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Items: 15


LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.

Sheffield NC, Bock C.

Bioinformatics. 2015 Oct 27. pii: btv612. [Epub ahead of print]


ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.

Schmidl C, Rendeiro AF, Sheffield NC, Bock C.

Nat Methods. 2015 Oct;12(10):963-5. doi: 10.1038/nmeth.3542. Epub 2015 Aug 17.


Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.

Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C.

Cell Rep. 2015 Mar 3;10(8):1386-97. doi: 10.1016/j.celrep.2015.02.001. Epub 2015 Feb 26.


Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1.

Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C, Kovar H.

Cell Rep. 2015 Feb 24;10(7):1082-95. doi: 10.1016/j.celrep.2015.01.042. Epub 2015 Feb 19.


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.


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.


Predicting cell-type-specific gene expression from regions of open chromatin.

Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U.

Genome Res. 2012 Sep;22(9):1711-22. doi: 10.1101/gr.135129.111.


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.


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.


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.


Mitochondrial genomics in Orthoptera using MOSAS.

Sheffield NC, Hiatt KD, Valentine MC, Song H, Whiting MF.

Mitochondrial DNA. 2010 Jun;21(3-4):87-104. doi: 10.3109/19401736.2010.500812.


Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.

Sheffield NC, Song H, Cameron SL, Whiting MF.

Syst Biol. 2009 Aug;58(4):381-94. doi: 10.1093/sysbio/syp037. Epub 2009 Jul 15.


Calculating expected DNA remnants from ancient founding events in human population genetics.

Stacey A, Sheffield NC, Crandall KA.

BMC Genet. 2008 Oct 17;9:66. doi: 10.1186/1471-2156-9-66.


A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

Sheffield NC, Song H, Cameron SL, Whiting MF.

Mol Biol Evol. 2008 Nov;25(11):2499-509. doi: 10.1093/molbev/msn198. Epub 2008 Sep 8.

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