ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

(2016) Maud de Dieuleveult et al.   NATURE

An interactive environment for agile analysis and visualization of ChIP-sequencing data

(2016) Mads Lerdrup et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

An interactive environment for agile analysis and visualization of ChIP-sequencing data

(2016) Mads Lerdrup et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters

(2016) Christopher A. Lavender et al.   PLoS Genetics

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

(2015) Lucy H. Williams et al.   MOLECULAR CELL

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

An integrated ChIP-seq analysis platform with customizable workflows

(2011) Eugenia G Giannopoulou et al.   BMC BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

GeneProf: analysis of high-throughput sequencing experiments

(2011) Florian Halbritter et al.   NATURE METHODS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells

(2009) Yasuto Araki et al.   IMMUNITY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY