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Items: 17

1.

Broad-Enrich: functional interpretation of large sets of broad genomic regions.

Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ, Sartor MA.

Bioinformatics. 2014 Sep 1;30(17):i393-400. doi: 10.1093/bioinformatics/btu444.

2.

ChIP-Enrich: gene set enrichment testing for ChIP-seq data.

Welch RP, Lee C, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA.

Nucleic Acids Res. 2014 Jul;42(13):e105. doi: 10.1093/nar/gku463. Epub 2014 May 30.

3.

Epigenetics: relevance and implications for public health.

Rozek LS, Dolinoy DC, Sartor MA, Omenn GS.

Annu Rev Public Health. 2014;35:105-22. doi: 10.1146/annurev-publhealth-032013-182513. Review.

4.

29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.

Lowe CB, Haussler D.

PLoS One. 2012;7(8):e43128. doi: 10.1371/journal.pone.0043128. Epub 2012 Aug 27.

5.

Epistasis network centrality analysis yields pathway replication across two GWAS cohorts for bipolar disorder.

Pandey A, Davis NA, White BC, Pajewski NM, Savitz J, Drevets WC, McKinney BA.

Transl Psychiatry. 2012 Aug 14;2:e154. doi: 10.1038/tp.2012.80.

6.

Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.

Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA.

Hum Mol Genet. 2012 May 15;21(10):2194-204. doi: 10.1093/hmg/dds034. Epub 2012 Feb 10.

7.

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.

Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP.

Cell. 2011 Dec 23;147(7):1537-50. doi: 10.1016/j.cell.2011.11.055. Erratum in: Cell. 2012 Oct 26;151(3):684-6.

8.

Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function.

Shen T, Aneas I, Sakabe N, Dirschinger RJ, Wang G, Smemo S, Westlund JM, Cheng H, Dalton N, Gu Y, Boogerd CJ, Cai CL, Peterson K, Chen J, Nobrega MA, Evans SM.

J Clin Invest. 2011 Dec;121(12):4640-54. doi: 10.1172/JCI59472. Epub 2011 Nov 14.

9.

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

Kazemian M, Zhu Q, Halfon MS, Sinha S.

Nucleic Acids Res. 2011 Dec;39(22):9463-72. doi: 10.1093/nar/gkr621. Epub 2011 Aug 5.

10.

Genome-wide identification of conserved regulatory function in diverged sequences.

Taher L, McGaughey DM, Maragh S, Aneas I, Bessling SL, Miller W, Nobrega MA, McCallion AS, Ovcharenko I.

Genome Res. 2011 Jul;21(7):1139-49. doi: 10.1101/gr.119016.110. Epub 2011 May 31.

11.

Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.

Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P.

PLoS One. 2011 Mar 18;6(3):e17753. doi: 10.1371/journal.pone.0017753.

12.

Length bias correction for RNA-seq data in gene set analyses.

Gao L, Fang Z, Zhang K, Zhi D, Cui X.

Bioinformatics. 2011 Mar 1;27(5):662-9. doi: 10.1093/bioinformatics/btr005. Epub 2011 Jan 19.

13.

Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function.

Raychaudhuri S, Korn JM, McCarroll SA; International Schizophrenia Consortium, Altshuler D, Sklar P, Purcell S, Daly MJ.

PLoS Genet. 2010 Sep 9;6(9):e1001097. doi: 10.1371/journal.pgen.1001097.

14.

Noncoding sequences near duplicated genes evolve rapidly.

Kostka D, Hahn MW, Pollard KS.

Genome Biol Evol. 2010;2:518-33. doi: 10.1093/gbe/evq037. Epub 2010 Jun 29.

15.

GREAT improves functional interpretation of cis-regulatory regions.

McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.

16.

Contrasts between adaptive coding and noncoding changes during human evolution.

Haygood R, Babbitt CC, Fedrigo O, Wray GA.

Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7853-7. doi: 10.1073/pnas.0911249107. Epub 2010 Apr 12.

17.

Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets.

Hazelett DJ, Lakeland DL, Weiss JB.

Bioinformatics. 2009 Jul 1;25(13):1617-24. doi: 10.1093/bioinformatics/btp282. Epub 2009 Apr 28.

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