SutA is a bacterial transcription factor expressed during slow growth inPseudomonas aeruginosa

Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum

(2015) Sebastian H. Kopf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation

(2015) Elise S. Cowley et al.   mBio

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture

(2014) John D. Bagert et al.   MOLECULAR & CELLULAR PROTEOMICS

DksA Guards Elongating RNA Polymerase against Ribosome-Stalling-Induced Arrest

(2014) Yan Zhang et al.   MOLECULAR CELL

Phenazine redox cycling enhances anaerobic survival inPseudomonas aeruginosaby facilitating generation of ATP and a proton-motive force

(2014) Nathaniel R. Glasser et al.   MOLECULAR MICROBIOLOGY

Biogeochemical Forces Shape the Composition and Physiology of Polymicrobial Communities in the Cystic Fibrosis Lung

(2014) R. A. Quinn et al.   mBio

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Bacterial Community Morphogenesis Is Intimately Linked to the Intracellular Redox State

(2013) L. E. P. Dietrich et al.   JOURNAL OF BACTERIOLOGY

A Proximal Promoter Element Required for Positive Transcriptional Control by Guanosine Tetraphosphate and DksA Protein during the Stringent Response

(2013) Bertil Gummesson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of secreted bacterial proteins by noncanonical amino acid tagging

(2013) A. Mahdavi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

easyRNASeq: a bioconductor package for processing RNA-Seq data

(2012) N. Delhomme et al.   BIOINFORMATICS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

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

(2012) Omri Wurtzel et al.   PLoS Pathogens

Genome-wide detection of novel regulatory RNAs in E. coli

(2011) R. Raghavan et al.   GENOME RESEARCH

Transcription Factor GreA Contributes to Resolving Promoter-Proximal Pausing of RNA Polymerase in Bacillus subtilis Cells

(2011) Y. Kusuya et al.   JOURNAL OF BACTERIOLOGY

Role of fimV in type II secretion system-dependent protein secretion of Pseudomonas aeruginosa on solid medium

(2011) G. P. F. Michel et al.   MICROBIOLOGY-SGM

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

(2011) J. J. Lemke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer

(2011) Anastasia Kalli et al.   PROTEOMICS

MochiView: versatile software for genome browsing and DNA motif analysis

(2010) Oliver R Homann et al.   BMC BIOLOGY

The Transcription Factor DksA Prevents Conflicts between DNA Replication and Transcription Machinery

(2010) Ashley K. Tehranchi et al.   CELL

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

(2010) Katharina Trunk et al.   ENVIRONMENTAL MICROBIOLOGY

Cleavable Biotin Probes for Labeling of Biomolecules via Azide−Alkyne Cycloaddition

(2010) Janek Szychowski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Role of a Zn-independent DksA in Zn homeostasis and stringent response

(2010) Crysten E. Blaby-Haas et al.   MOLECULAR MICROBIOLOGY

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

(2010) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

Analysis and Optimization of Copper-Catalyzed Azide–Alkyne Cycloaddition for Bioconjugation

(2009) Vu Hong et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Activation of gene expression by small RNA

(2009) Kathrin S. Fröhlich et al.   CURRENT OPINION IN MICROBIOLOGY

Endogenous Phenazine Antibiotics Promote Anaerobic Survival of Pseudomonas aeruginosa via Extracellular Electron Transfer

(2009) Y. Wang et al.   JOURNAL OF BACTERIOLOGY

Dynamics of Adaptive Microevolution of HypermutablePseudomonas aeruginosaduring Chronic Pulmonary Infection in Patients with Cystic Fibrosis

(2009) Christina Hoboth et al.   JOURNAL OF INFECTIOUS DISEASES

Genetic determinants of Pseudomonas aeruginosa biofilm establishment

(2009) M. Musken et al.   MICROBIOLOGY-SGM

Regulator Trafficking on Bacterial Transcription Units In Vivo

(2009) Rachel A. Mooney et al.   MOLECULAR CELL

Global position analysis of thePseudomonas aeruginosaquorum-sensing transcription factor LasR

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

The long-chain fatty acid sensor, PsrA, modulates the expression ofrpoSand the type III secretionexsCEBAoperon inPseudomonas aeruginosa

(2009) Yun Kang et al.   MOLECULAR MICROBIOLOGY

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY