John Capra

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Publications

The following timeline graph is generated from all co-authored publications.

1. Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Colbran LL, Gamazon ER, Zhou D, Evans P, Cox NJ, Capra JA (2019) Nat Ecol Evol 3(11): 1598-1606
   › Primary publication · 31591491 (PubMed) · PMC7046098 (PubMed Central)
2. The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins. Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A (2019) Genome Biol Evol 11(9): 2574-2592
   › Primary publication · 31504490 (PubMed) · PMC6751361 (PubMed Central)
3. Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation. Moon JM, Capra JA, Abbot P, Rokas A (2019) Bioessays 41(9): e1900072
   › Primary publication · 31373044 (PubMed)
4. Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A (2019) Evol Med Public Health 2019(1): 93-103
   › Primary publication · 31263560 (PubMed) · PMC6592264 (PubMed Central)
5. Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function. Benton ML, Talipineni SC, Kostka D, Capra JA (2019) BMC Genomics 20(1): 511
   › Primary publication · 31221079 (PubMed) · PMC6585034 (PubMed Central)
6. Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. Moon JM, Capra JA, Abbot P, Rokas A (2019) G3 (Bethesda) 9(8): 2761-2774
   › Primary publication · 31213516 (PubMed) · PMC6686946 (PubMed Central)
7. IgG4-related disease: Association with a rare gene variant expressed in cytotoxic T cells. 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, Undiagnosed Disease Network (2019) Mol Genet Genomic Med 7(6): e686
   › Primary publication · 30993913 (PubMed) · PMC6565556 (PubMed Central)
8. Protein structure aids predicting functional perturbation of missense variants in and . Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM (2019) Comput Struct Biotechnol J : 206-214
   › Primary publication · 30828412 (PubMed) · PMC6383132 (PubMed Central)
9. Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. Colbran LL, Chen L, Capra JA (2019) Genetics 211(4): 1205-1217
   › Primary publication · 30696717 (PubMed) · PMC6456323 (PubMed Central)
10. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR (2019) Chem Rev 119(9): 5537-5606
    › Primary publication · 30608666 (PubMed) · PMC6506414 (PubMed Central)
11. Genome-wide maps of distal gene regulatory enhancers active in the human placenta. Zhang J, Simonti CN, Capra JA (2018) PLoS One 13(12): e0209611
    › Primary publication · 30589856 (PubMed) · PMC6320013 (PubMed Central)
12. integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth. Eidem HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, Rokas A (2018) BMC Med Genomics 11(1): 107
    › Primary publication · 30453955 (PubMed) · PMC6245874 (PubMed Central)
13. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. Chen L, Fish AE, Capra JA (2018) PLoS Comput Biol 14(10): e1006484
    › Primary publication · 30286077 (PubMed) · PMC6191148 (PubMed Central)
14. The 2015 landslide and tsunami in Taan Fiord, Alaska. Higman B, Shugar DH, Stark CP, Ekström G, Koppes MN, Lynett P, Dufresne A, Haeussler PJ, Geertsema M, Gulick S, Mattox A, Venditti JG, Walton MAL, McCall N, Mckittrick E, MacInnes B, Bilderback EL, Tang H, Willis MJ, Richmond B, Reece RS, Larsen C, Olson B, Capra J, Ayca A, Bloom C, Williams H, Bonno D, Weiss R, Keen A, Skanavis V, Loso M (2018) Sci Rep 8(1): 12993
    › Primary publication · 30190595 (PubMed) · PMC6127189 (PubMed Central)
15. Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures. Sivley RM, Dou X, Meiler J, Bush WS, Capra JA (2018) Am J Hum Genet 102(3): 415-426
    › Primary publication · 29455857 (PubMed) · PMC5985282 (PubMed Central)
16. Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. Sivley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J, Capra JA (2018) BMC Bioinformatics 19(1): 18
    › Primary publication · 29361909 (PubMed) · PMC5781290 (PubMed Central)
17. Local ancestry transitions modify snp-trait associations. Fish AE, Crawford DC, Capra JA, Bush WS (2018) Pac Symp Biocomput : 424-435
    › Primary publication · 29218902 (PubMed) · PMC5728664 (PubMed Central)
18. Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity. Fish A, Chen L, Capra JA (2017) Genome Biol Evol 9(10): 2615-2625
    › Primary publication · 28985297 (PubMed) · PMC5737616 (PubMed Central)
19. Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints. Simonti CN, Pavlicev M, Capra JA (2017) Mol Biol Evol 34(11): 2856-2869
    › Primary publication · 28961735 (PubMed) · PMC5850124 (PubMed Central)
20. What is a placental mammal anyway? Abbot P, Capra JA (2017) Elife
    › Primary publication · 28895533 (PubMed) · PMC5595430 (PubMed Central)
21. The transformative potential of an integrative approach to pregnancy. Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A (2017) Placenta : 204-215
    › Primary publication · 28864013 (PubMed)
22. Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs. Patel VD, Capra JA (2017) BMC Genomics 18(1): 672
    › Primary publication · 28859623 (PubMed) · PMC5579935 (PubMed Central)
23. Short DNA sequence patterns accurately identify broadly active human enhancers. Colbran LL, Chen L, Capra JA (2017) BMC Genomics 18(1): 536
    › Primary publication · 28716036 (PubMed) · PMC5512948 (PubMed Central)
24. Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability. Wanzek K, Schwindt E, Capra JA, Paeschke K (2017) Nucleic Acids Res 45(13): 7796-7806
    › Primary publication · 28535251 (PubMed) · PMC5570088 (PubMed Central)
25. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. 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 (2017) Cell Metab 25(4): 838-855.e15
    › Primary publication · 28380376 (PubMed) · PMC5444661 (PubMed Central)
26. Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts? Fish AE, Capra JA, Bush WS (2016) Am J Hum Genet 99(4): 817-830
    › Primary publication · 27640306 (PubMed) · PMC5065654 (PubMed Central)
27. Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity. McDonald KR, Guise AJ, Pourbozorgi-Langroudi P, Cristea IM, Zakian VA, Capra JA, Sabouri N (2016) PLoS Genet 12(9): e1006238
    › Primary publication · 27611590 (PubMed) · PMC5017727 (PubMed Central)
28. Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y (2016) Genetics 204(3): 893-904
    › Primary publication · 27585849 (PubMed) · PMC5105867 (PubMed Central)
29. XPA: A key scaffold for human nucleotide excision repair. Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ (2016) DNA Repair (Amst) : 123-135
    › Primary publication · 27247238 (PubMed) · PMC4958585 (PubMed Central)
30. The phenotypic legacy of admixture between modern humans and Neandertals. 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 (2016) Science 351(6274): 737-41
    › Primary publication · 26912863 (PubMed) · PMC4849557 (PubMed Central)
31. Joint mouse-human phenome-wide association to test gene function and disease risk. 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 (2016) Nat Commun : 10464
    › Primary publication · 26833085 (PubMed) · PMC4740880 (PubMed Central)
32. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. 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 (2016) Nucleic Acids Res 44(D1): D908-16
    › Primary publication · 26567549 (PubMed) · PMC4702823 (PubMed Central)
33. The evolution of the human genome. Simonti CN, Capra JA (2015) Curr Opin Genet Dev : 9-15
    › Primary publication · 26338498 (PubMed) · PMC4695266 (PubMed Central)
34. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA (2015) BMC Evol Biol : 35
    › Primary publication · 25887984 (PubMed) · PMC4362643 (PubMed Central)
35. Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study. Capra JA (2015) BMC Genomics : 104
    › Primary publication · 25765133 (PubMed) · PMC4342796 (PubMed Central)
36. The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage. Sabouri N, Capra JA, Zakian VA (2014) BMC Biol : 101
    › Primary publication · 25471935 (PubMed) · PMC4275981 (PubMed Central)
37. Log-odds sequence logos. Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF (2015) Bioinformatics 31(3): 324-31
    › Primary publication · 25294922 (PubMed) · PMC4318935 (PubMed Central)
38. Modeling DNA methylation dynamics with approaches from phylogenetics. Capra JA, Kostka D (2014) Bioinformatics 30(17): i408-14
    › Primary publication · 25161227 (PubMed) · PMC4147898 (PubMed Central)
39. Integrating diverse datasets improves developmental enhancer prediction. Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA (2014) PLoS Comput Biol 10(6): e1003677
    › Primary publication · 24967590 (PubMed) · PMC4072507 (PubMed Central)
40. Many human accelerated regions are developmental enhancers. Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS (2013) Philos Trans R Soc Lond B Biol Sci 368(1632): 20130025
    › Primary publication · 24218637 (PubMed) · PMC3826498 (PubMed Central)
41. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. 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 (2013) Mol Cell 52(3): 314-24
    › Primary publication · 24207025 (PubMed) · PMC3936344 (PubMed Central)
42. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A (2013) PLoS Genet 9(8): e1003684
    › Primary publication · 23966869 (PubMed) · PMC3744432 (PubMed Central)
43. How old is my gene? Capra JA, Stolzer M, Durand D, Pollard KS (2013) Trends Genet 29(11): 659-68
    › Primary publication · 23915718 (PubMed) · PMC3812327 (PubMed Central)
44. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. 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 (2012) Cell 151(1): 206-20
    › Primary publication · 22981692 (PubMed) · PMC3462286 (PubMed Central)
45. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. Capra JA, Williams AG, Pollard KS (2012) PLoS Comput Biol 8(6): e1002567
    › Primary publication · 22761559 (PubMed) · PMC3386163 (PubMed Central)
46. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E (2011) Aging (Albany NY) 3(6): 635-42
    › Primary publication · 21701047 (PubMed) · PMC3164371 (PubMed Central)
47. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Katzman S, Capra JA, Haussler D, Pollard KS (2011) Genome Biol Evol : 614-26
    › Primary publication · 21697099 (PubMed) · PMC3157837 (PubMed Central)
48. Substitution patterns are GC-biased in divergent sequences across the metazoans. Capra JA, Pollard KS (2011) Genome Biol Evol : 516-27
    › Primary publication · 21670083 (PubMed) · PMC3138425 (PubMed Central)
49. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Paeschke K, Capra JA, Zakian VA (2011) Cell 145(5): 678-91
    › Primary publication · 21620135 (PubMed) · PMC3129610 (PubMed Central)
50. Novel genes exhibit distinct patterns of function acquisition and network integration. Capra JA, Pollard KS, Singh M (2010) Genome Biol 11(12): R127
    › Primary publication · 21187012 (PubMed) · PMC3046487 (PubMed Central)
51. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. Capra JA, Paeschke K, Singh M, Zakian VA (2010) PLoS Comput Biol 6(7): e1000861
    › Primary publication · 20676380 (PubMed) · PMC2908698 (PubMed Central)
52. Genomics through the lens of next-generation sequencing. Capra JA, Carbone L, Riesenfeld SJ, Wall JD (2010) Genome Biol 11(6): 306
    › Primary publication · 20587080 (PubMed) · PMC2911104 (PubMed Central)
53. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA (2009) PLoS Comput Biol 5(12): e1000585
    › Primary publication · 19997483 (PubMed) · PMC2777313 (PubMed Central)
54. Characterization and prediction of residues determining protein functional specificity. Capra JA, Singh M (2008) Bioinformatics 24(13): 1473-80
    › Primary publication · 18450811 (PubMed) · PMC2718669 (PubMed Central)
55. Predicting functionally important residues from sequence conservation. Capra JA, Singh M (2007) Bioinformatics 23(15): 1875-82
    › Primary publication · 17519246 (PubMed)

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