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。T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets
Yuanyuan Li et al.
BMC GENOMICS (2014)
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
Li Shen et al.
BMC GENOMICS (2014)
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
Anthony Mathelier et al.
NUCLEIC ACIDS RESEARCH (2014)
deepTools: a flexible platform for exploring deep-sequencing data
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2014)
Universal Count Correction for High-Throughput Sequencing
Tatsunori B. Hashimoto et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS
Yajie Yang et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2014)
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data
Haitham Ashoor et al.
BIOINFORMATICS (2013)
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
Parameswaran Ramachandran et al.
BIOINFORMATICS (2013)
Identification of transcription factor binding sites from ChIP-seq data at high resolution
Anais F. Bardet et al.
BIOINFORMATICS (2013)
QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions
Bin Liu et al.
BMC GENOMICS (2013)
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdottir et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Uniform, optimal signal processing of mapped deep-sequencing data
Vibhor Kumar et al.
NATURE BIOTECHNOLOGY (2013)
diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Li Shen et al.
PLOS ONE (2013)
jMOSAiCS: joint analysis of multiple ChIP-seq datasets
Xin Zeng et al.
GENOME BIOLOGY (2013)
Combining multiple ChIP-seq peak detection systems using combinatorial fusion
Christina Schweikert et al.
BMC GENOMICS (2012)
Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Dominic Schmidt et al.
CELL (2012)
Predicting cell-type-specific gene expression from regions of open chromatin
Anirudh Natarajan et al.
GENOME RESEARCH (2012)
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt et al.
GENOME RESEARCH (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham et al.
NATURE (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Summarizing and correcting the GC content bias in high-throughput sequencing
Yuval Benjamini et al.
NUCLEIC ACIDS RESEARCH (2012)
Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
Haipeng Xing et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS
Qunhua Li et al.
ANNALS OF APPLIED STATISTICS (2011)
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
Joseph K. Pickrell et al.
BIOINFORMATICS (2011)
Identifying dispersed epigenomic domains from ChIP-Seq data
Qiang Song et al.
BIOINFORMATICS (2011)
FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
BIOINFORMATICS (2011)
PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Xin Feng et al.
BMC BIOINFORMATICS (2011)
Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts
Adam M. Szalkowski et al.
BRIEFINGS IN BIOINFORMATICS (2011)
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
Qiye He et al.
NATURE GENETICS (2011)
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
Morten Beck Rye et al.
NUCLEIC ACIDS RESEARCH (2011)
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Naim U. Rashid et al.
GENOME BIOLOGY (2011)
A signal-noise model for significance analysis of ChIP-seq with negative control
Han Xu et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Genetic analysis of variation in transcription factor binding in yeast
Wei Zheng et al.
NATURE (2010)
Variation in Transcription Factor Binding Among Humans
Maya Kasowski et al.
SCIENCE (2010)
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
Dominic Schmidt et al.
SCIENCE (2010)
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Mei Zhong et al.
PLOS GENETICS (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
A transcription factor affinity-based code for mammalian transcription initiation
Molly Megraw et al.
GENOME RESEARCH (2009)
Computation for ChIP-seq and RNA-seq studies
Shirley Pepke et al.
NATURE METHODS (2009)
Extracting transcription factor targets from ChIP-Seq data
Geetu Tuteja et al.
NUCLEIC ACIDS RESEARCH (2009)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
A chromatin landmark and transcription initiation at most promoters in human cells
Matthew G. Guenther et al.
CELL (2007)
Genome-wide mapping of in vivo protein-DNA interactions
David S. Johnson et al.
SCIENCE (2007)
A method for selecting the bin size of a time histogram
Hideaki Shimazaki et al.
NEURAL COMPUTATION (2007)
Drosophila DNase I footprint database:: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
CM Bergman et al.
BIOINFORMATICS (2005)