ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
Authors
Keywords
-
Journal
NATURE BIOTECHNOLOGY
Volume 33, Issue 4, Pages 395-401
Publisher
Springer Nature
Online
2015-03-09
DOI
10.1038/nbt.3121
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Identification of transcription factor binding sites from ChIP-seq data at high resolution
- (2013) Anaïs F. Bardet et al. BIOINFORMATICS
- Q&A: A lateral thinker
- (2013) NATURE
- DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale
- (2013) Tianyin Zhou et al. NUCLEIC ACIDS RESEARCH
- TFBSshape: a motif database for DNA shape features of transcription factor binding sites
- (2013) Lin Yang et al. NUCLEIC ACIDS RESEARCH
- 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
- Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape
- (2013) Raluca Gordân et al. Cell Reports
- Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties
- (2013) Aurelien A Serandour et al. GENOME BIOLOGY
- Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers
- (2012) Kuangyu Yen et al. CELL
- Genome-wide structure and organization of eukaryotic pre-initiation complexes
- (2012) Ho Sung Rhee et al. NATURE
- Identifying ChIP-seq enrichment using MACS
- (2012) Jianxing Feng et al. Nature Protocols
- Transcription factors: from enhancer binding to developmental control
- (2012) François Spitz et al. NATURE REVIEWS GENETICS
- Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
- (2011) Ho Sung Rhee et al. CELL
- High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
- (2011) A. Ozdemir et al. GENOME RESEARCH
- High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
- (2011) Qiye He et al. NATURE GENETICS
- Counting absolute numbers of molecules using unique molecular identifiers
- (2011) Teemu Kivioja et al. NATURE METHODS
- A method for counting PCR template molecules with application to next-generation sequencing
- (2011) J. A. Casbon et al. NUCLEIC ACIDS RESEARCH
- Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo
- (2010) Walid D Fakhouri et al. Molecular Systems Biology
- iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
- (2010) Julian König et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
- (2010) Lihua Julie Zhu et al. NUCLEIC ACIDS RESEARCH
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- The role of DNA shape in protein–DNA recognition
- (2009) Remo Rohs et al. NATURE
- Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
- (2009) Jay R Hesselberth et al. NATURE METHODS
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk 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