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

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

(2013) C. D. Arnold et al.   SCIENCE

Principal component analysis reveals gender-specific predictors of cardiometabolic risk in 6th graders

(2012) Mark D Peterson et al.   Cardiovascular Diabetology

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner 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

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

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

(2012) Tali Raveh-Sadka et al.   NATURE GENETICS

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

(2011) Aaron T. Spivak et al.   NUCLEIC ACIDS RESEARCH

TAL Effectors: Customizable Proteins for DNA Targeting

(2011) A. J. Bogdanove et al.   SCIENCE

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

TATA is a modular component of synthetic promoters

(2010) I. Mogno et al.   GENOME RESEARCH

Environment-specific combinatorial cis-regulation in synthetic promoters

(2009) Jason Gertz et al.   Molecular Systems Biology

The incoherent feed-forward loop can generate non-monotonic input functions for genes

(2008) Shai Kaplan et al.   Molecular Systems Biology

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE