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Items: 1 to 20 of 105

1.

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A.

Bioinformatics. 2010 Oct 1;26(19):2438-44. doi: 10.1093/bioinformatics/btq466. Epub 2010 Aug 13.

2.

The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

BMC Immunol. 2008 Mar 5;9:7. doi: 10.1186/1471-2172-9-7.

3.

SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles.

Wong KC, Li Y, Peng C, Zhang Z.

Bioinformatics. 2015 Jan 1;31(1):17-24. doi: 10.1093/bioinformatics/btu604. Epub 2014 Sep 5.

PMID:
25192742
4.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

5.

Differential motif enrichment analysis of paired ChIP-seq experiments.

Lesluyes T, Johnson J, Machanick P, Bailey TL.

BMC Genomics. 2014 Sep 2;15:752. doi: 10.1186/1471-2164-15-752.

6.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.

7.

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

Auerbach RK, Chen B, Butte AJ.

Bioinformatics. 2013 Aug 1;29(15):1922-4. doi: 10.1093/bioinformatics/btt316. Epub 2013 Jun 3.

8.

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.

Qin J, Li MJ, Wang P, Zhang MQ, Wang J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W430-6. doi: 10.1093/nar/gkr332. Epub 2011 May 17.

9.

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.

Chen L, Wu G, Ji H.

Bioinformatics. 2011 May 15;27(10):1447-8. doi: 10.1093/bioinformatics/btr156. Epub 2011 Mar 30.

10.

Genome-wide in vivo cross-linking of sequence-specific transcription factors.

Li XY, Biggin MD.

Methods Mol Biol. 2012;809:3-26. doi: 10.1007/978-1-61779-376-9_1.

PMID:
22113265
11.

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.

12.

Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences.

Zambelli F, Pesole G, Pavesi G.

Curr Protoc Bioinformatics. 2014 Sep 8;47:2.11.1-31. doi: 10.1002/0471250953.bi0211s47.

PMID:
25199791
13.

Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data.

Yang CC, Chen MH, Lin SY, Andrews EH, Cheng C, Liu CC, Chen JJ.

BMC Genomics. 2017 Jan 10;18(1):61. doi: 10.1186/s12864-016-3450-3.

14.
15.

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.

Zambelli F, Prazzoli GM, Pesole G, Pavesi G.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W510-5. doi: 10.1093/nar/gks483. Epub 2012 Jun 4.

16.

MEME-ChIP: motif analysis of large DNA datasets.

Machanick P, Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1696-7. doi: 10.1093/bioinformatics/btr189. Epub 2011 Apr 12.

17.

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.

Liu L, Ramsay T, Zinkgraf M, Sundell D, Street NR, Filkov V, Groover A.

Plant J. 2015 Jun;82(5):887-98. doi: 10.1111/tpj.12850.

18.

Cistrome: an integrative platform for transcriptional regulation studies.

Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS.

Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83.

19.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

20.

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