Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

Bacterial Regulon Evolution: Distinct Responses and Roles for the Identical OmpR Proteins of Salmonella Typhimurium and Escherichia coli in the Acid Stress Response

(2014) Heather J. Quinn et al.   PLoS Genetics

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

(2014) George C. diCenzo et al.   PLoS Genetics

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021

(2013) Jan-Philip Schlüter et al.   BMC GENOMICS

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

(2013) E. Sallet et al.   DNA RESEARCH

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

(2013) Alexander E. Lobkovsky et al.   Genome Biology and Evolution

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

(2013) Marco Galardini et al.   Genome Biology and Evolution

DuctApe: A suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data

(2013) Marco Galardini et al.   GENOMICS

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia: Table 1.

(2013) Pieter Meysman et al.   NUCLEIC ACIDS RESEARCH

Molecular phylogeny of the nickel-resistance gene nreB and functional role in the nickel sensitive symbiotic nitrogen fixing bacterium Sinorhizobium meliloti

(2013) Francesco Pini et al.   PLANT AND SOIL

Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58

(2013) Marco Galardini et al.   Standards in Genomic Sciences

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

(2013) Masayuki Sugawara et al.   GENOME BIOLOGY

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

Draft Genome Sequence of Sinorhizobium meliloti CCNWSX0020, a Nitrogen-Fixing Symbiont with Copper Tolerance Capability Isolated from Lead-Zinc Mine Tailings

(2012) Z. Li et al.   JOURNAL OF BACTERIOLOGY

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

A Single Promoter Inversion Switches Photorhabdus Between Pathogenic and Mutualistic States

(2012) V. S. Somvanshi et al.   SCIENCE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

(2011) Marco Galardini et al.   BMC GENOMICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome

(2011) Susanne Schneiker-Bekel et al.   JOURNAL OF BIOTECHNOLOGY

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Plant-Bacteria Association and Symbiosis: Are There Common Genomic Traits in Alphaproteobacteria?

(2011) Francesco Pini et al.   Genes

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Comparative genomics of VirR regulons in Clostridium perfringens strains

(2010) Antonio Frandi et al.   BMC MICROBIOLOGY

The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis

(2010) Matteo Brilli et al.   BMC Systems Biology

RhizoRegNet—A database of rhizobial transcription factors and regulatory networks

(2010) Elizaveta Krol et al.   JOURNAL OF BIOTECHNOLOGY

Genomic repertoires of DNA-binding transcription factors across the tree of life

(2010) Varodom Charoensawan et al.   NUCLEIC ACIDS RESEARCH

Genetic flexibility of regulatory networks

(2010) A. Hunziker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation

(2009) S. A. F. T. van Hijum et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan et al.   NATURE

Pseudocounts for transcription factor binding sites

(2008) Keishin Nishida et al.   NUCLEIC ACIDS RESEARCH

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

(2008) Daniel J. Kvitek et al.   PLoS Genetics