 19: 18. PMID 29361909 DOI: 10.1186/S12859-018-2010-Z  1
2018 Fish AE, Crawford DC, Capra JA, Bush WS. Local ancestry transitions modify snp-trait associations. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 424-435. PMID 29218902  1
2017 Fish A, Chen L, Capra JA. Gene regulatory enhancers with evolutionarily conserved-activity are more pleiotropic than those with species-specific-activity. Genome Biology and Evolution. PMID 28985297 DOI: 10.1093/Gbe/Evx194  1
2017 Simonti CN, Pavlicev M, Capra JA. Transposable Element Exaptation into Regulatory Regions is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints. Molecular Biology and Evolution. PMID 28961735 DOI: 10.1093/Molbev/Msx219  1
2017 Abbot P, Capra JA. What is a placental mammal anyway? Elife. 6. PMID 28895533 DOI: 10.7554/Elife.30994  1
2017 Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A. The transformative potential of an integrative approach to pregnancy. Placenta. 57: 204-215. PMID 28864013 DOI: 10.1016/J.Placenta.2017.07.010  1
2017 Patel VD, Capra JA. Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs. Bmc Genomics. 18: 672. PMID 28859623 DOI: 10.1186/S12864-017-4073-Z  0.01
2017 Colbran LL, Chen L, Capra JA. Short DNA sequence patterns accurately identify broadly active human enhancers. Bmc Genomics. 18: 536. PMID 28716036 DOI: 10.1186/S12864-017-3934-9  1
2017 Wanzek K, Schwindt E, Capra JA, Paeschke K. Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability. Nucleic Acids Research. PMID 28535251 DOI: 10.1093/Nar/Gkx467  1
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, et al. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. Cell Metabolism. 25: 838-855.e15. PMID 28380376 DOI: 10.1016/J.Cmet.2017.03.003  1
2016 Fish AE, Capra JA, Bush WS. Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts? American Journal of Human Genetics. PMID 27640306 DOI: 10.1016/J.Ajhg.2016.07.022  1
2016 McDonald KR, Guise AJ, Pourbozorgi-Langroudi P, Cristea IM, Zakian VA, Capra JA, Sabouri N. Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity. Plos Genetics. 12: e1006238. PMID 27611590 DOI: 10.1371/Journal.Pgen.1006238  1
2016 Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y. Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Genetics. PMID 27585849 DOI: 10.1534/Genetics.116.189936  0.01
2016 Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ. XPA: A key scaffold for human nucleotide excision repair. Dna Repair. PMID 27247238 DOI: 10.1016/J.Dnarep.2016.05.018  1
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, ... ... Capra JA, et al. The phenotypic legacy of admixture between modern humans and Neandertals. Science (New York, N.Y.). 351: 737-41. PMID 26912863 DOI: 10.1126/Science.Aad2149  1
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, et al. Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications. 7: 10464. PMID 26833085 DOI: 10.1038/Ncomms10464  1
2015 Simonti CN, Capra JA. The evolution of the human genome. Current Opinion in Genetics & Development. 35: 9-15. PMID 26338498 DOI: 10.1016/J.Gde.2015.08.005  1
2015 Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. Bmc Evolutionary Biology. 15: 35. PMID 25887984 DOI: 10.1186/S12862-015-0327-Z  1
2015 Capra JA. Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study. Bmc Genomics. 16: 104. PMID 25765133 DOI: 10.1186/S12864-015-1264-3  1
2015 Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF. Log-odds sequence logos. Bioinformatics (Oxford, England). 31: 324-31. PMID 25294922 DOI: 10.1093/Bioinformatics/Btu634  1
2014 Sabouri N, Capra JA, Zakian VA. The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage. Bmc Biology. 12: 101. PMID 25471935 DOI: 10.1186/S12915-014-0101-5  1
2014 Capra JA, Kostka D. Modeling DNA methylation dynamics with approaches from phylogenetics. Bioinformatics (Oxford, England). 30: i408-14. PMID 25161227 DOI: 10.1093/Bioinformatics/Btu445  1
2014 Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. Plos Computational Biology. 10: e1003677. PMID 24967590 DOI: 10.1371/Journal.Pcbi.1003677  1
2013 Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. Many human accelerated regions are developmental enhancers. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20130025. PMID 24218637 DOI: 10.1098/Rstb.2013.0025  1
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, et al. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Molecular Cell. 52: 314-24. PMID 24207025 DOI: 10.1016/J.Molcel.2013.10.009  1
2013 Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes Plos Genetics. 9. PMID 23966869 DOI: 10.1371/Journal.Pgen.1003684  1
2013 Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene? Trends in Genetics : Tig. 29: 659-68. PMID 23915718 DOI: 10.1016/J.Tig.2013.07.001  1
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, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 151: 206-20. PMID 22981692 DOI: 10.1016/J.Cell.2012.07.035  1
2012 Capra JA, Williams AG, Pollard KS. Proteinhistorian: Tools for the comparative analysis of eukaryote protein origin Plos Computational Biology. 8. PMID 22761559 DOI: 10.1371/Journal.Pcbi.1002567  1
2011 Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2 Aging. 3: 635-642. PMID 21701047  1
2011 Katzman S, Capra JA, Haussler D, Pollard KS. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots Genome Biology and Evolution. 3: 614-626. PMID 21697099 DOI: 10.1093/Gbe/Evr058  1
2011 Capra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biology and Evolution. 3: 516-27. PMID 21670083 DOI: 10.1093/Gbe/Evr051  1
2011 Paeschke K, Capra JA, Zakian VA. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell. 145: 678-91. PMID 21620135 DOI: 10.1016/J.Cell.2011.04.015  1
2011 Capra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans Genome Biology and Evolution. 3: 516-527. DOI: 10.1093/gbe/evr051  1
2010 Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration Genome Biology. 11. PMID 21187012 DOI: 10.1186/Gb-2010-11-12-R127  1
2010 Capra JA, Paeschke K, Singh M, Zakian VA. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. Plos Computational Biology. 6: e1000861. PMID 20676380 DOI: 10.1371/Journal.Pcbi.1000861  1
2010 Capra JA, Carbone L, Riesenfeld SJ, Wall JD. Genomics through the lens of next-generation sequencing. Genome Biology. 11: 306. PMID 20587080 DOI: 10.1186/Gb-2010-11-6-306  1
2009 Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Plos Computational Biology. 5: e1000585. PMID 19997483 DOI: 10.1371/Journal.Pcbi.1000585  1
2008 Capra JA, Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics (Oxford, England). 24: 1473-80. PMID 18450811 DOI: 10.1093/Bioinformatics/Btn214  1
2007 Capra JA, Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics (Oxford, England). 23: 1875-82. PMID 17519246 DOI: 10.1093/Bioinformatics/Btm270  1
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, et al. Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics. 1: 327-42. PMID 15043219 DOI: 10.1385/Ni:1:4:327  1
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