Measuring cis-regulatory energetics in living cells using allelic manifolds

Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

(2018) Nathan M. Belliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Activity Profile and Context Dependence of All Human 5′ Splice Sites

(2018) Mandy S. Wong et al.   MOLECULAR CELL

Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants

(2018) Tal Einav et al.   PLoS One

Isolation and characterization of novel mutations in the pSC101 origin that increase copy number

(2018) Mitchell G. Thompson et al.   Scientific Reports

Local and global regulation of transcription initiation in bacteria

(2016) Douglas F. Browning et al.   NATURE REVIEWS MICROBIOLOGY

A Simple Grammar Defines Activating and Repressing cis -Regulatory Elements in Photoreceptors

(2016) Michael A. White et al.   Cell Reports

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

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

(2013) Ilaria Mogno et al.   GENOME RESEARCH

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Enhancer-like long-range transcriptional activation by   CI-mediated DNA looping

(2013) L. Cui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activating Transcription in Bacteria

(2012) David J. Lee et al.   Annual Review of Microbiology

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

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

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

Thermodynamic State Ensemble Models of cis-Regulation

(2012) Marc S. Sherman et al.   PLoS Computational Biology

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

(2012) Robert C. Brewster et al.   PLoS Computational Biology

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

Quantitative dissection of the simple repression input-output function

(2011) H. G. Garcia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

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

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE