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Cited In for PubMed (Select 15550541)


Incorporating Chromatin Accessibility Data into Sequence-to-Expression Modeling.

Peng PC, Hassan Samee MA, Sinha S.

Biophys J. 2015 Mar 10;108(5):1257-67. doi: 10.1016/j.bpj.2014.12.037.


An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape.

Chen H, Li H, Liu F, Zheng X, Wang S, Bo X, Shu W.

Sci Rep. 2015 Feb 16;5:8465. doi: 10.1038/srep08465.


Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation.

Wan J, Oliver VF, Wang G, Zhu H, Zack DJ, Merbs SL, Qian J.

BMC Genomics. 2015 Feb 5;16:49. doi: 10.1186/s12864-015-1271-4.


Chromatin accessibility: a window into the genome.

Tsompana M, Buck MJ.

Epigenetics Chromatin. 2014 Nov 20;7(1):33. doi: 10.1186/1756-8935-7-33. eCollection 2014. Review.


Estrogen induces global reorganization of chromatin structure in human breast cancer cells.

Mourad R, Hsu PY, Juan L, Shen C, Koneru P, Lin H, Liu Y, Nephew K, Huang TH, Li L.

PLoS One. 2014 Dec 3;9(12):e113354. doi: 10.1371/journal.pone.0113354. eCollection 2014.


Replicon: a software to accurately predict DNA replication timing in metazoan cells.

Gindin Y, Meltzer PS, Bilke S.

Front Genet. 2014 Nov 3;5:378. doi: 10.3389/fgene.2014.00378. eCollection 2014.


SuRFing the genomics wave: an R package for prioritising SNPs by functionality.

Ryan NM, Morris SW, Porteous DJ, Taylor MS, Evans KL.

Genome Med. 2014 Oct 14;6(10):79. doi: 10.1186/s13073-014-0079-1. eCollection 2014.


Multiple functional risk variants in a SMAD7 enhancer implicate a colorectal cancer risk haplotype.

Fortini BK, Tring S, Plummer SJ, Edlund CK, Moreno V, Bresalier RS, Barry EL, Church TR, Figueiredo JC, Casey G.

PLoS One. 2014 Nov 6;9(11):e111914. doi: 10.1371/journal.pone.0111914. eCollection 2014.


Regulation of the Th1 genomic locus from Ifng through Tmevpg1 by T-bet.

Collier SP, Henderson MA, Tossberg JT, Aune TM.

J Immunol. 2014 Oct 15;193(8):3959-65. doi: 10.4049/jimmunol.1401099. Epub 2014 Sep 15.


Functional annotation signatures of disease susceptibility loci improve SNP association analysis.

Iversen ES, Lipton G, Clyde MA, Monteiro AN.

BMC Genomics. 2014 May 24;15:398. doi: 10.1186/1471-2164-15-398.


Cell-Type Specific Determinants of NRAMP1 Expression in Professional Phagocytes.

Cellier MF.

Biology (Basel). 2013 Jan 25;2(1):233-83. doi: 10.3390/biology2010233.


The histone lysine demethylase JMJD3/KDM6B is recruited to p53 bound promoters and enhancer elements in a p53 dependent manner.

Williams K, Christensen J, Rappsilber J, Nielsen AL, Johansen JV, Helin K.

PLoS One. 2014 May 5;9(5):e96545. doi: 10.1371/journal.pone.0096545. eCollection 2014.


Identifying and mapping cell-type-specific chromatin programming of gene expression.

Marstrand TT, Storey JD.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):E645-54. doi: 10.1073/pnas.1312523111. Epub 2014 Jan 27.


Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1.

Biancolella M, Fortini BK, Tring S, Plummer SJ, Mendoza-Fandino GA, Hartiala J, Hitchler MJ, Yan C, Schumacher FR, Conti DV, Edlund CK, Noushmehr H, Coetzee SG, Bresalier RS, Ahnen DJ, Barry EL, Berman BP, Rice JC, Coetzee GA, Casey G.

Hum Mol Genet. 2014 Apr 15;23(8):2198-209. doi: 10.1093/hmg/ddt584. Epub 2013 Nov 20.


Efficient subtractive cloning of genes activated by lipopolysaccharide and interferon γ in primary-cultured cortical cells of newborn mice.

Miyauchi O, Iwase K, Itoh K, Kato M, Seki N, Braissant O, Bachmann C, Shozu M, Sekiya S, Osada H, Takiguchi M.

PLoS One. 2013 Nov 11;8(11):e79236. doi: 10.1371/journal.pone.0079236. eCollection 2013.


Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

Koohy H, Down TA, Hubbard TJ.

PLoS One. 2013 Jul 26;8(7):e69853. doi: 10.1371/journal.pone.0069853. Print 2013.


Genome-scale mapping of DNase I hypersensitivity.

John S, Sabo PJ, Canfield TK, Lee K, Vong S, Weaver M, Wang H, Vierstra J, Reynolds AP, Thurman RE, Stamatoyannopoulos JA.

Curr Protoc Mol Biol. 2013 Jul;Chapter 27:Unit 21.27. doi: 10.1002/0471142727.mb2127s103.


DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.

Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA.

Nat Genet. 2013 Aug;45(8):852-9. doi: 10.1038/ng.2677. Epub 2013 Jun 23.


Drosophila functional elements are embedded in structurally constrained sequences.

Kenigsberg E, Tanay A.

PLoS Genet. 2013 May;9(5):e1003512. doi: 10.1371/journal.pgen.1003512. Epub 2013 May 30.


PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.

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