Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs

(2012) Søren Mørk et al.   BIOINFORMATICS

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

(2012) Elena S Peterson et al.   BMC GENOMICS

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

Noncoding RNAs Binding to the Nucleoid Protein HU in Escherichia coli

(2012) M. Macvanin et al.   JOURNAL OF BACTERIOLOGY

Analysis of the Regulated Transcriptome of Neisseria meningitidis in Human Blood Using a Tiling Array

(2012) E. Del Tordello et al.   JOURNAL OF BACTERIOLOGY

Dual RpoH Sigma Factors and Transcriptional Plasticity in a Symbiotic Bacterium

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

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Sinorhizobium meliloti Sigma Factors RpoE1 and RpoE4 Are Activated in Stationary Phase in Response to Sulfite

(2012) Bénédicte Bastiat et al.   PLoS One

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

(2012) Pablo Pareja-Tobes et al.   PLoS One

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

(2012) Ina Wilms et al.   RNA Biology

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics

(2011) Sarah Frank et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

The genome of Tetranychus urticae reveals herbivorous pest adaptations

(2011) Miodrag Grbić et al.   NATURE

Transcription Reprogramming during Root Nodule Development in Medicago truncatula

(2011) Sandra Moreau et al.   PLoS One

Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs

(2011) Barbara A. Weissenmayer et al.   PLoS One

A high resolution map of a cyanobacterial transcriptome

(2011) Vikram Vijayan et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt 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

The role of sigma factor RpoH1 in the pH stress response of Sinorhizobium meliloti

(2010) Daniella K C de Lucena et al.   BMC MICROBIOLOGY

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

Structural and operational complexity of the Geobacter sulfurreducens genome

(2010) Y. Qiu et al.   GENOME RESEARCH

Dual Control of Sinorhizobium meliloti RpoE2 Sigma Factor Activity by Two PhyR-Type Two-Component Response Regulators

(2010) B. Bastiat et al.   JOURNAL OF BACTERIOLOGY

RpoE2 of Sinorhizobium meliloti is necessary for trehalose synthesis and growth in hyperosmotic media

(2010) M. Flechard et al.   MICROBIOLOGY-SGM

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Differentiation of Symbiotic Cells and Endosymbionts in Medicago truncatula Nodulation Are Coupled to Two Transcriptome-Switches

(2010) Nicolas Maunoury et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Identification of a Hydroxyproline Transport System in the Legume EndosymbiontSinorhizobium meliloti

(2009) Allyson M. MacLean et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The transcription unit architecture of the Escherichia coli genome

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

Stability of the pstS transcript of Escherichia coli

(2008) Meire Aguena et al.   ARCHIVES OF MICROBIOLOGY

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

(2008) Claudio Valverde et al.   BMC GENOMICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics

Sinorhizobium meliloti rpoE2is necessary for H2O2stress resistance during the stationary growth phase

(2008) Maud Flechard et al.   FEMS MICROBIOLOGY LETTERS

Auxotrophy Accounts for Nodulation Defect of MostSinorhizobium melilotiMutants in the Branched-Chain Amino Acid Biosynthesis Pathway

(2008) Maria de las Nieves Peltzer et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

The model legumeMedicago truncatulaA17 is poorly matched for N2fixation with the sequenced microsymbiontSinorhizobium meliloti1021

(2008) Jason J. Terpolilli et al.   NEW PHYTOLOGIST