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

STAR: an integrated solution to management and visualization of sequencing data

(2013) T. Wang et al.   BIOINFORMATICS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation and Hydroxymethylation in Reprogramming

(2013) Yawei Gao et al.   Cell Stem Cell

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

A brief introduction to web-based genome browsers

(2012) J. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Spark: A navigational paradigm for genomic data exploration

(2012) C. B. Nielsen et al.   GENOME RESEARCH

Morphine Epigenomically Regulates Behavior through Alterations in Histone H3 Lysine 9 Dimethylation in the Nucleus Accumbens

(2012) H. Sun et al.   JOURNAL OF NEUROSCIENCE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

(2012) Aurélien A. Sérandour et al.   NUCLEIC ACIDS RESEARCH

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

(2011) Kian Peng Koh et al.   Cell Stem Cell

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

(2011) Yufei Xu et al.   MOLECULAR CELL

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

(2011) Hao Wu et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach et al.   PLoS Genetics

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

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

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Essential Role of the Histone Methyltransferase G9a in Cocaine-Induced Plasticity

(2010) I. Maze et al.   SCIENCE

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

(2009) F. Tie et al.   DEVELOPMENT

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY