Towards a processual microbial ontology

Biological individuality: the case of biofilms

(2012) Marc Ereshefsky et al.   BIOLOGY & PHILOSOPHY

Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

(2012) Elizabeth Skippington et al.   Genome Biology and Evolution

The Rhizome of the Multidrug-Resistant Enterobacter aerogenes Genome Reveals How New “Killer Bugs” Are Created because of a Sympatric Lifestyle

(2012) Seydina M. Diene et al.   MOLECULAR BIOLOGY AND EVOLUTION

Suppression of the antiviral response by an influenza histone mimic

(2012) Ivan Marazzi et al.   NATURE

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

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

Insights into the bovine rumen plasmidome

(2012) A. B. Kav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella

(2011) Elizabeth Skippington et al.   BMC GENOMICS

50 ways to build a spindle: the complexity of microtubule generation during mitosis

(2011) Tommy Duncan et al.   CHROMOSOME RESEARCH

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

(2011) O. Popa et al.   GENOME RESEARCH

The 2010 Garrod Lecture: The dimensions of evolution in antibiotic resistance: ex unibus plurum et ex pluribus unum

(2011) F. Baquero   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2011) Chris S. Smillie et al.   NATURE

Mainstreams of Horizontal Gene Exchange in Enterobacteria: Consideration of the Outbreak of Enterohemorrhagic E. coli O104:H4 in Germany in 2011

(2011) Oliver Bezuidt et al.   PLoS One

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Moonlighting proteins: An intriguing mode of multitasking

(2010) Daphne H.E.W. Huberts et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

On the need for integrative phylogenomics, and some steps toward its creation

(2010) Eric Bapteste et al.   BIOLOGY & PHILOSOPHY

Symbiosis, lateral function transfer and the (many) saplings of life

(2010) Frédéric Bouchard   BIOLOGY & PHILOSOPHY

The myth of bacterial species and speciation

(2010) Jeffrey G. Lawrence et al.   BIOLOGY & PHILOSOPHY

Uniting sex and eukaryote origins in an emerging oxygenic world

(2010) Jeferson Gross et al.   Biology Direct

Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets

(2010) Ariella Alperovitch-Lavy et al.   ENVIRONMENTAL MICROBIOLOGY

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

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

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

Defining Life: The Virus Viewpoint

(2010) Patrick Forterre   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Moonlighting enzymes in parasitic protozoa

(2010) PETER W. COLLINGRIDGE et al.   PARASITOLOGY

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Persistence pays: how viruses promote host group survival

(2009) Luis P Villarreal   CURRENT OPINION IN MICROBIOLOGY

Carrying photosynthesis genes increases ecological fitness of cyanophagein silico

(2009) Ferdi L. Hellweger   ENVIRONMENTAL MICROBIOLOGY

On the origin of prokaryotic species

(2009) W. F. Doolittle et al.   GENOME RESEARCH

Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance

(2009) Stephen A. McMahon et al.   NUCLEIC ACIDS RESEARCH

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

(2009) O. Zhaxybayeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

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

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

(2008) Ani Qu et al.   PLoS One

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

The convergence of carbohydrate active gene repertoires in human gut microbes

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

A unified hydrophobicity scale for multispan membrane proteins

(2008) Julia Koehler et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution

(2008) Graham F. Hatfull et al.   RESEARCH IN MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

The eukaryotic tree of life: endosymbiosis takes its TOL

(2008) Christopher E. Lane et al.   TRENDS IN ECOLOGY & EVOLUTION