MAnorm2 for quantitatively comparing groups of ChIP-seq samples

Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

(2019) Guoqiang Yi et al.   Cell Reports

The Open Chromatin Landscape of Non-small Cell Lung Carcinoma

(2019) Zhoufeng Wang et al.   CANCER RESEARCH

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia

(2018) Christopher J. Ott et al.   CANCER CELL

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation

(2016) Ryuichiro Nakato et al.   BRIEFINGS IN BIOINFORMATICS

A comprehensive comparison of tools for differential ChIP-seq analysis

(2016) Sebastian Steinhauser et al.   BRIEFINGS IN BIOINFORMATICS

Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles

(2016) Paloma Cejas et al.   NATURE MEDICINE

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets

(2015) Li Chen et al.   BIOINFORMATICS

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Enhancer Sequence Variants and Transcription-Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B-Cell Lymphoma

(2015) Olivia I. Koues et al.   IMMUNITY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data

(2014) Yanxiao Zhang et al.   BIOINFORMATICS

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines

(2014) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

(2012) Jian Xu et al.   DEVELOPMENTAL CELL

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments

(2011) M. j. Nueda et al.   BIOSTATISTICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY