Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon

Non-canonical protein-DNA interactions identified by ChIP are not artifacts

(2013) Richard P Bonocora et al.   BMC GENOMICS

Database resources for the tuberculosis community

(2013) Jocelyne M. Lew et al.   TUBERCULOSIS

FRUIT, a Scar-Free System for Targeted Chromosomal Mutagenesis, Epitope Tagging, and Promoter Replacement in Escherichia coli and Salmonella enterica

(2012) Anne M. Stringer et al.   PLoS One

RNIE: genome-wide prediction of bacterial intrinsic terminators

(2011) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

WebGeSTer DB—a transcription terminator database

(2010) Anirban Mitra et al.   NUCLEIC ACIDS RESEARCH

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

Regulation of Arabinose and Xylose Metabolism in Escherichia coli

(2009) T. A. Desai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolution of Transcriptional Regulatory Circuits in Bacteria

(2009) J. Christian Perez et al.   CELL

Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome

(2009) T. Jarvik et al.   JOURNAL OF BACTERIOLOGY

Furanose-specific Sugar Transport

(2009) Richard S. P. Horler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Evolution of a Bacterial Regulon Controlling Virulence and Mg2+ Homeostasis

(2009) J. Christian Perez et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Technical considerations in using DNA microarrays to define regulons

(2008) Virgil A. Rhodius et al.   METHODS

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

(2008) Tomohiro Shimada et al.   NUCLEIC ACIDS RESEARCH