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

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

(2010) Lucie Bittner et al.   Biology Direct

The Tree and Net Components of Prokaryote Evolution

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

Type I Restriction-Modification Loci Reveal High Allelic Diversity in ClinicalHelicobacter pyloriIsolates

(2010) Sönke Andres et al.   HELICOBACTER

The post-Darwinist rhizome of life

(2010) Didier Raoult   LANCET

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees

(2010) K. Schliep et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Quantifying Nonvertical Inheritance in the Evolution of Legionella pneumophila

(2010) M. Coscolla et al.   MOLECULAR BIOLOGY AND EVOLUTION

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Clanistics: a multi-level perspective for harvesting unrooted gene trees

(2010) François-Joseph Lapointe et al.   TRENDS IN MICROBIOLOGY

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

(2009) Teresa Nogueira et al.   CURRENT BIOLOGY

The Genome of Thermosipho africanus TCF52B: Lateral Genetic Connections to the Firmicutes and Archaea

(2009) C. L. Nesbo et al.   JOURNAL OF BACTERIOLOGY

The Modern Concept of the Procaryote

(2009) W. B. Whitman   JOURNAL OF BACTERIOLOGY

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

(2009) Konstantinos Liolios et al.   NUCLEIC ACIDS RESEARCH

The network of life: genome beginnings and evolution

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

Lateral genetic transfer: open issues

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

Getting a better picture of microbial evolution en route to a network of genomes

(2009) T. Dagan et al.   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

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

(2009) Marie Touchon et al.   PLoS Genetics

Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network

(2008) Matteo Brilli et al.   BMC BIOINFORMATICS

Molecular phylogeny: reconstructing the forest

(2008) Philippe Lopez et al.   COMPTES RENDUS BIOLOGIES

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

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

Dealing with incongruence in phylogenomic analyses

(2008) N. Galtier et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Genome evolution in cyanobacteria: The stable core and the variable shell

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

The prokaryotic tree of life: past, present…and future?

(2008) James O. McInerney et al.   TRENDS IN ECOLOGY & EVOLUTION