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Results: 1 to 20 of 56


Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations.

Weiser M, Mukherjee S, Furey TS.

Genetics. 2014 Nov;198(3):879-93. doi: 10.1534/genetics.114.167791. Epub 2014 Sep 16.


GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.

Xiong Q, Mukherjee S, Furey TS.

Sci Rep. 2014 Sep 12;4:6347. doi: 10.1038/srep06347.


Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.

Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y.

PLoS One. 2014 Sep 8;9(9):e107156. doi: 10.1371/journal.pone.0107156. eCollection 2014.


Genetics. Genetics driving epigenetics.

Furey TS, Sethupathy P.

Science. 2013 Nov 8;342(6159):705-6. doi: 10.1126/science.1246755. No abstract available.


Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects.

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ.

Genome Res. 2014 Feb;24(2):241-50. doi: 10.1101/gr.158253.113. Epub 2013 Oct 24.


A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function.

Bischof JM, Gillen AE, Song L, Gosalia N, London D, Furey TS, Crawford GE, Harris A.

Biol Reprod. 2013 Oct 31;89(4):104. doi: 10.1095/biolreprod.113.110403. Print 2013 Oct.


DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types.

Winter DR, Song L, Mukherjee S, Furey TS, Crawford GE.

Genome Res. 2013 Jul;23(7):1118-29. doi: 10.1101/gr.150482.112. Epub 2013 May 8.


Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS.

Genome Res. 2013 May;23(5):777-88. doi: 10.1101/gr.152140.112. Epub 2013 Mar 12.


ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.

Furey TS.

Nat Rev Genet. 2012 Dec;13(12):840-52. doi: 10.1038/nrg3306. Epub 2012 Oct 23. Review.


Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.

Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG.

Genome Biol. 2012 Oct 3;13(10):R88. doi: 10.1186/gb-2012-13-10-r88.


A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning.

Bennett BD, Xiong Q, Mukherjee S, Furey TS.

PLoS One. 2012;7(9):e44635. doi: 10.1371/journal.pone.0044635. Epub 2012 Sep 13. Erratum in: PLoS One. 2013;8(9). doi:10.1371/annotation/c04cea96-35f4-4578-a891-639e30fddd59.


The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.


Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.

Parker SC, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, Crawford GE, Rosenberg SA, Samuels Y, Margulies EH.

PLoS Genet. 2012;8(8):e1002871. doi: 10.1371/journal.pgen.1002871. Epub 2012 Aug 9.


Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE.

PLoS Genet. 2012 Jun;8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28.


Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays.

Sheffield NC, Furey TS.

Genes (Basel). 2012 Oct 15;3(4):651-70. doi: 10.3390/genes3040651.


A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.

Bischof JM, Ott CJ, Leir SH, Gosalia N, Song L, London D, Furey TS, Cotton CU, Crawford GE, Harris A.

Thorax. 2012 May;67(5):385-91. doi: 10.1136/thoraxjnl-2011-200880. Epub 2011 Dec 14.


Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.

Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.

Genome Res. 2012 Jan;22(1):9-24. doi: 10.1101/gr.127597.111. Epub 2011 Nov 16.


Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.

Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS.

Genome Res. 2012 Feb;22(2):386-97. doi: 10.1101/gr.124370.111. Epub 2011 Sep 22. Erratum in: Genome Res. 2013 May;23(5):905.


Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC.

Genome Res. 2011 Oct;21(10):1659-71. doi: 10.1101/gr.125088.111. Epub 2011 Jul 27.


Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12.

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