Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

Bacterial RNA polymerase can retain σ70throughout transcription

(2016) Timothy T. Harden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane inEscherichia coli

(2015) Matthias Urfer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

(2014) Andrey Feklístov et al.   Annual Review of Microbiology

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

(2014) Marion Koch et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

READemption--a tool for the computational analysis of deep-sequencing-based transcriptome data

(2014) K. U. Forstner et al.   BIOINFORMATICS

Differential RNA-seq: the approach behind and the biological insight gained

(2014) Cynthia M Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

(2014) Karsten Voigt et al.   ISME Journal

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

(2014) W. Shao et al.   mBio

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

(2013) Eric I Sun et al.   BMC GENOMICS

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021

(2013) Jan-Philip Schlüter et al.   BMC GENOMICS

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

(2013) Ulrich Omasits et al.   GENOME RESEARCH

Proteogenomic Analysis ofBradyrhizobium japonicumUSDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline

(2013) Dhirendra Kumar et al.   MOLECULAR & CELLULAR PROTEOMICS

High-Resolution Transcriptomic Analyses of Sinorhizobium sp. NGR234 Bacteroids in Determinate Nodules of Vigna unguiculata and Indeterminate Nodules of Leucaena leucocephala

(2013) Yan Li et al.   PLoS One

Dual RpoH Sigma Factors and Transcriptional Plasticity in a Symbiotic Bacterium

(2012) Melanie J. Barnett et al.   JOURNAL OF BACTERIOLOGY

ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics

(2012) Serena Di Palma et al.   Nature Protocols

The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

(2012) Nina Sesto et al.   NATURE REVIEWS MICROBIOLOGY

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Positive Regulation of psbA Gene Expression by cis-Encoded Antisense RNAs in Synechocystis sp. PCC 6803

(2012) I. Sakurai et al.   PLANT PHYSIOLOGY

Reactive Oxygen Species-Inducible ECF σ Factors of Bradyrhizobium japonicum

(2012) Nadezda Masloboeva et al.   PLoS One

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

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

Small RNAs of theBradyrhizobium/Rhodopseudomonaslineage and their analysis

(2012) Ramakanth Madhugiri et al.   RNA Biology

Selective Translation of Leaderless mRNAs by Specialized Ribosomes Generated by MazF in Escherichia coli

(2011) Oliver Vesper et al.   CELL

Root Nodulation: A Paradigm for How Plant-Microbe Symbiosis Influences Host Developmental Pathways

(2011) Guilhem J. Desbrosses et al.   Cell Host & Microbe

A Comparative Transcriptome Analysis ofRhizobium etliBacteroids: Specific Gene Expression During Symbiotic Nongrowth

(2011) Maarten Vercruysse et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A Role forBradyrhizobium japonicumECF16 Sigma Factor EcfS in the Formation of a Functional Symbiosis with Soybean

(2011) S. B. Stockwell et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

ProOpDB: Prokaryotic Operon DataBase

(2011) B. Taboada et al.   NUCLEIC ACIDS RESEARCH

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

(2011) Cornelius Schmidtke et al.   NUCLEIC ACIDS RESEARCH

An experimentally anchored map of transcriptional start sites in the model cyanobacteriumSynechocystissp. PCC6803

(2011) Jan Mitschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ARNold: A web tool for the prediction of Rho-independent transcription terminators

(2011) Magali Naville et al.   RNA Biology

An Ergatis-based prokaryotic genome annotation web server

(2010) Chris Hemmerich et al.   BIOINFORMATICS

Missing genes in the annotation of prokaryotic genomes

(2010) Andrew S Warren et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Rhizobial Adaptation to Hosts, a New Facet in the Legume Root-Nodule Symbiosis

(2010) Marion Koch et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

PeptideClassifier for protein inference and targeted quantitative proteomics

(2010) Ermir Qeli et al.   NATURE BIOTECHNOLOGY

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

WebGeSTer DB—a transcription terminator database

(2010) Anirban Mitra et al.   NUCLEIC ACIDS RESEARCH

Protein and gene model inference based on statistical modeling in k-partite graphs

(2010) S. Gerster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules

(2010) Nathanaël Delmotte et al.   PROTEOMICS

The PhyR-σEcfGsignalling cascade is involved in stress response and symbiotic efficiency inBradyrhizobium japonicum

(2009) Benjamin Gourion et al.   MOLECULAR MICROBIOLOGY

Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability

(2009) D. Jager et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Small RNAs Establish Delays and Temporal Thresholds in Gene Expression

(2008) Stefan Legewie et al.   BIOPHYSICAL JOURNAL

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK2-FixK1 Cascade in Bradyrhizobium japonicum

(2008) S. Mesa et al.   JOURNAL OF BACTERIOLOGY

Expression of theBradyrhizobium japonicumType III Secretion System in Legume Nodules and Analysis of the Associatedttsbox Promoter

(2008) Susanne Zehner et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

(2008) Alexandra Sittka et al.   PLoS Genetics