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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.
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67 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
2024 Moth CW, Sheehan JH, Mamun AA, Sivley RM, Gulsevin A, Rinker D, Capra JA, Meiler J. VUStruct: a compute pipeline for high throughput and personalized structural biology. Biorxiv : the Preprint Server For Biology. PMID 39149406 DOI: 10.1101/2024.08.06.606224  0.309
2023 Velazquez-Arcelay K, Colbran LL, McArthur E, Brand CM, Rinker DC, Siemann JK, McMahon DG, Capra JA. Archaic Introgression Shaped Human Circadian Traits. Genome Biology and Evolution. 15. PMID 38095367 DOI: 10.1093/gbe/evad203  0.326
2023 Brand CM, Colbran LL, Capra JA. Resurrecting the alternative splicing landscape of archaic hominins using machine learning. Nature Ecology & Evolution. PMID 37142741 DOI: 10.1038/s41559-023-02053-5  0.303
2022 Fong SL, Capra JA. Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins. Genome Biology and Evolution. 14. PMID 36314566 DOI: 10.1093/gbe/evac159  0.33
2022 Li B, Jin B, Capra JA, Bush WS. Integration of Protein Structure and Population-Scale DNA Sequence Data for Disease Gene Discovery and Variant Interpretation. Annual Review of Biomedical Data Science. PMID 35508071 DOI: 10.1146/annurev-biodatasci-122220-112147  0.323
2022 Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annual Review of Genomics and Human Genetics. PMID 35440148 DOI: 10.1146/annurev-genom-111521-121903  0.316
2022 Colbran LL, Johnson MR, Mathieson I, Capra JA. Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment. Genome Biology and Evolution. 13. PMID 34718543 DOI: 10.1093/gbe/evab237  0.308
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  0.317
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  0.372
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  0.33
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  0.322
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  0.379
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  0.355
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  0.431
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  0.36
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  0.436
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  0.438
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  0.311
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  0.329
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  0.417
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  0.367
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  0.331
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  0.376
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  0.33
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  0.306
2019 Davis L, Beiter E, Khramtsova E, Van Der Merwe C, Chimusa E, Simonti C, Stein D, Capra J, Knowles J, Straub P, Hucks D, Stranger B. Polygenic Adaptation Underlies Evolution of Brain Structures and Behavioral Traits European Neuropsychopharmacology. 29: S755-S756. DOI: 10.1016/J.Euroneuro.2017.06.102  0.302
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  0.425
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  0.384
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  0.398
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  0.389
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  0.367
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  0.393
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  0.366
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  0.404
2017 Abbot P, Capra JA. What is a placental mammal anyway? Elife. 6. PMID 28895533 DOI: 10.7554/Elife.30994  0.335
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  0.324
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  0.392
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  0.352
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  0.353
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  0.353
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  0.33
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  0.358
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  0.36
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  0.428
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  0.431
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  0.417
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  0.408
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  0.38
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  0.358
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  0.485
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  0.457
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  0.306
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  0.449
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  0.347
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  0.352
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  0.345
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  0.376
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  0.401
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  0.307
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  0.562
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  0.539
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  0.357
2010 Wang X, Agarwala R, Capra JA, Chen Z, Church DM, Ciobanu DC, Li Z, Lu L, Mozhui K, Mulligan MK, Nelson SF, Pollard KS, Taylor WL, Thomason DB, Williams RW. High-throughput sequencing of the DBA/2J mouse genome Bmc Bioinformatics. 11. DOI: 10.1186/1471-2105-11-S4-O7  0.376
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  0.548
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  0.559
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  0.566
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  0.321
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