Predicting the impact of promoter variability on regulatory outputs

Reliable scaling of position weight matrices for binding strength comparisons between transcription factors

(2015) Xiaoyan Ma et al.   BMC BIOINFORMATICS

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

Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

(2014) M Razo-Mejia et al.   PHYSICAL BIOLOGY

Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes

(2014) Alinne P. de Castro et al.   Frontiers in Microbiology

Ligand-Enhanced Abiotic Iron Oxidation and the Effects of Chemical versus Biological Iron Cycling in Anoxic Environments

(2013) Sebastian H. Kopf et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

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

(2013) Robin P Smith et al.   NATURE GENETICS

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal

(2013) Jonathan S. Z. Aow et al.   NUCLEIC ACIDS RESEARCH

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

(2013) James Q Boedicker et al.   PHYSICAL BIOLOGY

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Ferrous Iron Is a Significant Component of Bioavailable Iron in Cystic Fibrosis Airways

(2013) R. C. Hunter et al.   mBio

Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic

(2013) Ah-Ram Kim et al.   PLoS Genetics

Activating Transcription in Bacteria

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

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Sequence-dependent sliding kinetics of p53

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

Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria

(2012) Hernan G. Garcia et al.   Cell Reports

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

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

The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

(2012) Omri Wurtzel et al.   PLoS Pathogens

Quorum Sensing in Chromobacterium violaceum: DNA Recognition and Gene Regulation by the CviR Receptor

(2011) D. L. Stauff et al.   JOURNAL OF BACTERIOLOGY

BqsR/BqsS Constitute a Two-Component System That Senses Extracellular Fe(II) in Pseudomonas aeruginosa

(2011) N. N. K. Kreamer et al.   JOURNAL OF BACTERIOLOGY

Analysis of the Pseudomonas aeruginosa Regulon Controlled by the Sensor Kinase KinB and Sigma Factor RpoN

(2011) F. H. Damron et al.   JOURNAL OF BACTERIOLOGY

Accurate Prediction of Gene Expression by Integration of DNA Sequence Statistics with Detailed Modeling of Transcription Regulation

(2010) Jose M.G. Vilar   BIOPHYSICAL JOURNAL

Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons

(2010) Katharina Trunk et al.   ENVIRONMENTAL MICROBIOLOGY

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu 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

Global position analysis of thePseudomonas aeruginosaquorum-sensing transcription factor LasR

(2009) Kerrigan B. Gilbert et al.   MOLECULAR MICROBIOLOGY

Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa

(2009) Zhe-Xian Tian et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

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

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE