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.

29 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
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  0.36
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  0.36
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  0.56
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  0.56
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
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