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Items: 1 to 50 of 55

1.

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.

Genome Biol Evol. 2019 Sep 1;11(9):2574-2592. doi: 10.1093/gbe/evz183.

PMID:
31504490
2.

Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation.

Moon JM, Capra JA, Abbot P, Rokas A.

Bioessays. 2019 Sep;41(9):e1900072. doi: 10.1002/bies.201900072. Epub 2019 Aug 2. Review.

PMID:
31373044
3.

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.

Evol Med Public Health. 2019 May 17;2019(1):93-103. doi: 10.1093/emph/eoz015. eCollection 2019.

4.

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function.

Benton ML, Talipineni SC, Kostka D, Capra JA.

BMC Genomics. 2019 Jun 20;20(1):511. doi: 10.1186/s12864-019-5779-x.

5.

Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues.

Moon JM, Capra JA, Abbot P, Rokas A.

G3 (Bethesda). 2019 Aug 8;9(8):2761-2774. doi: 10.1534/g3.119.400186.

6.

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 3rd; Undiagnosed Disease Network.

Mol Genet Genomic Med. 2019 Jun;7(6):e686. doi: 10.1002/mgg3.686. Epub 2019 Apr 16.

7.

Protein structure aids predicting functional perturbation of missense variants in SCN5A and KCNQ1.

Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM.

Comput Struct Biotechnol J. 2019 Feb 1;17:206-214. doi: 10.1016/j.csbj.2019.01.008. eCollection 2019.

8.

Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity.

Colbran LL, Chen L, Capra JA.

Genetics. 2019 Apr;211(4):1205-1217. doi: 10.1534/genetics.118.301895. Epub 2019 Jan 29.

PMID:
30696717
9.

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.

Chem Rev. 2019 May 8;119(9):5537-5606. doi: 10.1021/acs.chemrev.8b00532. Epub 2019 Jan 4.

10.

Genome-wide maps of distal gene regulatory enhancers active in the human placenta.

Zhang J, Simonti CN, Capra JA.

PLoS One. 2018 Dec 27;13(12):e0209611. doi: 10.1371/journal.pone.0209611. eCollection 2018.

11.

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.

BMC Med Genomics. 2018 Nov 19;11(1):107. doi: 10.1186/s12920-018-0426-y.

12.

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.

Chen L, Fish AE, Capra JA.

PLoS Comput Biol. 2018 Oct 4;14(10):e1006484. doi: 10.1371/journal.pcbi.1006484. eCollection 2018 Oct.

13.

Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology.

Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A.

G3 (Bethesda). 2018 Mar 28;8(4):1315-1325. doi: 10.1534/g3.118.200035.

14.

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.

Am J Hum Genet. 2018 Mar 1;102(3):415-426. doi: 10.1016/j.ajhg.2018.01.017. Epub 2018 Feb 15.

15.

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.

BMC Bioinformatics. 2018 Jan 23;19(1):18. doi: 10.1186/s12859-018-2010-z.

16.

Local ancestry transitions modify snp-trait associations.

Fish AE, Crawford DC, Capra JA, Bush WS.

Pac Symp Biocomput. 2018;23:424-435.

17.

Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity.

Fish A, Chen L, Capra JA.

Genome Biol Evol. 2017 Oct 1;9(10):2615-2625. doi: 10.1093/gbe/evx194.

18.

Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints.

Simonti CN, Pavlicev M, Capra JA.

Mol Biol Evol. 2017 Nov 1;34(11):2856-2869. doi: 10.1093/molbev/msx219.

19.

What is a placental mammal anyway?

Abbot P, Capra JA.

Elife. 2017 Sep 12;6. pii: e30994. doi: 10.7554/eLife.30994.

20.

The transformative potential of an integrative approach to pregnancy.

Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A.

Placenta. 2017 Sep;57:204-215. doi: 10.1016/j.placenta.2017.07.010. Epub 2017 Jul 15. Review.

PMID:
28864013
21.

Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs.

Patel VD, Capra JA.

BMC Genomics. 2017 Aug 31;18(1):672. doi: 10.1186/s12864-017-4073-z.

22.

Short DNA sequence patterns accurately identify broadly active human enhancers.

Colbran LL, Chen L, Capra JA.

BMC Genomics. 2017 Jul 17;18(1):536. doi: 10.1186/s12864-017-3934-9.

23.

Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability.

Wanzek K, Schwindt E, Capra JA, Paeschke K.

Nucleic Acids Res. 2017 Jul 27;45(13):7796-7806. doi: 10.1093/nar/gkx467.

24.

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.

Cell Metab. 2017 Apr 4;25(4):838-855.e15. doi: 10.1016/j.cmet.2017.03.003.

25.

Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?

Fish AE, Capra JA, Bush WS.

Am J Hum Genet. 2016 Oct 6;99(4):817-830. doi: 10.1016/j.ajhg.2016.07.022. Epub 2016 Sep 15.

26.

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.

PLoS Genet. 2016 Sep 9;12(9):e1006238. doi: 10.1371/journal.pgen.1006238. eCollection 2016 Sep.

27.

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.

Genetics. 2016 Nov;204(3):893-904. doi: 10.1534/genetics.116.189936. Epub 2016 Aug 31.

28.

XPA: A key scaffold for human nucleotide excision repair.

Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ.

DNA Repair (Amst). 2016 Aug;44:123-135. doi: 10.1016/j.dnarep.2016.05.018. Epub 2016 May 20. Review.

29.

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.

Science. 2016 Feb 12;351(6274):737-41. doi: 10.1126/science.aad2149.

30.

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.

Nat Commun. 2016 Feb 2;7:10464. doi: 10.1038/ncomms10464.

31.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D908-16. doi: 10.1093/nar/gkv1137. Epub 2015 Nov 14.

32.

The evolution of the human genome.

Simonti CN, Capra JA.

Curr Opin Genet Dev. 2015 Dec;35:9-15. doi: 10.1016/j.gde.2015.08.005. Epub 2015 Sep 9. Review.

33.

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.

BMC Evol Biol. 2015 Mar 10;15:35. doi: 10.1186/s12862-015-0327-z.

34.
35.

The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage.

Sabouri N, Capra JA, Zakian VA.

BMC Biol. 2014 Dec 4;12:101. doi: 10.1186/s12915-014-0101-5.

36.

Log-odds sequence logos.

Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.

Bioinformatics. 2015 Feb 1;31(3):324-31. doi: 10.1093/bioinformatics/btu634. Epub 2014 Oct 6.

37.

Modeling DNA methylation dynamics with approaches from phylogenetics.

Capra JA, Kostka D.

Bioinformatics. 2014 Sep 1;30(17):i408-14. doi: 10.1093/bioinformatics/btu445.

38.

Integrating diverse datasets improves developmental enhancer prediction.

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003677. doi: 10.1371/journal.pcbi.1003677. eCollection 2014 Jun.

39.

Many human accelerated regions are developmental enhancers.

Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130025. doi: 10.1098/rstb.2013.0025. Print 2013 Dec 19.

40.

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.

Mol Cell. 2013 Nov 7;52(3):314-24. doi: 10.1016/j.molcel.2013.10.009.

41.

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.

PLoS Genet. 2013;9(8):e1003684. doi: 10.1371/journal.pgen.1003684. Epub 2013 Aug 15.

42.

How old is my gene?

Capra JA, Stolzer M, Durand D, Pollard KS.

Trends Genet. 2013 Nov;29(11):659-68. doi: 10.1016/j.tig.2013.07.001. Epub 2013 Aug 1. Review.

43.

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.

Cell. 2012 Sep 28;151(1):206-20. doi: 10.1016/j.cell.2012.07.035. Epub 2012 Sep 12.

44.

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

Capra JA, Williams AG, Pollard KS.

PLoS Comput Biol. 2012;8(6):e1002567. doi: 10.1371/journal.pcbi.1002567. Epub 2012 Jun 28.

45.

SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.

Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E.

Aging (Albany NY). 2011 Jun;3(6):635-42.

46.

Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.

Katzman S, Capra JA, Haussler D, Pollard KS.

Genome Biol Evol. 2011;3:614-26. doi: 10.1093/gbe/evr058. Epub 2011 Jun 21.

47.

Substitution patterns are GC-biased in divergent sequences across the metazoans.

Capra JA, Pollard KS.

Genome Biol Evol. 2011;3:516-27. doi: 10.1093/gbe/evr051. Epub 2011 Jun 13.

48.

DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase.

Paeschke K, Capra JA, Zakian VA.

Cell. 2011 May 27;145(5):678-91. doi: 10.1016/j.cell.2011.04.015.

49.

Novel genes exhibit distinct patterns of function acquisition and network integration.

Capra JA, Pollard KS, Singh M.

Genome Biol. 2010;11(12):R127. doi: 10.1186/gb-2010-11-12-r127. Epub 2010 Dec 27.

50.

G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

Capra JA, Paeschke K, Singh M, Zakian VA.

PLoS Comput Biol. 2010 Jul 22;6(7):e1000861. doi: 10.1371/journal.pcbi.1000861.

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