ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
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Title
ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
Authors
Keywords
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Journal
NATURE REVIEWS GENETICS
Volume 13, Issue 12, Pages 840-852
Publisher
Springer Nature
Online
2012-10-23
DOI
10.1038/nrg3306
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Note: Only part of the references are listed.- A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data
- (2012) Vanessa M. Kvam et al. AMERICAN JOURNAL OF BOTANY
- Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments
- (2012) Ekaterina E Khrameeva et al. BMC BIOINFORMATICS
- A Census of Human Soluble Protein Complexes
- (2012) Pierre C. Havugimana et al. CELL
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- (2012) Guoliang Li et al. CELL
- Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
- (2012) Aaron L. Statham et al. GENOME RESEARCH
- Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
- (2012) Arie B. Brinkman et al. GENOME RESEARCH
- Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics
- (2012) Housheng Hansen He et al. GENOME RESEARCH
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- (2012) S. G. Landt et al. GENOME RESEARCH
- An expansive human regulatory lexicon encoded in transcription factor footprints
- (2012) Shane Neph et al. NATURE
- DNase I sensitivity QTLs are a major determinant of human expression variation
- (2012) Jacob F. Degner et al. NATURE
- Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function
- (2012) Colin R. Lickwar et al. NATURE
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman et al. NATURE
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Systematic evaluation of factors influencing ChIP-seq fidelity
- (2012) Yiwen Chen et al. NATURE METHODS
- Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA
- (2012) Jeremy M Simon et al. Nature Protocols
- Summarizing and correcting the GC content bias in high-throughput sequencing
- (2012) Yuval Benjamini 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
- Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes
- (2012) Stephen C. J. Parker et al. PLoS Genetics
- Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo
- (2012) Michael J. Guertin et al. PLoS Genetics
- Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
- (2012) Yoichiro Shibata et al. PLoS Genetics
- A Protein Complex Network of Drosophila melanogaster
- (2011) K.G. Guruharsha et al. CELL
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- (2011) Ho Sung Rhee et al. CELL
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- (2011) Peter N. Cockerill FEBS Journal
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- (2011) W. Wu et al. GENOME RESEARCH
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- (2011) L. Song et al. GENOME RESEARCH
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- (2011) C. S. Ku et al. JOURNAL OF MEDICAL GENETICS
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- (2011) J. Rozowsky et al. Molecular Systems Biology
- Single-tube linear DNA amplification (LinDA) for robust ChIP-seq
- (2011) Pattabhiraman Shankaranarayanan et al. NATURE METHODS
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- (2011) Eda Yildirim et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Sequence-specific error profile of Illumina sequencers
- (2011) Kensuke Nakamura 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
- Database resources of the National Center for Biotechnology Information
- (2011) E. W. Sayers et al. NUCLEIC ACIDS RESEARCH
- Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads
- (2011) Schraga Schwartz et al. PLoS One
- Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data
- (2011) Brandon M. Malone et al. PLoS One
- A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function
- (2011) Jared M Bischof et al. THORAX
- Overcoming bias and systematic errors in next generation sequencing data
- (2011) Margaret A Taub et al. Genome Medicine
- Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
- (2011) Dongjun Chung et al. PLoS Computational Biology
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- (2011) Chao Cheng et al. PLoS Computational Biology
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- (2011) Hironori Waki et al. PLoS Genetics
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- (2011) Jason Gertz et al. PLoS Genetics
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- (2011) Luca Magnani et al. PLoS Genetics
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- (2011) André E Minoche et al. GENOME BIOLOGY
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- (2010) I. V. Kulakovskiy et al. BIOINFORMATICS
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- (2010) Jianrong Wang et al. BIOINFORMATICS
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- (2010) T. D. Wu et al. BIOINFORMATICS
- A survey of sequence alignment algorithms for next-generation sequencing
- (2010) H. Li et al. BRIEFINGS IN BIOINFORMATICS
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- (2010) Michael L. Stitzel et al. Cell Metabolism
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- (2010) Valentina Boeva et al. NUCLEIC ACIDS RESEARCH
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- (2010) Elizabeth G. Wilbanks et al. PLoS One
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- (2010) R. McDaniell et al. SCIENCE
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- (2010) Song Wu et al. Theoretical Biology and Medical Modelling
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- (2010) Guoliang Li et al. GENOME BIOLOGY
- Evidence-ranked motif identification
- (2010) Stoyan Georgiev et al. GENOME BIOLOGY
- A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
- (2009) Teemu D Laajala et al. BMC GENOMICS
- High-resolution analysis of epigenetic changes associated with X inactivation
- (2009) H. Marks et al. GENOME RESEARCH
- ChIP-based methods for the identification of long-range chromatin interactions
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- Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
- (2009) Paul G. Giresi et al. METHODS
- Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
- (2009) Jay R Hesselberth et al. NATURE METHODS
- Insights from genomic profiling of transcription factors
- (2009) Peggy J. Farnham NATURE REVIEWS GENETICS
- ChIP–seq: advantages and challenges of a maturing technology
- (2009) Peter J. Park NATURE REVIEWS GENETICS
- Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome
- (2009) Folkert J van Werven et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
- (2009) L. A. Hindorff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Proteome Organization in a Genome-Reduced Bacterium
- (2009) S. Kuhner et al. SCIENCE
- Diversity and Complexity in DNA Recognition by Transcription Factors
- (2009) G. Badis et al. SCIENCE
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
- (2009) Pingzhao Hu et al. PLOS BIOLOGY
- Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq
- (2009) Mehdi Motallebipour et al. GENOME BIOLOGY
- CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features
- (2009) Kobby Essien et al. GENOME BIOLOGY
- High-Resolution Mapping and Characterization of Open Chromatin across the Genome
- (2008) Alan P. Boyle et al. CELL
- Design and analysis of ChIP-seq experiments for DNA-binding proteins
- (2008) Peter V Kharchenko et al. NATURE BIOTECHNOLOGY
- Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
- (2008) Anton Valouev et al. NATURE METHODS
- UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
- (2008) D. E. Newburger et al. NUCLEIC ACIDS RESEARCH
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