EGN: a wizard for construction of gene and genome similarity networks

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

(2012) E. Bapteste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The public goods hypothesis for the evolution of life on Earth

(2011) James O McInerney et al.   Biology Direct

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli

(2011) Julie Beauregard-Racine et al.   Biology Direct

A Rooted Net of Life

(2011) David Williams et al.   Biology Direct

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

(2011) O. Popa et al.   GENOME RESEARCH

Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks

(2011) M. Tamminen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Structure, Function, and Evolution of Linear Replicons inBorrelia

(2010) George Chaconas et al.   Annual Review of Microbiology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

(2010) Lucie Bittner et al.   Biology Direct

The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks

(2010) Marco Fondi et al.   ENVIRONMENTAL MICROBIOLOGY

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome Biology and Evolution

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Lateral genetic transfer: open issues

(2009) M. A. Ragan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conjugative plasmids: vessels of the communal gene pool

(2009) A. Norman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The not so universal tree of life or the place of viruses in the living world

(2009) H. Brussow   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

Microbial co-habitation and lateral gene transfer: what transposases can tell us

(2009) Sean D Hooper et al.   GENOME BIOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA