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

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

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

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Oncogenic Kras Maintains Pancreatic Tumors through Regulation of Anabolic Glucose Metabolism

(2012) Haoqiang Ying et al.   CELL

Cancer in Light of Experimental Evolution

(2012) Kathleen Sprouffske et al.   CURRENT BIOLOGY

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

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

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Evolution of the cancer genome

(2012) Ondrej Podlaha et al.   TRENDS IN GENETICS

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

Loss of Genetic Redundancy in Reductive Genome Evolution

(2011) André G. Mendonça et al.   PLoS Computational Biology

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

(2011) Daniel J. Kvitek et al.   PLoS Genetics

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

(2011) Jared W. Wenger et al.   PLoS Genetics

Whole-genome sequencing of a laboratory-evolved yeast strain

(2010) Carlos L Araya et al.   BMC GENOMICS

A High Frequency of Beneficial Mutations Across Multiple Fitness Components in Saccharomyces cerevisiae

(2010) D. W. Hall et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

(2010) D. Gresham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

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

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

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

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

(2008) David Gresham et al.   PLoS Genetics