标题
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions
作者
关键词
-
出版物
Briefings in Functional Genomics
Volume 9, Issue 5-6, Pages 466-476
出版商
Oxford University Press (OUP)
发表日期
2011-05-05
DOI
10.1093/bfgp/elq022
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- The value of position-specific priors in motif discovery using MEME
- (2010) Timothy L Bailey 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
- The Telomere-Binding Protein Tbf1 Demarcates snoRNA Gene Promoters in Saccharomyces cerevisiae
- (2010) Milena Preti et al. MOLECULAR CELL
- De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis
- (2010) Valentina Boeva et al. NUCLEIC ACIDS RESEARCH
- On the detection and refinement of transcription factor binding sites using ChIP-Seq data
- (2010) Ming Hu et al. NUCLEIC ACIDS RESEARCH
- MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites
- (2010) Christoph D. Schmid et al. PLoS One
- Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
- (2010) Elizabeth G. Wilbanks et al. PLoS One
- Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
- (2010) D. Schmidt et al. SCIENCE
- Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans
- (2010) R. McDaniell et al. SCIENCE
- A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression
- (2010) Kenzie D. MacIsaac et al. PLoS Computational Biology
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson 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
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- BayesPeak: Bayesian analysis of ChIP-seq data
- (2009) Christiana Spyrou et al. BMC BIOINFORMATICS
- A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
- (2009) Teemu D Laajala et al. BMC GENOMICS
- Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
- (2009) Philippe Lefrançois et al. BMC GENOMICS
- Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder
- (2009) A. A. Sharov et al. DNA RESEARCH
- Genomic location analysis by ChIP-Seq
- (2009) Artem Barski et al. JOURNAL OF CELLULAR BIOCHEMISTRY
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
- (2009) Joel Rozowsky et al. NATURE BIOTECHNOLOGY
- Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
- (2009) Jay R Hesselberth et al. NATURE METHODS
- Computation for ChIP-seq and RNA-seq studies
- (2009) Shirley Pepke et al. NATURE METHODS
- ChIP–seq: advantages and challenges of a maturing technology
- (2009) Peter J. Park NATURE REVIEWS GENETICS
- Extracting transcription factor targets from ChIP-Seq data
- (2009) Geetu Tuteja et al. NUCLEIC ACIDS RESEARCH
- The UCSC Genome Browser database: update 2010
- (2009) B. Rhead et al. NUCLEIC ACIDS RESEARCH
- MEME SUITE: tools for motif discovery and searching
- (2009) T. L. Bailey et al. NUCLEIC ACIDS RESEARCH
- Impact of Chromatin Structures on DNA Processing for Genomic Analyses
- (2009) Leonid Teytelman et al. PLoS One
- Mapping accessible chromatin regions using Sono-Seq
- (2009) R. K. Auerbach et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
- (2009) Christoph Bock et al. GENOME BIOLOGY
- A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
- (2009) Desmond S Lun et al. GENOME BIOLOGY
- A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
- (2009) Cizhong Jiang et al. GENOME BIOLOGY
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- F-Seq: a feature density estimator for high-throughput sequence tags
- (2008) A. P. Boyle et al. BIOINFORMATICS
- An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
- (2008) Han Xu et al. BIOINFORMATICS
- CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data
- (2008) M. Cesaroni et al. BIOINFORMATICS
- FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
- (2008) A. P. Fejes et al. BIOINFORMATICS
- Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
- (2008) David A Nix et al. BMC BIOINFORMATICS
- Dynamic Regulation of Nucleosome Positioning in the Human Genome
- (2008) Dustin E. Schones et al. CELL
- The DNA-encoded nucleosome organization of a eukaryotic genome
- (2008) Noam Kaplan et al. NATURE
- 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
- Combinatorial patterns of histone acetylations and methylations in the human genome
- (2008) Zhibin Wang et al. NATURE GENETICS
- Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
- (2008) Anton Valouev et al. NATURE METHODS
- A universal classification of eukaryotic transposable elements implemented in Repbase
- (2008) Vladimir V. Kapitonov et al. NATURE REVIEWS GENETICS
- Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
- (2008) R. Jothi et al. NUCLEIC ACIDS RESEARCH
- Ensembl 2009
- (2008) T. J. P. Hubbard et al. NUCLEIC ACIDS RESEARCH
- Modeling ChIP Sequencing In Silico with Applications
- (2008) Zhengdong D. Zhang et al. PLoS Computational Biology
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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