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Items: 1 to 20 of 28

1.

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY.

Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898.

PMID:
30361341
2.

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space.

Klughammer J, Kiesel B, Roetzer T, Fortelny N, Nemc A, Nenning KH, Furtner J, Sheffield NC, Datlinger P, Peter N, Nowosielski M, Augustin M, Mischkulnig M, Ströbel T, Alpar D, Ergüner B, Senekowitsch M, Moser P, Freyschlag CF, Kerschbaumer J, Thomé C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, Haybaeck J, Krassnig S, Mahdy Ali K, von Campe G, Payer F, Sherif C, Preiser J, Hauser T, Winkler PA, Kleindienst W, Würtz F, Brandner-Kokalj T, Stultschnig M, Schweiger S, Dieckmann K, Preusser M, Langs G, Baumann B, Knosp E, Widhalm G, Marosi C, Hainfellner JA, Woehrer A, Bock C.

Nat Med. 2018 Oct;24(10):1611-1624. doi: 10.1038/s41591-018-0156-x. Epub 2018 Aug 27.

PMID:
30150718
3.

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

Nagraj VP, Magee NE, Sheffield NC.

Nucleic Acids Res. 2018 Jul 2;46(W1):W194-W199. doi: 10.1093/nar/gky464.

4.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK.

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474.

5.

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles.

Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, Zang C.

Bioinformatics. 2018 Aug 15;34(16):2867-2869. doi: 10.1093/bioinformatics/bty194.

PMID:
29608647
6.

MIRA: an R package for DNA methylation-based inference of regulatory activity.

Lawson JT, Tomazou EM, Bock C, Sheffield NC.

Bioinformatics. 2018 Aug 1;34(15):2649-2650. doi: 10.1093/bioinformatics/bty083.

7.

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.

Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Álava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, Holter W, Windhager R, Dirksen U, Ambros PF, Delattre O, Kovar H, Bock C, Tomazou EM.

Nat Med. 2017 Mar;23(3):386-395. doi: 10.1038/nm.4273. Epub 2017 Jan 30.

8.

Single-cell epigenomic variability reveals functional cancer heterogeneity.

Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY.

Genome Biol. 2017 Jan 24;18(1):15. doi: 10.1186/s13059-016-1133-7.

9.

Multi-Omics of Single Cells: Strategies and Applications.

Bock C, Farlik M, Sheffield NC.

Trends Biotechnol. 2016 Aug;34(8):605-608. doi: 10.1016/j.tibtech.2016.04.004. Epub 2016 May 20.

10.

The second European interdisciplinary Ewing sarcoma research summit--A joint effort to deconstructing the multiple layers of a complex disease.

Kovar H, Amatruda J, Brunet E, Burdach S, Cidre-Aranaz F, de Alava E, Dirksen U, van der Ent W, Grohar P, Grünewald TG, Helman L, Houghton P, Iljin K, Korsching E, Ladanyi M, Lawlor E, Lessnick S, Ludwig J, Meltzer P, Metzler M, Mora J, Moriggl R, Nakamura T, Papamarkou T, Radic Sarikas B, Rédini F, Richter GH, Rossig C, Schadler K, Schäfer BW, Scotlandi K, Sheffield NC, Shelat A, Snaar-Jagalska E, Sorensen P, Stegmaier K, Stewart E, Sweet-Cordero A, Szuhai K, Tirado OM, Tirode F, Toretsky J, Tsafou K, Üren A, Zinovyev A, Delattre O.

Oncotarget. 2016 Feb 23;7(8):8613-24. doi: 10.18632/oncotarget.6937. Review.

11.

Differential DNA Methylation Analysis without a Reference Genome.

Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C.

Cell Rep. 2015 Dec 22;13(11):2621-2633. doi: 10.1016/j.celrep.2015.11.024. Epub 2015 Dec 8.

12.

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

Sheffield NC, Bock C.

Bioinformatics. 2016 Feb 15;32(4):587-9. doi: 10.1093/bioinformatics/btv612. Epub 2015 Oct 27.

13.

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):963-965. doi: 10.1038/nmeth.3542. Epub 2015 Aug 17.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

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