Rye MB - Search Results

1

MACPET: model-based analysis for ChIA-PET.

Vardaxis I, Drabløs F, Rye MB, Lindqvist BH. Vardaxis I, et al. Among authors: rye mb. Biostatistics. 2020 Jul 1;21(3):625-639. doi: 10.1093/biostatistics/kxy084. Biostatistics. 2020. PMID: 30698663 Free PMC article.

2

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Liang C; FANTOM Consortium; Forrest AR, Wagner GP. Liang C, et al. Nat Commun. 2015 Jan 14;6:6066. doi: 10.1038/ncomms7066. Nat Commun. 2015. PMID: 25585899 Free article.

3

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.

Rye MB, Sætrom P, Drabløs F. Rye MB, et al. Nucleic Acids Res. 2011 Mar;39(4):e25. doi: 10.1093/nar/gkq1187. Epub 2010 Nov 26. Nucleic Acids Res. 2011. PMID: 21113027 Free PMC article.

4

A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

Håndstad T, Rye MB, Drabløs F, Sætrom P. Håndstad T, et al. Among authors: rye mb. PLoS One. 2011 Apr 14;6(4):e18430. doi: 10.1371/journal.pone.0018430. PLoS One. 2011. PMID: 21533218 Free PMC article.

5

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F. Rye M, et al. BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80. BMC Biol. 2011. PMID: 22115494 Free PMC article.

6

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.

Kornacker K, Rye MB, Håndstad T, Drabløs F. Kornacker K, et al. Among authors: rye mb. BMC Bioinformatics. 2012 Jul 24;13:176. doi: 10.1186/1471-2105-13-176. BMC Bioinformatics. 2012. PMID: 22827163 Free PMC article.

7

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P. Håndstad T, et al. BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372. BMC Genomics. 2012. PMID: 22863112 Free PMC article.

8

The Genomic HyperBrowser: an analysis web server for genome-scale data.

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E. Sandve GK, et al. Among authors: rye mb. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41. doi: 10.1093/nar/gkt342. Epub 2013 Apr 30. Nucleic Acids Res. 2013. PMID: 23632163 Free PMC article.

9

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.

Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F; FANTOM consortium. Rye M, et al. BMC Genomics. 2014 Mar 26;15:120. doi: 10.1186/1471-2164-15-120. BMC Genomics. 2014. PMID: 24669905 Free PMC article.

10

An atlas of active enhancers across human cell types and tissues.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. Andersson R, et al. Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787. Nature. 2014. PMID: 24670763 Free PMC article.

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