Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

(2010) Mazhar Adli et al.   NATURE METHODS

Efficient Double Fragmentation ChIP-seq Provides Nucleotide Resolution Protein-DNA Binding Profiles

(2010) Michal Mokry et al.   PLoS One

Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

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

Visualization of genomic data with the Hilbert curve

(2009) S. Anders   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast genomic μChIP-chip from 1,000 cells

(2009) John Arne Dahl et al.   GENOME BIOLOGY

Poised RNA Polymerase II Gives Pause for Thought

(2008) Thanasis Margaritis et al.   CELL

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

(2008) Xi Chen et al.   CELL

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Messenger RNA regulation: to translate or to degrade

(2008) Ann-Bin Shyu et al.   EMBO JOURNAL

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Genome-Wide Pattern of TCF7L2/TCF4 Chromatin Occupancy in Colorectal Cancer Cells

(2008) P. Hatzis et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

A rapid micro chromatin immunoprecipitation assay (ChIP)

(2008) John Arne Dahl et al.   Nature Protocols

μChIP—a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies

(2008) John Arne Dahl et al.   NUCLEIC ACIDS RESEARCH

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE