Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes

Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts

(2016) Dorota Matelska et al.   Genome Biology and Evolution

Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems

(2016) Emilie Dumas et al.   Genome Biology and Evolution

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Global repositioning of transcription start sites in a plant-fermenting bacterium

(2016) Magali Boutard et al.   Nature Communications

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae

(2015) Isabelle Rosinski-Chupin et al.   BMC GENOMICS

Development of live attenuated Streptococcus agalactiae vaccine for tilapia via continuous passage in vitro

(2015) L.P. Li et al.   FISH & SHELLFISH IMMUNOLOGY

Genome Rearrangements Can Make and Break Small RNA Genes

(2015) Rahul Raghavan et al.   Genome Biology and Evolution

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.

(2015) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

RNA sequencing uncovers antisense RNAs and novel small RNAs inStreptococcus pyogenes

(2015) Anaïs Le Rhun et al.   RNA Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Resistance to rifampicin: a review

(2014) Beth P Goldstein   JOURNAL OF ANTIBIOTICS

Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

(2014) Chen-Hsun Tsai et al.   JOURNAL OF BACTERIOLOGY

Rfam 12.0: updates to the RNA families database

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

Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

(2014) Violette Da Cunha et al.   Nature Communications

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment

(2013) Vincent P Richards et al.   BMC GENOMICS

Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage

(2013) Isabelle Rosinski-Chupin et al.   BMC GENOMICS

Novel Regulatory Small RNAs in Streptococcus pyogenes

(2013) Rafael A. Tesorero et al.   PLoS One

Adaptive Response of Group B Streptococcus to High Glucose Conditions: New Insights on the CovRS Regulation Network

(2013) Benedetta Di Palo et al.   PLoS One

Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

(2012) Elizabeth Skippington et al.   Genome Biology and Evolution

The highly dynamic CRISPR1 system ofStreptococcus agalactiaecontrols the diversity of its mobilome

(2012) Maria-José Lopez-Sanchez et al.   MOLECULAR MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

nocoRNAc: Characterization of non-coding RNAs in prokaryotes

(2011) Alexander Herbig et al.   BMC BIOINFORMATICS

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains

(2011) Christophe Pichon et al.   NUCLEIC ACIDS RESEARCH

The Staphylococcus aureus RNome and Its Commitment to Virulence

(2011) Brice Felden et al.   PLoS Pathogens

Regulatory RNA in Bacterial Pathogens

(2010) Kai Papenfort et al.   Cell Host & Microbe

Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype

(2010) Luay F. Abu-Qatouseh et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Cartography of Methicillin-Resistant S. aureus Transcripts: Detection, Orientation and Temporal Expression during Growth Phase and Stress Conditions

(2010) Marie Beaume et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The RNase P family

(2010) J. Christopher Ellis et al.   RNA Biology

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Identification and Characterization of Noncoding Small RNAs in Streptococcus pneumoniae Serotype 2 Strain D39

(2009) H.-C. T. Tsui et al.   JOURNAL OF BACTERIOLOGY

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

(2009) Alexander Serganov et al.   NATURE

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

Transcriptome Adaptation of Group B Streptococcus to Growth in Human Amniotic Fluid

(2009) Izabela Sitkiewicz et al.   PLoS One

Group B Streptococcus and pregnancy: a review

(2008) John W. Larsen et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Remodeling of the Streptococcus agalactiae Transcriptome in Response to Growth Temperature

(2008) Laurent Mereghetti et al.   PLoS One

Extensive Adaptive Changes Occur in the Transcriptome of Streptococcus agalactiae (Group B Streptococcus) in Response to Incubation with Human Blood

(2008) Laurent Mereghetti et al.   PLoS One

Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae

(2008) M. Brochet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aspects of the natural history and virulence of S. agalactiae infection in Nile tilapia

(2008) G.F. Mian et al.   VETERINARY MICROBIOLOGY

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

(2008) Alexandra Sittka et al.   PLoS Genetics