A Genome-Wide Survey of Highly Expressed Non-Coding RNAs and Biological Validation of Selected Candidates in Agrobacterium tumefaciens

Hfq Influences Multiple Transport Systems and Virulence in the Plant Pathogen Agrobacterium tumefaciens

(2012) I. Wilms et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals

(2012) X. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Riboswitch control of Rho-dependent transcription termination

(2012) K. Hollands et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens

(2012) Ina Wilms et al.   RNA Biology

Transcription attenuation in bacteria: theme and variations

(2011) M. Naville et al.   Briefings in Functional Genomics

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

(2011) Oliver Vesper et al.   CELL

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

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

Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein

(2011) Ina Wilms et al.   MOLECULAR MICROBIOLOGY

Molecular aspects of bacterial pH sensing and homeostasis

(2011) Terry A. Krulwich et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial transcriptomics: what is beyond the RNA horiz-ome?

(2011) Marc Güell et al.   NATURE REVIEWS MICROBIOLOGY

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

A high resolution map of a cyanobacterial transcriptome

(2011) Vikram Vijayan et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

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

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation

(2010) Andrea Pitzschke et al.   EMBO JOURNAL

SsrA (tmRNA) acts as an antisense RNA to regulateStaphylococcus aureuspigment synthesis by base pairing withcrtMNmRNA

(2010) Yu Liu et al.   FEBS LETTERS

The cspA mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA

(2010) Anna Maria Giuliodori et al.   MOLECULAR CELL

Proteomic and transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant

(2010) Sonja Klüsener et al.   MOLECULAR GENETICS AND GENOMICS

A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon

(2010) Matthias Gimpel et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

RNAs: regulators of bacterial virulence

(2010) Jonas Gripenland et al.   NATURE REVIEWS MICROBIOLOGY

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes

(2009) Edmund Loh et al.   CELL

Experimental approaches for the discovery and characterization of regulatory small RNA

(2009) Cynthia Mira Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

The T box mechanism: tRNA as a regulatory molecule

(2009) Nicholas J. Green et al.   FEBS LETTERS

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

(2009) S. C. Slater et al.   JOURNAL OF BACTERIOLOGY

Molecular Basis of ChvE Function in Sugar Binding, Sugar Utilization, and Virulence in Agrobacterium tumefaciens

(2009) F. He et al.   JOURNAL OF BACTERIOLOGY

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

A simple method for directional transcriptome sequencing using Illumina technology

(2009) N. J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011

(2008) Claudio Valverde et al.   BMC GENOMICS

Comparative transcriptome analysis ofAgrobacterium tumefaciensin response to plant signal salicylic acid, indole-3-acetic acid and γ-amino butyric acid reveals signalling cross-talk andAgrobacterium-plant co-evolution

(2008) Ze-Chun Yuan et al.   CELLULAR MICROBIOLOGY

Riboswitch RNAs: using RNA to sense cellular metabolism

(2008) T. M. Henkin   GENES & DEVELOPMENT

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

(2008) Elizabeth M. Fozo et al.   MOLECULAR MICROBIOLOGY

The 5′ end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator

(2008) Maude Guillier et al.   NUCLEIC ACIDS RESEARCH

High-density seedling expression system for the production of bioactive human cardiotrophin-1, a potential therapeutic cytokine, in transgenic tobacco chloroplasts

(2008) Imma Farran et al.   PLANT BIOTECHNOLOGY JOURNAL