Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Published 2013 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Authors
Keywords
-
Journal
PLoS Computational Biology
Volume 9, Issue 11, Pages e1003326
Publisher
Public Library of Science (PLoS)
Online
2013-11-15
DOI
10.1371/journal.pcbi.1003326
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- A fast weak motif-finding algorithm based on community detection in graphs
- (2013) Caiyan Jia et al. BMC BIOINFORMATICS
- Predicting the molecular complexity of sequencing libraries
- (2013) Timothy Daley et al. NATURE METHODS
- LOcating Non-Unique matched Tags (LONUT) to Improve the Detection of the Enriched Regions for ChIP-seq Data
- (2013) Rui Wang et al. PLoS One
- Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
- (2013) M. A. White et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Is junk DNA bunk? A critique of ENCODE
- (2013) W. F. Doolittle PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MULTOVL: fast multiple overlaps of genomic regions
- (2012) A. Aszodi BIOINFORMATICS
- Normalization of ChIP-seq data with control
- (2012) Kun Liang et al. BMC BIOINFORMATICS
- Combining multiple ChIP-seq peak detection systems using combinatorial fusion
- (2012) Christina Schweikert et al. BMC GENOMICS
- The UCSC genome browser and associated tools
- (2012) R. M. Kuhn et al. BRIEFINGS IN BIOINFORMATICS
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- (2012) S. G. Landt et al. GENOME RESEARCH
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman et al. NATURE
- Systematic evaluation of factors influencing ChIP-seq fidelity
- (2012) Yiwen Chen et al. NATURE METHODS
- Robust 4C-seq data analysis to screen for regulatory DNA interactions
- (2012) Harmen J G van de Werken et al. NATURE METHODS
- ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
- (2012) Terrence S. Furey NATURE REVIEWS GENETICS
- Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes
- (2012) Hui-wen Liu et al. NUCLEIC ACIDS RESEARCH
- Inferring direct DNA binding from ChIP-seq
- (2012) Timothy L. Bailey et al. NUCLEIC ACIDS RESEARCH
- High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
- (2012) Yuchun Guo et al. PLoS Computational Biology
- CHANCE: comprehensive software for quality control and validation of ChIP-seq data
- (2012) Aaron Diaz et al. GENOME BIOLOGY
- MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
- (2012) Zhen Shao et al. GENOME BIOLOGY
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
- (2012) Kevin Y Yip et al. GENOME BIOLOGY
- Measuring reproducibility of high-throughput experiments
- (2011) Qunhua Li et al. Annals of Applied Statistics
- DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models
- (2011) C. Taslim et al. BIOINFORMATICS
- Identifying dispersed epigenomic domains from ChIP-Seq data
- (2011) Qiang Song et al. BIOINFORMATICS
- Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
- (2011) Paweł P. Łabaj et al. BIOINFORMATICS
- Detecting differential binding of transcription factors with ChIP-seq
- (2011) Kun Liang et al. BIOINFORMATICS
- MEME-ChIP: motif analysis of large DNA datasets
- (2011) Philip Machanick et al. BIOINFORMATICS
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- RecMotif: a novel fast algorithm for weak motif discovery
- (2011) He Sun et al. BMC BIOINFORMATICS
- PeakRanger: A cloud-enabled peak caller for ChIP-seq data
- (2011) Xin Feng et al. BMC BIOINFORMATICS
- Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
- (2011) Ho Sung Rhee et al. CELL
- Studying the epigenome using next generation sequencing
- (2011) C. S. Ku et al. JOURNAL OF MEDICAL GENETICS
- Integrative genomics viewer
- (2011) James T Robinson et al. NATURE BIOTECHNOLOGY
- Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq
- (2011) Mazhar Adli et al. Nature Protocols
- A computational pipeline for comparative ChIP-seq analyses
- (2011) Anaïs F Bardet et al. Nature Protocols
- POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization
- (2011) Marco A. Mendoza-Parra et al. NUCLEIC ACIDS RESEARCH
- Systematic bias in high-throughput sequencing data and its correction by BEADS
- (2011) Ming-Sin Cheung et al. NUCLEIC ACIDS RESEARCH
- Inferring transcription factor complexes from ChIP-seq data
- (2011) Tom Whitington et al. NUCLEIC ACIDS RESEARCH
- RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
- (2011) Morgane Thomas-Chollier et al. NUCLEIC ACIDS RESEARCH
- ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
- (2011) Jose M Muiño et al. Plant Methods
- Cistrome: an integrative platform for transcriptional regulation studies
- (2011) Tao Liu et al. GENOME BIOLOGY
- ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
- (2011) Naim U Rashid et al. GENOME BIOLOGY
- Deep and wide digging for binding motifs in ChIP-Seq data
- (2010) I. V. Kulakovskiy et al. BIOINFORMATICS
- A signal–noise model for significance analysis of ChIP-seq with negative control
- (2010) Han Xu et al. BIOINFORMATICS
- Discovering homotypic binding events at high spatial resolution
- (2010) Yuchun Guo et al. BIOINFORMATICS
- CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
- (2010) Lakshmi Kuttippurathu et al. BIOINFORMATICS
- BigWig and BigBed: enabling browsing of large distributed datasets
- (2010) W. J. Kent et al. BIOINFORMATICS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
- (2010) Congmao Wang et al. BMC BIOINFORMATICS
- PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
- (2010) Mali Salmon-Divon et al. BMC BIOINFORMATICS
- HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
- (2010) Zhaohui S Qin et al. BMC BIOINFORMATICS
- ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
- (2010) Lihua J Zhu et al. BMC BIOINFORMATICS
- Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts
- (2010) A. M. Szalkowski et al. BRIEFINGS IN BIOINFORMATICS
- GREAT improves functional interpretation of cis-regulatory regions
- (2010) Cory Y McLean et al. NATURE BIOTECHNOLOGY
- Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
- (2010) Mitchell Guttman et al. NATURE BIOTECHNOLOGY
- An assessment of histone-modification antibody quality
- (2010) Thea A Egelhofer et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
- (2010) Elizabeth G. Wilbanks et al. PLoS One
- ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
- (2010) Guoliang Li et al. GENOME BIOLOGY
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
- (2010) Jeremy Goecks et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Comparative study on ChIP-seq data: normalization and binding pattern characterization
- (2009) Cenny Taslim et al. BIOINFORMATICS
- CEAS: cis-regulatory element annotation system
- (2009) Hyunjin Shin et al. BIOINFORMATICS
- A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
- (2009) Chongzhi Zang et al. BIOINFORMATICS
- The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
- (2009) J. W. Nicol et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- BayesPeak: Bayesian analysis of ChIP-seq data
- (2009) Christiana Spyrou et al. BMC BIOINFORMATICS
- High-resolution DNA-binding specificity analysis of yeast transcription factors
- (2009) C. Zhu et al. GENOME RESEARCH
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
- (2009) Joel Rozowsky et al. NATURE BIOTECHNOLOGY
- Computation for ChIP-seq and RNA-seq studies
- (2009) Shirley Pepke et al. NATURE METHODS
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest
- (2009) L. Ryan Baugh et al. SCIENCE
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
- (2008) Han Xu et al. BIOINFORMATICS
- SOAP: short oligonucleotide alignment program
- (2008) R. Li et al. BIOINFORMATICS
- Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
- (2008) David A Nix et al. BMC BIOINFORMATICS
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
- (2008) H. Li et al. GENOME RESEARCH
- An integrated software system for analyzing ChIP-chip and ChIP-seq data
- (2008) Hongkai Ji et al. NATURE BIOTECHNOLOGY
- Design and analysis of ChIP-seq experiments for DNA-binding proteins
- (2008) Peter V Kharchenko et al. NATURE BIOTECHNOLOGY
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
- (2008) R. Jothi et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started