Detecting Horizontal Gene Transfer between Closely Related Taxa

Stability along with Extreme Variability in Core Genome Evolution

(2013) Yuri I. Wolf et al.   Genome Biology and Evolution

A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation

(2012) Yan Zhang et al.   BMC EVOLUTIONARY BIOLOGY

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

(2012) Rolf S Kaas et al.   BMC GENOMICS

Universal Pacemaker of Genome Evolution

(2012) Sagi Snir et al.   PLoS Computational Biology

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous Identification of Duplications and Lateral Gene Transfers

(2010) A Tofigh et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting Plasmid Promiscuity Based on Genomic Signature

(2010) H. Suzuki et al.   JOURNAL OF BACTERIOLOGY

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity

(2010) Alix Boc et al.   SYSTEMATIC BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Uniting Alignments and Trees

(2009) A. Loytynoja et al.   SCIENCE

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

(2008) P. S. Novichkov et al.   JOURNAL OF BACTERIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE