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Items: 1 to 20 of 134

1.

Identifying Direct Downstream Targets: WT1 ChIP-Seq Analysis.

da Silva F, Massa F, Schedl A.

Methods Mol Biol. 2016;1467:177-88. doi: 10.1007/978-1-4939-4023-3_15.

PMID:
27417969
2.

High-Resolution Chromatin Immunoprecipitation: ChIP-Sequencing.

Diaz RE, Sanchez A, Anton Le Berre V, Bouet JY.

Methods Mol Biol. 2017;1624:61-73. doi: 10.1007/978-1-4939-7098-8_6.

3.

ChIPulate: A comprehensive ChIP-seq simulation pipeline.

Datta V, Hannenhalli S, Siddharthan R.

PLoS Comput Biol. 2019 Mar 21;15(3):e1006921. doi: 10.1371/journal.pcbi.1006921. eCollection 2019 Mar.

4.

Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis.

Cortijo S, Charoensawan V, Roudier F, Wigge PA.

Methods Mol Biol. 2018;1761:231-248. doi: 10.1007/978-1-4939-7747-5_18.

PMID:
29525962
5.

Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe.

Vallabh S, Kartashov AV, Barski A.

Methods Mol Biol. 2018;1783:343-360. doi: 10.1007/978-1-4939-7834-2_17.

6.

NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.

Mendoza-Parra MA, Saleem MA, Blum M, Cholley PE, Gronemeyer H.

Methods Mol Biol. 2016;1418:243-65. doi: 10.1007/978-1-4939-3578-9_13.

PMID:
27008019
7.

Computational analysis of protein-DNA interactions from ChIP-seq data.

Rougemont J, Naef F.

Methods Mol Biol. 2012;786:263-73. doi: 10.1007/978-1-61779-292-2_16.

PMID:
21938632
8.

Next-generation sequencing applied to flower development: ChIP-Seq.

Graciet E, O'Maoiléidigh DS, Wellmer F.

Methods Mol Biol. 2014;1110:413-29. doi: 10.1007/978-1-4614-9408-9_24.

PMID:
24395273
9.

Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.

Lefrançois P, Gallagher JE, Snyder M.

Methods Mol Biol. 2014;1205:231-55. doi: 10.1007/978-1-4939-1363-3_15.

10.

ChIP-Seq: Library Preparation and Sequencing.

Sheaffer KL, Schug J.

Methods Mol Biol. 2016;1402:101-117. doi: 10.1007/978-1-4939-3378-5_9.

PMID:
26721486
11.

ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses.

Lelandais G, Blugeon C, Merhej J.

Methods Mol Biol. 2016;1361:185-202. doi: 10.1007/978-1-4939-3079-1_11.

PMID:
26483023
12.

Chromatin Immunoprecipitation.

Wiehle L, Breiling A.

Methods Mol Biol. 2016;1480:7-21. doi: 10.1007/978-1-4939-6380-5_2.

PMID:
27659971
13.

Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development.

Hartwig S, Ho J, Pandey P, Macisaac K, Taglienti M, Xiang M, Alterovitz G, Ramoni M, Fraenkel E, Kreidberg JA.

Development. 2010 Apr;137(7):1189-203. doi: 10.1242/dev.045732.

14.

Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.

Stanton KP, Jin J, Lederman RR, Weissman SM, Kluger Y.

Nucleic Acids Res. 2017 Dec 1;45(21):e173. doi: 10.1093/nar/gkx799.

15.

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.

16.

Design and analysis of ChIP-seq experiments for DNA-binding proteins.

Kharchenko PV, Tolstorukov MY, Park PJ.

Nat Biotechnol. 2008 Dec;26(12):1351-9. doi: 10.1038/nbt.1508. Epub 2008 Nov 16.

17.

Analysis of LXR Nuclear Receptor Cistrome Through ChIP-Seq Data Bioinformatics.

de la Rosa JV, Ramón-Vázquez A, Tabraue C, Castrillo A.

Methods Mol Biol. 2019;1951:99-109. doi: 10.1007/978-1-4939-9130-3_8.

PMID:
30825147
18.

Direct ChIP-Seq significance analysis improves target prediction.

Bansal M, Mendiratta G, Anand S, Kushwaha R, Kim R, Kustagi M, Iyer A, Chaganti RS, Califano A, Sumazin P.

BMC Genomics. 2015;16 Suppl 5:S4. doi: 10.1186/1471-2164-16-S5-S4. Epub 2015 May 26.

19.

ChIP-Seq Data Analysis to Define Transcriptional Regulatory Networks.

Pavesi G.

Adv Biochem Eng Biotechnol. 2017;160:1-14. doi: 10.1007/10_2016_43. Review.

20.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

Xing H, Mo Y, Liao W, Zhang MQ.

PLoS Comput Biol. 2012;8(7):e1002613. doi: 10.1371/journal.pcbi.1002613. Epub 2012 Jul 26.

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