Escherichia colicultures maintain stable subpopulation structure during long-term evolution

Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli

(2017) Sylvie Létoffé et al.   PLoS Genetics

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Evolutionary convergence in experimental Pseudomonas populations

(2016) Peter A Lind et al.   ISME Journal

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Insertion sequence-caused large-scale rearrangements in the genome ofEscherichia coli

(2016) Heewook Lee et al.   NUCLEIC ACIDS RESEARCH

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

(2016) Marta Lourenço et al.   PLoS Genetics

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

(2015) Rohan Maddamsetti et al.   GENETICS

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin

(2015) Milya Davlieva et al.   NUCLEIC ACIDS RESEARCH

Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations

(2015) Evgeni M. Frenkel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel sRNAs involved in biofilm formation, motility and fimbriae formation in Escherichia coli

(2015) Geunu Bak et al.   Scientific Reports

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

(2015) Rohan Maddamsetti et al.   GENETICS

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

(2014) Jeffrey E Barrick et al.   BMC GENOMICS

Detection of Structural Variants Involving Repetitive Regions in the Reference Genome

(2014) Heewook Lee et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community

(2014) Margie Kinnersley et al.   PLoS Genetics

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

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

Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments

(2012) Pilar Eliana Puentes-Téllez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

POPULATION SUBDIVISION AND ADAPTATION IN ASEXUAL POPULATIONS OF SACCHAROMYCES CEREVISIAE

(2012) Sergey Kryazhimskiy et al.   EVOLUTION

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2012) Zachary D. Blount et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

(2012) Sung Yoon et al.   GENOME BIOLOGY

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

(2010) Tim F Cooper et al.   BMC EVOLUTIONARY BIOLOGY

NOVEL COOPERATION EXPERIMENTALLY EVOLVED BETWEEN SPECIES

(2010) William Harcombe   EVOLUTION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Repeatability of Adaptive Radiation During Long-Term Experimental Evolution of Escherichia coli in a Multiple Nutrient Environment

(2010) Gerda Saxer et al.   PLoS One

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

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

Inactivation of Efflux Pumps Abolishes Bacterial Biofilm Formation

(2008) M. Kvist et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Death and cannibalism in a seasonal environment facilitate bacterial coexistence

(2008) Daniel E. Rozen et al.   ECOLOGY LETTERS

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

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