Flexible comparative genomics of prokaryotic transcriptional regulatory networks

Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes

(2018) Blanca Taboada et al.   BIOINFORMATICS

Comparative genomics of the DNA damage-inducible network in the Patescibacteria

(2017) Miquel Sánchez-Osuna et al.   ENVIRONMENTAL MICROBIOLOGY

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

(2017) Bruno T. L. Nichio et al.   Frontiers in Genetics

A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data

(2016) Elizabeth T. Hobbs et al.   Algorithms for Molecular Biology

Assessment of transfer methods for comparative genomics of regulatory networks in bacteria

(2016) Sefa Kılıç et al.   BMC BIOINFORMATICS

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

(2016) Bingqiang Liu et al.   Scientific Reports

Genome-Based Taxonomic Classification of Bacteroidetes

(2016) Richard L. Hahnke et al.   Frontiers in Microbiology

Identification of 17 HrpX-Regulated Proteins Including Two Novel Type III Effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola

(2014) Xiao-bo Xue et al.   PLoS One

RecA Protein Plays a Role in the Chemotactic Response and Chemoreceptor Clustering of Salmonella enterica

(2014) Albert Mayola et al.   PLoS One

Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems

(2013) L Aravind et al.   Biology Direct

LASAGNA: A novel algorithm for transcription factor binding site alignment

(2013) Chih Lee et al.   BMC BIOINFORMATICS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria

(2013) Sefa Kılıç et al.   NUCLEIC ACIDS RESEARCH

Hidden Markov Models for Evolution and Comparative Genomics Analysis

(2013) Nadezda A. Bykova et al.   PLoS One

scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes

(2013) Patrick K. O'Neill et al.   PLoS One

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

(2012) Neus Sanchez-Alberola et al.   BMC GENOMICS

Features for computational operon prediction in prokaryotes

(2012) L.-Y. Chuang et al.   Briefings in Functional Genomics

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

FITBAR: a web tool for the robust prediction of prokaryotic regulons

(2010) Jacques Oberto   BMC BIOINFORMATICS

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

(2010) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

Genomic Analysis of "Elusimicrobium minutum," the First Cultivated Representative of the Phylum "Elusimicrobia" (Formerly Termite Group 1)

(2009) D. P. R. Herlemann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A reexamination of information theory-based methods for DNA-binding site identification

(2009) Ivan Erill et al.   BMC BIOINFORMATICS

The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis

(2009) S. van der Veen et al.   MICROBIOLOGY-SGM

Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays

(2009) N. Jochmann et al.   MICROBIOLOGY-SGM

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH