Selection on Horizontally Transferred and Duplicated Genes in Sinorhizobium (Ensifer), the Root-Nodule Symbionts of Medicago

The Evolution of Natural Competence: Disentangling Costs and Benefits of Sex in Bacteria

(2013) Danesh Moradigaravand et al.   AMERICAN NATURALIST

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

(2013) Daniel R. Schrider et al.   GENETICS

The Evolution of Genomic Instability in the Obligate Endosymbionts of Whiteflies

(2013) Daniel B. Sloan et al.   Genome Biology and Evolution

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

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

Functional genotypes are associated with commensalEscherichia colistrain abundance within-host individuals and populations

(2013) Michaela D. J. Blyton et al.   MOLECULAR ECOLOGY

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

(2013) Masayuki Sugawara et al.   GENOME BIOLOGY

Evolutionary Effects of Translocations in Bacterial Genomes

(2012) Jarrett D. Morrow 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

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

(2012) Brendan Epstein et al.   PLoS Genetics

Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

(2012) Ming-Chun Lee et al.   PLoS Genetics

Selection-Driven Gene Loss in Bacteria

(2012) Sanna Koskiniemi et al.   PLoS Genetics

High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans

(2011) Kendra J. Lipinski et al.   CURRENT BIOLOGY

Lateral gene transfer

(2011) Olga Zhaxybayeva et al.   CURRENT BIOLOGY

A Method for Inferring the Rate of Occurrence and Fitness Effects of Advantageous Mutations

(2011) Adrian Schneider et al.   GENETICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

(2011) Yingrui Li et al.   NATURE BIOTECHNOLOGY

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS Genetics

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

(2010) A. B. Reams et al.   GENETICS

Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster

(2010) Julie M. Cridland et al.   Genome Biology and Evolution

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

(2010) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene copy-number polymorphism in nature

(2010) D. R. Schrider et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419

(2010) Wayne Reeve et al.   Standards in Genomic Sciences

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

On the origin of prokaryotic species

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

MicroScope: a platform for microbial genome annotation and comparative genomics

(2009) D. Vallenet et al.   Database-The Journal of Biological Databases and Curation

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

(2009) Marie Touchon et al.   PLoS Genetics

Evolution of new gene functions: simulation and analysis of the amplification model

(2008) Mats E. Pettersson et al.   GENETICA

The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products

(2008) D. M. Stoebel et al.   GENETICS

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

(2008) J. J. Emerson et al.   SCIENCE

The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli

(2008) Mark W. J. van Passel et al.   PLoS Computational Biology