Simple Phenotypic Sweeps Hide Complex Genetic Changes in Populations

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

The form of a trade-off determines the response to competition

(2013) Ram Maharjan et al.   ECOLOGY LETTERS

EPISTATIC INTERACTIONS DETERMINE THE MUTATIONAL PATHWAYS AND COEXISTENCE OF LINEAGES IN CLONALESCHERICHIA COLIPOPULATIONS

(2013) Ram Prasad Maharjan et al.   EVOLUTION

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

(2013) Katherine Phan et al.   ISME Journal

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

The basis of antagonistic pleiotropy in hfq mutations that have opposite effects on fitness at slow and fast growth rates

(2012) R Maharjan et al.   HEREDITY

The multiplicity of divergence mechanisms in a single evolving population

(2012) Ram P Maharjan et al.   GENOME BIOLOGY

Insertion Sequence-Driven Evolution of Escherichia coli in Chemostats

(2011) Joël Gaffé et al.   JOURNAL OF MOLECULAR EVOLUTION

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

(2010) Lei Wang et al.   Genome Biology and Evolution

Genomic Identification of a Novel Mutation in hfq That Provides Multiple Benefits in Evolving Glucose-Limited Populations of Escherichia coli

(2010) R. Maharjan et al.   JOURNAL OF BACTERIOLOGY

Molecular and Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli Extraintestinal Infections

(2010) Maxime Levert et al.   PLoS Pathogens

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genomic Sequencing Reveals Regulatory Mutations and Recombinational Events in the Widely Used MC4100 Lineage of Escherichia coli K-12

(2009) T. Ferenci et al.   JOURNAL OF BACTERIOLOGY

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli

(2009) Margie A. Kinnersley et al.   PLoS Genetics

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics