FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

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

(2013) Warren A. Whyte et al.   CELL

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

(2013) Ilaria Mogno et al.   GENOME RESEARCH

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

(2013) Stephen S Gisselbrecht et al.   NATURE METHODS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

(2012) Chih-yu Chen et al.   BMC GENOMICS

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

CTCF: insights into insulator function during development

(2012) M. Herold et al.   DEVELOPMENT

PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes

(2012) Zhonghua Gao et al.   MOLECULAR CELL

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Structure and function of active chromatin and DNase I hypersensitive sites

(2011) Peter N. Cockerill   FEBS Journal

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Quantification of lentiviral vector copy numbers in individual hematopoietic colony-forming cells shows vector dose-dependent effects on the frequency and level of transduction

(2010) S Charrier et al.   GENE THERAPY

Sequence features that drive human promoter function and tissue specificity

(2010) J. M. Landolin et al.   GENOME RESEARCH

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Functional cis-regulatory genomics for systems biology

(2010) Jongmin Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

MEME SUITE: tools for motif discovery and searching

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

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

(2008) Xi Chen et al.   CELL

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions

(2008) M. Yaragatti et al.   GENOME RESEARCH