Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

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

(2011) Andrey O Kislyuk et al.   BMC GENOMICS

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

(2010) Guanqun Shi 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

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer

(2010) Wolfgang Fischer et al.   NUCLEIC ACIDS RESEARCH

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

(2009) Jochen Blom et al.   BMC BIOINFORMATICS

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

Comparative genomics: the bacterial pan-genome

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

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

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

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH

Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis

(2008) C. Schoen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CLUSTERING OF MAIN ORTHOLOGS FOR MULTIPLE GENOMES

(2008) ZHENG FU et al.   Journal of Bioinformatics and Computational Biology