标题
Analysis of computational footprinting methods for DNase sequencing experiments
作者
关键词
-
出版物
NATURE METHODS
Volume 13, Issue 4, Pages 303-309
出版商
Springer Nature
发表日期
2016-02-23
DOI
10.1038/nmeth.3772
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data
- (2015) Juhani Kähärä et al. BIOINFORMATICS
- The difficulty of a fair comparison
- (2015) NATURE METHODS
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications
- (2014) Eduardo G. Gusmao et al. BIOINFORMATICS
- DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence
- (2014) Myong-Hee Sung et al. MOLECULAR CELL
- Transient Estrogen Receptor Binding and p300 Redistribution Support a Squelching Mechanism for Estradiol-Repressed Genes
- (2014) Michael J. Guertin et al. MOLECULAR ENDOCRINOLOGY
- Conservation of trans-acting circuitry during mammalian regulatory evolution
- (2014) Andrew B. Stergachis et al. NATURE
- Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
- (2014) Richard I Sherwood et al. NATURE BIOTECHNOLOGY
- Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
- (2014) Clifford A. Meyer et al. NATURE REVIEWS GENETICS
- Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
- (2014) Galip Gürkan Yardımcı et al. NUCLEIC ACIDS RESEARCH
- Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
- (2013) Housheng Hansen He et al. NATURE METHODS
- Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data
- (2013) Jason Piper et al. NUCLEIC ACIDS RESEARCH
- JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
- (2013) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
- (2013) L. Teytelman et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Probing DNA shape and methylation state on a genomic scale with DNase I
- (2013) A. Lazarovici et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
- (2013) Hirotaka Nakahashi et al. Cell Reports
- An expansive human regulatory lexicon encoded in transcription factor footprints
- (2012) Shane Neph et al. NATURE
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
- (2012) Alok K Tewari et al. GENOME BIOLOGY
- Epigenetic priors for identifying active transcription factor binding sites
- (2011) Gabriel Cuellar-Partida et al. BIOINFORMATICS
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
- (2011) Sam John et al. NATURE GENETICS
- An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression
- (2010) Jindan Yu et al. CANCER CELL
- High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
- (2010) A. P. Boyle et al. GENOME RESEARCH
- Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
- (2010) R. Pique-Regi et al. GENOME RESEARCH
- Heterodimerization with Different Jun Proteins Controls c-Fos Intranuclear Dynamics and Distribution
- (2010) Cécile E. Malnou et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
- (2010) K. Robasky et al. NUCLEIC ACIDS RESEARCH
- MOODS: fast search for position weight matrix matches in DNA sequences
- (2009) J. Korhonen et al. BIOINFORMATICS
- Biopython: freely available Python tools for computational molecular biology and bioinformatics
- (2009) P. J. A. Cock et al. BIOINFORMATICS
- Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
- (2009) Bartek Wilczynski et al. BMC BIOINFORMATICS
- Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
- (2009) Jay R Hesselberth et al. NATURE METHODS
- ChIP–seq: advantages and challenges of a maturing technology
- (2009) Peter J. Park NATURE REVIEWS GENETICS
- F-Seq: a feature density estimator for high-throughput sequence tags
- (2008) A. P. Boyle et al. BIOINFORMATICS
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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