Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

The infinitely many genes model with horizontal gene transfer

(2014) Franz Baumdicker et al.   ELECTRONIC JOURNAL OF PROBABILITY

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives

(2014) Mohammad Howard-Azzeh et al.   PHOTOSYNTHESIS RESEARCH

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

(2013) Jaroslav Flegr   Biology Direct

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

(2013) Alexander E. Lobkovsky et al.   Genome Biology and Evolution

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

(2013) P. M. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

(2012) Tal Dagan et al.   Genome Biology and Evolution

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The diversity of a distributed genome in bacterial populations

(2010) F. Baumdicker et al.   ANNALS OF APPLIED PROBABILITY

Signature proteins for the major clades of Cyanobacteria

(2010) Radhey S Gupta et al.   BMC EVOLUTIONARY BIOLOGY

Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium

(2010) H. James Tripp et al.   NATURE

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

A Phylogenetic Mixture Model for Gene Family Loss in Parasitic Bacteria

(2009) Matthew Spencer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference and Characterization of Horizontally Transferred Gene Families Using Stochastic Mapping

(2009) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

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

A likelihood framework to analyse phyletic patterns

(2008) O. Cohen 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

Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina

(2008) W. D. Swingley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA