Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome of Pseudomonas putida

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

(2016) Eugeni Belda et al.   ENVIRONMENTAL MICROBIOLOGY

Pseudomonas putida—a versatile host for the production of natural products

(2015) Anita Loeschcke et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Quantitative bacterial transcriptomics with RNA-seq

(2015) James P Creecy et al.   CURRENT OPINION IN MICROBIOLOGY

The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism inPseudomonas putida

(2015) Ruggero La Rosa et al.   ENVIRONMENTAL MICROBIOLOGY

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

(2015) Thorsten Bischler et al.   METHODS

Differential RNA-seq ofVibrio choleraeidentifies the VqmR small RNA as a regulator of biofilm formation

(2015) Kai Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second messenger – Sensing riboswitches in bacteria

(2015) Arati Ramesh   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria

(2015) Matthias Kopf et al.   Scientific Reports

Accurate DNA Assembly and Genome Engineering with Optimized Uracil Excision Cloning

(2015) Ana Mafalda Cavaleiro et al.   ACS Synthetic Biology

Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs

(2015) Aaron M. Nuss et al.   PLoS Genetics

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

(2015) Scarlet S. Shell et al.   PLoS Genetics

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

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

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

Comparative Genome Analysis of the Closely Related Synechocystis Strains PCC 6714 and PCC 6803

(2014) M. Kopf et al.   DNA RESEARCH

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

Biotechnological domestication of pseudomonads using synthetic biology

(2014) Pablo I. Nikel et al.   NATURE REVIEWS MICROBIOLOGY

Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome

(2014) Leelavati Narlikar   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from theChloroflexiphylum

(2014) Irina A. Rodionova et al.   Environmental Microbiology Reports

Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

(2014) T. Conway et al.   mBio

The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101

(2014) Ulrike Pfreundt et al.   Scientific Reports

How to find RNA thermometers

(2014) Francesco Righetti et al.   Frontiers in Cellular and Infection Microbiology

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

(2013) Eric I Sun et al.   BMC GENOMICS

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

(2013) Sandra Wiegand 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

The promise of riboswitches as potential antibacterial drug targets

(2013) Christina E. Lünse et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia spumigena CCY9414 Based on a Genome-Transcriptome Analysis

(2013) Björn Voß et al.   PLoS One

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

(2013) Andrea Haller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptomic fingerprinting ofPseudomonas putidaunder alternative physiological regimes

(2013) Juhyun Kim et al.   Environmental Microbiology Reports

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

(2013) Teresa Cortes et al.   Cell Reports

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

Industrial biotechnology of Pseudomonas putida and related species

(2012) Ignacio Poblete-Castro et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods

(2012) Marc Sultan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa

(2012) María Gómez-Lozano et al.   ENVIRONMENTAL MICROBIOLOGY

The Entner-Doudoroff pathway empowersPseudomonas putida KT2440 with a high tolerance to oxidative stress

(2012) Max Chavarría et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

(2012) Omri Wurtzel et al.   Molecular Systems Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dual-acting riboswitch control of translation initiation and mRNA decay

(2012) M.-P. Caron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

(2011) Xiaobin Zheng et al.   BMC GENOMICS

Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics

(2011) Sarah Frank et al.   ENVIRONMENTAL MICROBIOLOGY

Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440

(2011) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals

(2011) Linda Jeanguenin et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

cis-Antisense RNA, Another Level of Gene Regulation in Bacteria

(2011) J. Georg et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2011) Cornelius Schmidtke et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification of Transcriptional Start Sites in the Plant Pathogen Pseudomonas syringae pv. tomato str. DC3000

(2011) Melanie J. Filiatrault et al.   PLoS One

Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120

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

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

In silicogenome-scale metabolic analysis ofPseudomonas putidaKT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

(2010) Seung Bum Sohn et al.   Biotechnology Journal

A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering

(2010) Morten HH Nørholm   BMC BIOTECHNOLOGY

A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

(2010) Jan-Philip Schlüter et al.   BMC GENOMICS

Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity

(2010) M. J. Filiatrault et al.   JOURNAL OF BACTERIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Dynamic evolution of translation initiation mechanisms in prokaryotes

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

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation

(2010) Magali Naville et al.   GENOME BIOLOGY

The Structural and Biochemical Foundations of Thiamin Biosynthesis

(2009) Christopher T. Jurgenson et al.   Annual Review of Biochemistry

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Identification of small RNAs inMycobacterium tuberculosis

(2009) Kristine B. Arnvig et al.   MOLECULAR MICROBIOLOGY

Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

(2009) Jens Georg et al.   Molecular Systems Biology

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

(2009) Jane M. Liu et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

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

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

A Novel Class of Modular Transporters for Vitamins in Prokaryotes

(2008) D. A. Rodionov et al.   JOURNAL OF BACTERIOLOGY

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG

(2008) J. E. Brock et al.   RNA

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology

Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1

(2008) Mark W. Silby et al.   PLoS Genetics