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John Capra

Title(s)Assoc Professor in Residence, Epidemiology & Biostatistics
SchoolSchool of Medicine
Address550 16th. Street
San Francisco CA 94158
Phone--
ORCID ORCID Icon0000-0001-9743-1795 Additional info
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    Collapse Overview 
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    The Capra Lab uses the tools of computer science and statistics to address problems in genetics, evolution, and biomedicine.

    Collapse Research 
    Collapse Research Activities and Funding
    The Evolution of Gene Regulation and Human Disease
    NIH/NIGMS R35GM127087Apr 1, 2018 - Mar 31, 2023
    Role: Principal Investigator
    Integrating ’Omics and EHRs to Elucidate the Genetic Architecture of Preterm Birth
    Burroughs Wellcome Fund Jun 1, 2017 - Mar 31, 2021
    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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    Collapse Bibliographic 
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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. The influence of evolutionary history on human health and disease. Nat Rev Genet. 2021 Jan 06. Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. PMID: 33408383.
      View in: PubMed   Mentions:    Fields:    
    2. Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS Comput Biol. 2020 Nov; 16(11):e1008291. Li B, Yang YT, Capra JA, Gerstein MB. PMID: 33253214.
      View in: PubMed   Mentions:    Fields:    
    3. Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput Biol. 2020 Nov; 16(11):e1008334. Chen L, Capra JA. PMID: 33137083.
      View in: PubMed   Mentions:    Fields:    
    4. Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species. FASEB J. 2020 12; 34(12):15946-15960. Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. PMID: 33015868.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    5. PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. Genome Biol. 2020 08 26; 21(1):217. Tang ZZ, Sliwoski GR, Chen G, Jin B, Bush WS, Li B, Capra JA. PMID: 32847609.
      View in: PubMed   Mentions:    Fields:    
    6. Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations. Nat Ecol Evol. 2020 10; 4(10):1332-1341. Rinker DC, Simonti CN, McArthur E, Shaw D, Hodges E, Capra JA. PMID: 32719451.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    7. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nat Commun. 2020 07 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:    Translation:Humans
    8. 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:
    9. Phenotypic Profiling in Subjects Heterozygous for 1 of 2 Rare Variants in the Hypophosphatasia Gene (ALPL). J Endocr Soc. 2020 Aug 01; 4(8):bvaa084. Tilden DR, Sheehan JH, Newman JH, Meiler J, Capra JA, Ramirez A, Simmons J, Dahir K. PMID: 32803091.
      View in: PubMed   Mentions:
    10. 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 09; 223(3):312-321. 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:    Translation:Humans
    11. High-Throughput Reclassification of SCN5A Variants. Am J Hum Genet. 2020 07 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: 2     Fields:    Translation:HumansCells
    12. Functional annotation of rare structural variation in the human brain. Nat Commun. 2020 06 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: 1     Fields:    Translation:Humans
    13. 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:    
    14. 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: 2     Fields:    Translation:HumansAnimals
    15. 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: 1     Fields:    Translation:HumansAnimals
    16. 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
    17. 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
    18. 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: 3     Fields:    Translation:HumansCells
    19. 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:
    20. 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: 1     Fields:    Translation:HumansCells
    21. 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:
    22. 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: 4     Fields:    Translation:HumansCells
    23. 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: 18     Fields:    Translation:HumansCells
    24. 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: 4     Fields:    Translation:HumansCells
    25. 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: 1     Fields:    Translation:Humans
    26. 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: 5     Fields:    Translation:HumansAnimalsCells
    27. 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
    28. 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: 15     Fields:    Translation:HumansCells
    29. 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: 3     Fields:    Translation:HumansCells
    30. 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: 3     Fields:    Translation:HumansCells
    31. 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: 15     Fields:    Translation:HumansAnimalsCells
    32. 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
    33. What is a placental mammal anyway? Elife. 2017 09 12; 6. Abbot P, Capra JA. PMID: 28895533.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    34. 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: 6     Fields:    Translation:HumansAnimalsCells
    35. 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: 5     Fields:    Translation:AnimalsCells
    36. 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: 7     Fields:    Translation:HumansAnimalsCells
    37. 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: 4     Fields:    Translation:Humans
    38. 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: 65     Fields:    Translation:HumansAnimalsCells
    39. 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: 11     Fields:    Translation:HumansCells
    40. 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: 12     Fields:    Translation:AnimalsCells
    41. 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: 6     Fields:    Translation:Humans
    42. 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: 30     Fields:    Translation:HumansAnimalsCells
    43. 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: 46     Fields:    Translation:HumansAnimals
    44. 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: 40     Fields:    Translation:HumansAnimals
    45. 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
    46. 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: 2     Fields:    Translation:HumansCells
    47. 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: 10     Fields:    Translation:HumansAnimalsCells
    48. 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
    49. 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: 26     Fields:    Translation:AnimalsCells
    50. 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
    51. 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
    52. 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: 47     Fields:    Translation:HumansAnimalsCells
    53. 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: 43     Fields:    Translation:HumansAnimalsCells
    54. 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: 40     Fields:    Translation:HumansAnimalsCells
    55. 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: 22     Fields:    Translation:HumansAnimalsCells
    56. 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: 20     Fields:    
    57. 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: 261     Fields:    Translation:HumansAnimalsCells
    58. 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
    59. 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: 21     Fields:    Translation:HumansCells
    60. 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
    61. 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: 40     Fields:    Translation:HumansAnimalsCells
    62. 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: 211     Fields:    Translation:AnimalsCells
    63. 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: 35     Fields:    Translation:AnimalsCells
    64. 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: 81     Fields:    Translation:AnimalsCells
    65. 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
    66. 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: 131     Fields:    Translation:Cells
    67. 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: 56     Fields:    Translation:Cells
    68. 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: 192     Fields:    Translation:Cells
    69. 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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