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Results: 18

1.

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.

PMID:
24967590
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24218637
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
24207025
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23966869
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23915718
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
22981692
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22761559
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
21701047
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21697099
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21670083
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
21620135
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
21187012
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
20676380
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Genomics through the lens of next-generation sequencing.

Capra JA, Carbone L, Riesenfeld SJ, Wall JD.

Genome Biol. 2010;11(6):306. doi: 10.1186/gb-2010-11-6-306. Epub 2010 Jun 25.

PMID:
20587080
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.

PLoS Comput Biol. 2009 Dec;5(12):e1000585. doi: 10.1371/journal.pcbi.1000585. Epub 2009 Dec 4.

PMID:
19997483
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Characterization and prediction of residues determining protein functional specificity.

Capra JA, Singh M.

Bioinformatics. 2008 Jul 1;24(13):1473-80. doi: 10.1093/bioinformatics/btn214. Epub 2008 May 1.

PMID:
18450811
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Predicting functionally important residues from sequence conservation.

Capra JA, Singh M.

Bioinformatics. 2007 Aug 1;23(15):1875-82. Epub 2007 May 22.

PMID:
17519246
[PubMed - indexed for MEDLINE]
Free Article
18.

Informatics center for mouse genomics: the dissection of complex traits of the nervous system.

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.

Neuroinformatics. 2003;1(4):327-42.

PMID:
15043219
[PubMed - indexed for MEDLINE]

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