BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis

(2019) Dingyu Liu et al.   Biotechnology for Biofuels

Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry

(2018) Jean-Benoît Lalanne et al.   CELL

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes

(2018) Sung-Huan Yu et al.   GigaScience

BRENDA in 2019: a European ELIXIR core data resource

(2018) Lisa Jeske et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence

(2018) Indu Warrier et al.   PLoS Pathogens

SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis

(2017) Bingyao Zhu et al.   NUCLEIC ACIDS RESEARCH

RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets

(2017) Ferhat Alkan et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

(2017) Zasha Weinberg et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement

(2017) Rainer Borriss et al.   Microbial Biotechnology

Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis

(2016) Adam W. Westbrook et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Editing of the Bacillus subtilis Genome by the CRISPR-Cas9 System

(2016) Josef Altenbuchner   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrated genome browser: visual analytics platform for genomics

(2016) Nowlan H. Freese et al.   BIOINFORMATICS

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

A multistress responsive type I toxin-antitoxin system:bsrE/SR5 from theB. subtilischromosome

(2016) Peter Müller et al.   RNA Biology

Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

(2016) D. Dar et al.   SCIENCE

Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High-Salinity Environments Using RNA Sequencing

(2016) Katja Nagler et al.   Frontiers in Microbiology

Diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes

(2015) Kelly A Fimlaid et al.   CURRENT OPINION IN MICROBIOLOGY

Where does transcription start? 5′-RACE adapted to next-generation sequencing

(2015) Fleur A.D. Leenen et al.   NUCLEIC ACIDS RESEARCH

Structured RNAs and synteny regions in the pig genome

(2014) Christian Anthon et al.   BMC GENOMICS

Genome-Wide Analysis of Small RNAs Expressed by Yersinia pestis Identifies a Regulator of the Yop-Ysc Type III Secretion System

(2014) C. A. Schiano et al.   JOURNAL OF BACTERIOLOGY

The tmRNA website

(2014) Corey M. Hudson et al.   NUCLEIC ACIDS RESEARCH

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

(2014) T. Conway et al.   mBio

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

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

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

The FsrA sRNA and FbpB Protein Mediate the Iron-Dependent Induction of the Bacillus subtilis LutABC Iron-Sulfur-Containing Oxidases

(2012) G. T. Smaldone et al.   JOURNAL OF BACTERIOLOGY

BsrG/SR4 from Bacillus subtilis- the first temperature-dependent type I toxin-antitoxin system

(2012) Natalie Jahn et al.   MOLECULAR MICROBIOLOGY

BSRD: a repository for bacterial small regulatory RNA

(2012) Lei Li et al.   NUCLEIC ACIDS RESEARCH

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

(2012) P. Nicolas et al.   SCIENCE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The UCSC Archaeal Genome Browser: 2012 update

(2011) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2010) Anna Maria Giuliodori et al.   MOLECULAR CELL

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

(2009) V. Barbe et al.   MICROBIOLOGY-SGM

The transcriptionally active regions in the genome ofBacillus subtilis

(2009) Simon Rasmussen et al.   MOLECULAR MICROBIOLOGY

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH