Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes

(2017) So Nakagawa et al.   NUCLEIC ACIDS RESEARCH

Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1

(2017) Suhyung Cho et al.   Scientific Reports

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

(2016) Julia Babski et al.   BMC GENOMICS

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Initiation of mRNA translation in bacteria: structural and dynamic aspects

(2015) Claudio O. Gualerzi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Quantitative bacterial transcriptomics with RNA-seq

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

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

(2015) Jie Li et al.   Scientific Reports

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

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

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

(2014) Dominik Jäger et al.   BMC GENOMICS

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

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

RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti

(2014) Arjan de Groot et al.   Genome Biology and Evolution

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

A comparison of key aspects of gene regulation inStreptomyces coelicolorandEscherichia coliusing nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

(2014) David A. Romero et al.   MOLECULAR MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Defining the Bacteroides Ribosomal Binding Site

(2013) Udo Wegmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) Sandra Wiegand et al.   BMC GENOMICS

Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique

(2013) Katharina Pfeifer-Sancar et al.   BMC GENOMICS

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

RNA at 92°C

(2013) Claire Toffano-Nioche et al.   RNA Biology

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

Large Variations in Bacterial Ribosomal RNA Genes

(2012) K. Lim et al.   MOLECULAR BIOLOGY AND EVOLUTION

EcoGene 3.0

(2012) Jindan Zhou et al.   NUCLEIC ACIDS RESEARCH

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

(2012) P. Nicolas et al.   SCIENCE

A Pilot Study of Bacterial Genes with Disrupted ORFs Reveals a Surprising Profusion of Protein Sequence Recoding Mediated by Ribosomal Frameshifting and Transcriptional Realignment

(2011) V. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

(2011) Eli Venter et al.   PLoS One

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Prevalence of transcription promoters within archaeal operons and coding sequences

(2009) Tie Koide et al.   Molecular Systems Biology

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