A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design

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

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

(2011) Aaron W. Aday et al.   DEVELOPMENTAL BIOLOGY

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

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

(2011) Jason Ernst et al.   NATURE

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

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

(2011)   PLOS BIOLOGY

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Synthetic design of strong promoters

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

A systematic approach to identify functional motifs within vertebrate developmental enhancers

(2009) Qiang Li et al.   DEVELOPMENTAL BIOLOGY

Functional autonomy of distant-acting human enhancers

(2009) Axel Visel et al.   GENOMICS

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

(2009) Nathaniel D. Heintzman et al.   NATURE

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

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors

(2008) Sarah De Val et al.   CELL

Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli

(2008) J. Y. Lee et al.   NUCLEIC ACIDS RESEARCH

The Sphingolipid Transporter Spns2 Functions in Migration of Zebrafish Myocardial Precursors

(2008) A. Kawahara et al.   SCIENCE