Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
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Title
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
Authors
Keywords
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Journal
NATURE REVIEWS GENETICS
Volume 15, Issue 11, Pages 709-721
Publisher
Springer Nature
Online
2014-09-16
DOI
10.1038/nrg3788
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Note: Only part of the references are listed.- Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
- (2014) N. Bonhoure et al. GENOME RESEARCH
- Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
- (2014) Richard I Sherwood et al. NATURE BIOTECHNOLOGY
- Impact of sequencing depth in ChIP-seq experiments
- (2014) Youngsook L. Jung et al. NUCLEIC ACIDS RESEARCH
- Universal Count Correction for High-Throughput Sequencing
- (2014) Tatsunori B. Hashimoto et al. PLoS Computational Biology
- BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets
- (2013) Jianrong Wang et al. BIOINFORMATICS
- Uniform, optimal signal processing of mapped deep-sequencing data
- (2013) Vibhor Kumar et al. NATURE BIOTECHNOLOGY
- Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH
- (2013) Jeff Vierstra et al. NATURE METHODS
- Predicting the molecular complexity of sequencing libraries
- (2013) Timothy Daley et al. NATURE METHODS
- Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
- (2013) Housheng Hansen He et al. NATURE METHODS
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
- (2013) Simon Anders et al. Nature Protocols
- Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data
- (2013) Jason Piper 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
- Identification of Genetic Variants That Affect Histone Modifications in Human Cells
- (2013) G. McVicker et al. SCIENCE
- Cancer Genome Landscapes
- (2013) B. Vogelstein et al. SCIENCE
- Large-Scale Quality Analysis of Published ChIP-seq Data
- (2013) Georgi K. Marinov et al. G3-Genes Genomes Genetics
- dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
- (2013) Dongjun Chung et al. PLoS Computational Biology
- Bayesian Inference of Spatial Organizations of Chromosomes
- (2013) Ming Hu et al. PLoS Computational Biology
- Systematic biases in DNA copy number originate from isolation procedures
- (2013) Sebastiaan van Heesch et al. GENOME BIOLOGY
- HiCNorm: removing biases in Hi-C data via Poisson regression
- (2012) Ming Hu et al. BIOINFORMATICS
- RSeQC: quality control of RNA-seq experiments
- (2012) Liguo Wang et al. BIOINFORMATICS
- RNA-SeQC: RNA-seq metrics for quality control and process optimization
- (2012) David S. DeLuca et al. BIOINFORMATICS
- The sva package for removing batch effects and other unwanted variation in high-throughput experiments
- (2012) Jeffrey T. Leek et al. BIOINFORMATICS
- Removing technical variability in RNA-seq data using conditional quantile normalization
- (2012) K. D. Hansen et al. BIOSTATISTICS
- Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
- (2012) Jesse Dabney et al. BIOTECHNIQUES
- The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
- (2012) Karl Kornacker et al. BMC BIOINFORMATICS
- Limitations and possibilities of low cell number ChIP-seq
- (2012) Gregor D Gilfillan et al. BMC GENOMICS
- A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
- (2012) M.-A. Dillies et al. BRIEFINGS IN BIOINFORMATICS
- 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
- Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- (2012) J. Wang 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
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Technical considerations for functional sequencing assays
- (2012) Weihua Zeng et al. NATURE IMMUNOLOGY
- Systematic evaluation of factors influencing ChIP-seq fidelity
- (2012) Yiwen Chen et al. NATURE METHODS
- Iterative correction of Hi-C data reveals hallmarks of chromosome organization
- (2012) Maxim Imakaev et al. NATURE METHODS
- Unsupervised pattern discovery in human chromatin structure through genomic segmentation
- (2012) Michael M Hoffman et al. NATURE METHODS
- Dfam: a database of repetitive DNA based on profile hidden Markov models
- (2012) Travis J. Wheeler et al. NUCLEIC ACIDS RESEARCH
- Summarizing and correcting the GC content bias in high-throughput sequencing
- (2012) Yuval Benjamini et al. NUCLEIC ACIDS RESEARCH
- Fast Computation and Applications of Genome Mappability
- (2012) Thomas Derrien et al. PLoS One
- Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"
- (2012) J. K. Pickrell et al. SCIENCE
- Rapid genome-scale mapping of chromatin accessibility in tissue
- (2012) Lars Grøntved et al. Epigenetics & Chromatin
- Controls of Nucleosome Positioning in the Human Genome
- (2012) Daniel J. Gaffney et al. PLoS Genetics
- CHANCE: comprehensive software for quality control and validation of ChIP-seq data
- (2012) Aaron Diaz et al. GENOME BIOLOGY
- MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
- (2012) Zhen Shao et al. GENOME BIOLOGY
- Surveying the epigenomic landscape, one base at a time
- (2012) Gabriel E Zentner et al. GENOME BIOLOGY
- False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
- (2011) Joseph K. Pickrell et al. BIOINFORMATICS
- Identifying dispersed epigenomic domains from ChIP-Seq data
- (2011) Qiang Song et al. BIOINFORMATICS
- Detecting differential binding of transcription factors with ChIP-seq
- (2011) Kun Liang et al. BIOINFORMATICS
- htSeqTools: high-throughput sequencing quality control, processing and visualization in R
- (2011) Evarist Planet et al. BIOINFORMATICS
- ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
- (2011) Joshua WK Ho et al. BMC GENOMICS
- AlleleSeq: analysis of allele-specific expression and binding in a network framework
- (2011) J. Rozowsky et al. Molecular Systems Biology
- Determinants of nucleosome organization in primary human cells
- (2011) Anton Valouev et al. NATURE
- ChIP-Seq: technical considerations for obtaining high-quality data
- (2011) Benjamin L Kidder et al. NATURE IMMUNOLOGY
- Epigenome characterization at single base-pair resolution
- (2011) J. G. Henikoff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
- (2011) Naim U Rashid et al. GENOME BIOLOGY
- SAMStat: monitoring biases in next generation sequencing data
- (2010) T. Lassmann et al. BIOINFORMATICS
- A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data
- (2010) Xiaoyu Chen et al. BIOINFORMATICS
- Discovering homotypic binding events at high spatial resolution
- (2010) Yuchun Guo et al. BIOINFORMATICS
- PICS: Probabilistic Inference for ChIP-seq
- (2010) Xuekui Zhang et al. BIOMETRICS
- 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
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- Understanding mechanisms underlying human gene expression variation with RNA sequencing
- (2010) Joseph K. Pickrell et al. NATURE
- Discovery and characterization of chromatin states for systematic annotation of the human genome
- (2010) Jason Ernst et al. NATURE BIOTECHNOLOGY
- Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks
- (2010) Xionglei He et al. NATURE GENETICS
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- Tackling the widespread and critical impact of batch effects in high-throughput data
- (2010) Jeffrey T. Leek et al. NATURE REVIEWS GENETICS
- iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
- (2010) Julian König et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
- (2010) Desiree Tillo et al. PLoS One
- The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data
- (2010) Ho-Ryun Chung et al. PLoS One
- Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation
- (2010) X. Fan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes
- (2010) Andreas Ruepp et al. GENOME BIOLOGY
- Estimating enrichment of repetitive elements from high-throughput sequence data
- (2010) Daniel S Day et al. GENOME BIOLOGY
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
- (2009) Jacob F. Degner et al. BIOINFORMATICS
- A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
- (2009) Chongzhi Zang et al. BIOINFORMATICS
- SOAP2: an improved ultrafast tool for short read alignment
- (2009) R. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data
- (2009) Héctor Corrada Bravo et al. BIOMETRICS
- Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
- (2009) Paul G. Giresi et al. METHODS
- An oestrogen-receptor-α-bound human chromatin interactome
- (2009) Melissa J. Fullwood et al. NATURE
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
- (2009) Joel Rozowsky et al. NATURE BIOTECHNOLOGY
- Personalized copy number and segmental duplication maps using next-generation sequencing
- (2009) Can Alkan et al. NATURE GENETICS
- 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
- Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
- (2009) Yong Zhang et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Impact of Chromatin Structures on DNA Processing for Genomic Analyses
- (2009) Leonid Teytelman et al. PLoS One
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- 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
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
- (2008) H. Li et al. GENOME RESEARCH
- 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
- Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
- (2008) Anton Valouev et al. NATURE METHODS
- The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome
- (2008) Yutao Fu et al. PLoS Genetics
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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