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

Exploring the plant-associated bacterial communities in Medicago sativa L

(2012) Francesco Pini et al.   BMC MICROBIOLOGY

Phylo-MCOA: A Fast and Efficient Method to Detect Outlier Genes and Species in Phylogenomics Using Multiple Co-inertia Analysis

(2012) D. M. de Vienne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

(2012) C. F. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

(2012) Brendan Epstein et al.   PLoS Genetics

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Genomic fluidity: an integrative view of gene diversity within microbial populations

(2011) Andrey O Kislyuk et al.   BMC GENOMICS

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

(2011) Marco Galardini et al.   BMC GENOMICS

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

(2011) Xavier Bailly et al.   ISME Journal

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

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are There Laws of Genome Evolution?

(2011) Eugene V. Koonin   PLoS Computational Biology

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

(2011) Francesco Pini et al.   Genes

Genetic diversity and salt tolerance of Sinorhizobium populations from two Tunisian soils

(2010) Darine Trabelsi et al.   ANNALS OF MICROBIOLOGY

Composition bias and the origin of ORFan genes

(2010) Inbal Yomtovian et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

(2010) Xiangyu Deng et al.   BMC GENOMICS

Comparative genomics of VirR regulons in Clostridium perfringens strains

(2010) Antonio Frandi et al.   BMC MICROBIOLOGY

Genomic evolution of Vibrio cholerae

(2010) Yong-Joon Cho et al.   CURRENT OPINION IN MICROBIOLOGY

Dual Control of Sinorhizobium meliloti RpoE2 Sigma Factor Activity by Two PhyR-Type Two-Component Response Regulators

(2010) B. Bastiat et al.   JOURNAL OF BACTERIOLOGY

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Constraints and plasticity in genome and molecular-phenome evolution

(2010) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

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

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

Metabolic Capacity of Sinorhizobium (Ensifer) meliloti Strains as Determined by Phenotype MicroArray Analysis

(2009) E. G. Biondi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

(2009) Yeşim Soyer et al.   BMC EVOLUTIONARY BIOLOGY

Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

(2009) Hong Guo et al.   GENOME

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Development of real-time PCR assay for detection and quantification ofSinorhizobium melilotiin soil and plant tissue

(2009) D. Trabelsi et al.   LETTERS IN APPLIED MICROBIOLOGY

Darwinian evolution in the light of genomics

(2009) E. V. Koonin   NUCLEIC ACIDS RESEARCH

Horizontal gene transfer in evolution: facts and challenges

(2009) L. Boto   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Molecular Determinants of a Symbiotic Chronic Infection

(2008) Katherine E. Gibson et al.   Annual Review of Genetics

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Diversity ofSinorhizobiumstrains nodulatingMedicago sativafrom different Iranian regions

(2008) Majid Bedaf Talebi et al.   FEMS MICROBIOLOGY LETTERS

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Mutational Analysis of theSinorhizobium melilotiShort-Chain Dehydrogenase/Reductase Family Reveals Substantial Contribution to Symbiosis and Catabolic Diversity

(2008) Asha I. Jacob et al.   MOLECULAR PLANT-MICROBE INTERACTIONS