Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum

(2016) Jessica Baude et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

(2016) George C. diCenzo et al.   Nature Communications

Horizontally transferred genes cluster spatially and metabolically

(2015) Alexander Dilthey et al.   Biology Direct

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

(2015) Yujun Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis

(2015) Florent Lassalle et al.   RESEARCH IN MICROBIOLOGY

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations

(2015) Seyed Abdollah Mousavi et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics

(2015) Ernesto Ormeño-Orrillo et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

(2015) N. Kumar et al.   Open Biology

Genomic Heterogeneity and Ecological Speciation within One Subspecies of Bacillus subtilis

(2014) Sarah Kopac et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

(2014) Tony Campillo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid

(2014) Martha H. Ramírez-Bahena et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

TPMS: a set of utilities for querying collections of gene trees

(2013) Thomas Bigot et al.   BMC BIOINFORMATICS

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconciliation of Sequence Data and Updated Annotation of the Genome of Agrobacterium tumefaciens C58, and Distribution of a Linear Chromosome in the Genus Agrobacterium

(2012) Steven Slater et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome Sequence and Mutational Analysis of Plant-Growth-Promoting Bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a Zinc-Lead Mine Tailing

(2012) Xiuli Hao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantifying Homologous Replacement of Loci between Haloarchaeal Species

(2012) David Williams et al.   Genome Biology and Evolution

Genome Sequence of the Arsenite-Oxidizing Strain Agrobacterium tumefaciens 5A

(2012) X. Hao et al.   JOURNAL OF BACTERIOLOGY

Progressive genome-wide introgression in agriculturalCampylobacter coli

(2012) Samuel K. Sheppard et al.   MOLECULAR ECOLOGY

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral gene transfer as a support for the tree of life

(2012) S. S. Abby 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

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Models, algorithms and programs for phylogeny reconciliation

(2011) J.-P. Doyon et al.   BRIEFINGS IN BIOINFORMATICS

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

(2011) Florent Lassalle et al.   Genome Biology and Evolution

Genome Sequence of the Curdlan-Producing Agrobacterium sp. Strain ATCC 31749

(2011) A. M. Ruffing et al.   JOURNAL OF BACTERIOLOGY

Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin

(2011) F. Aujoulat et al.   JOURNAL OF BACTERIOLOGY

Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid

(2011) Daniel Wibberg et al.   JOURNAL OF BIOTECHNOLOGY

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

(2010) Sophie S Abby et al.   BMC BIOINFORMATICS

Rapid and Efficient Identification of Agrobacterium Species by recA Allele Analysis

(2010) Denis Costechareyre et al.   MICROBIAL ECOLOGY

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

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

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

The consequences of genetic drift for bacterial genome complexity

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

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

(2009) S. C. Slater et al.   JOURNAL OF BACTERIOLOGY

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics

The Origins of Ecological Diversity in Prokaryotes

(2008) Frederick M. Cohan et al.   CURRENT BIOLOGY