Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment

(2015) Erin R. Reichenberger et al.   Genome Biology and Evolution

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.

(2015) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

(2015) Florent Lassalle et al.   PLoS Genetics

PanGP: A tool for quickly analyzing bacterial pan-genome profile

(2014) Yongbing Zhao et al.   BIOINFORMATICS

Translational selection in human: more pronounced in housekeeping genes

(2014) Lina Ma et al.   Biology Direct

Variation, Evolution, and Correlation Analysis of C+G Content and Genome or Chromosome Size in Different Kingdoms and Phyla

(2014) Xiu-Qing Li et al.   PLoS One

Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

(2014) W. Ran et al.   mBio

Effective population size does not predict codon usage bias in mammals

(2014) Michael D. Kessler et al.   Ecology and Evolution

Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation

(2013) Emmanuel F Mongodin et al.   BMC GENOMICS

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

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

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

(2012) Zhang Zhang et al.   BMC BIOINFORMATICS

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

(2012) Rolf S Kaas et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A selective force favoring increased G+C content in bacterial genes

(2012) R. Raghavan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg et al.   PLoS Genetics

Sequencing the species pan-genome

(2009) Stephen Bentley   NATURE REVIEWS MICROBIOLOGY

Molecular mechanisms of Escherichia coli pathogenicity

(2009) Matthew A. Croxen et al.   NATURE REVIEWS MICROBIOLOGY

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

(2009) Marie Touchon et al.   PLoS Genetics

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

(2008) Wagied Davids et al.   BMC EVOLUTIONARY BIOLOGY

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

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