Keyword

ChIP-seq

Description: A genomic method combining chromatin immunoprecipitation and DNA sequencing to identify protein-binding sites across the genome.

Primary topic: Genomics and Chromatin Dynamics (48%)

Wikidata ID: wiki/Q5065899

OpenAlex ID: keywords/chip-seq

Model-based Analysis of ChIP-Seq (MACS)

2008 · Yong Zhang, Tao Liu, et al. · Genome biology · 18,330

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Differential expression analysis for sequence count data

2010 · Simon Anders, Wolfgang Huber · Genome biology · 15,532

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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

2012 · Davis J. McCarthy, Yunshun Chen, et al. · Nucleic Acids Research · 5,187

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GREAT improves functional interpretation of cis-regulatory regions

2010 · Cory Y McLean, Dave Bristor, et al. · Nature Biotechnology · 4,493

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

2007 · Tarjei S. Mikkelsen, Manching Ku, et al. · Nature · 4,127

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

2007 · David S. Johnson, Ali Mortazavi, et al. · Science · 2,917

ChIP–seq: advantages and challenges of a maturing technology

2009 · Peter J. Park · Nature Reviews Genetics · 2,213

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

2012 · Stephen G. Landt, Georgi K. Marinov, et al. · Genome Research · 2,030

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Identifying ChIP-seq enrichment using MACS

2012 · Jianxing Feng, Tao Liu, et al. · Nature Protocols · 1,877

ChIP-seq accurately predicts tissue-specific activity of enhancers

2009 · Axel Visel, Matthew J. Blow, et al. · Nature · 1,640

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Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

2007 · Gordon Robertson, Martin Hirst, et al. · Nature Methods · 1,455

Comprehensive single-cell transcriptional profiling of a multicellular organism

2017 · Junyue Cao, Jonathan S. Packer, et al. · Science · 1,401

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Sequencing depth and coverage: key considerations in genomic analyses

2014 · David Sims, Ian Sudbery, et al. · Nature Reviews Genetics · 1,395

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

2008 · Alexander Marson, Stuart S. Levine, et al. · Cell · 1,370

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A map of the cis-regulatory sequences in the mouse genome

2012 · Yin Shen, Feng Yue, et al. · Nature · 1,362

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

2010 · Lihua J Zhu, Claude Gazin, et al. · BMC Bioinformatics · 1,181

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A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

2006 · Chia-Lin Wei, Qiang Wu, et al. · Cell · 1,142

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ChEA3: transcription factor enrichment analysis by orthogonal omics integration

2019 · Alexandra B Keenan, Denis Torre, et al. · Nucleic Acids Research · 1,131

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Streaming fragment assignment for real-time analysis of sequencing experiments

2012 · Adam Roberts, Lior Pachter · Nature Methods · 1,059

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

2009 · Chongzhi Zang, Dustin E. Schones, et al. · Bioinformatics · 1,059

Nucleosome positioning and gene regulation: advances through genomics

2009 · Cizhong Jiang, B. Franklin Pugh · Nature Reviews Genetics · 1,058

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

2010 · Alexander Lachmann, Huilei Xu, et al. · Bioinformatics · 1,031

Measuring reproducibility of high-throughput experiments

2011 · Qunhua Li, James B. Brown, et al. · The Annals of Applied Statistics · 1,019

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Counting absolute numbers of molecules using unique molecular identifiers

2011 · Teemu Kivioja, Anna Vähärautio, et al. · Nature Methods · 1,006

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

2013 · Anthony Mathelier, Xiaobei Zhao, et al. · Nucleic Acids Research · 983

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Works count: 6,526

Citation count: 188,000