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ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.

Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, Kawaji H, Nakaki R, Sese J, Meno C.

EMBO Rep. 2018 Dec;19(12). pii: e46255. doi: 10.15252/embr.201846255. Epub 2018 Nov 9.


TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data.

Zeng J, Li G.

Int J Biol Sci. 2018 Sep 7;14(12):1724-1731. doi: 10.7150/ijbs.28850. eCollection 2018.


ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B.

Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. doi: 10.1093/nar/gkx1092.


ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.

Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS.

BMC Bioinformatics. 2016 Oct 3;17(1):404.


Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T.

Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Review.


HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.

Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP.

BMC Bioinformatics. 2014 Aug 15;15:280. doi: 10.1186/1471-2105-15-280.


Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX.

Nucleic Acids Res. 2012 Sep;40(16):7690-704. Epub 2012 Jun 6.


BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.

Ramachandran P, Palidwor GA, Perkins TJ.

Epigenetics Chromatin. 2015 Sep 17;8:33. doi: 10.1186/s13072-015-0028-2. eCollection 2015.


Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.

Piechota M, Korostynski M, Ficek J, Tomski A, Przewlocki R.

BMC Bioinformatics. 2016 Feb 12;17:85. doi: 10.1186/s12859-016-0938-4.


Integrative analysis of ChIP-chip and ChIP-seq dataset.

Zhu LJ.

Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8.


GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

Yevshin I, Sharipov R, Valeev T, Kel A, Kolpakov F.

Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67. doi: 10.1093/nar/gkw951. Epub 2016 Oct 24.


ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.


iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C.

BMC Genomics. 2016 Aug 12;17(1):632. doi: 10.1186/s12864-016-2963-0.


i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.

Imrichová H, Hulselmans G, Atak ZK, Potier D, Aerts S.

Nucleic Acids Res. 2015 Jul 1;43(W1):W57-64. doi: 10.1093/nar/gkv395. Epub 2015 Apr 29.


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.


Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.

Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X, Meyer CA, Liu XS.

Nucleic Acids Res. 2019 Jan 8;47(D1):D729-D735. doi: 10.1093/nar/gky1094.


Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering.

Müller L, Gerighausen D, Farman M, Zeckzer D.

BMC Bioinformatics. 2016 Sep 15;17(1):377. doi: 10.1186/s12859-016-1248-6.


An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue.

David SA, Piégu B, Hennequet-Antier C, Pannetier M, Aguirre-Lavin T, Crochet S, Bordeau T, Couroussé N, Brionne A, Bigot Y, Collin A, Coustham V.

Biol Proced Online. 2017 Aug 29;19:10. doi: 10.1186/s12575-017-0059-0. eCollection 2017.


The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

Ambrosini G, Dreos R, Kumar S, Bucher P.

BMC Genomics. 2016 Nov 18;17(1):938.

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