Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system

Experimental evolution of recombination and crossover interference in Drosophila caused by directional selection for stress-related traits

(2015) Dau Dayal Aggarwal et al.   BMC BIOLOGY

A Coalescent Model for a Sweep of a Unique Standing Variant

(2015) Jeremy J. Berg et al.   GENETICS

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps

(2015) D. R. Schrider et al.   GENETICS

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation inDrosophila melanogaster

(2015) Aashish R. Jha et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

A Coalescent Model for a Sweep of a Unique Standing Variant

(2015) Jeremy J. Berg et al.   GENETICS

Genomics of Rapid Adaptation to Antibiotics: Convergent Evolution and Scalable Sequence Amplification

(2014) David Laehnemann et al.   Genome Biology and Evolution

Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation

(2014) C Schlötterer et al.   HEREDITY

Patterns of Linkage Disequilibrium and Long Range Hitchhiking in Evolving ExperimentalDrosophila melanogasterPopulations

(2014) Susanne U. Franssen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic changes under rapid evolution: selection for parasitoid resistance

(2014) K. M. Jalvingh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans

(2014) C. H. Chandler   G3-Genes Genomes Genetics

forqs: forward-in-time simulation of recombination, quantitative traits and selection

(2013) Darren Kessner et al.   BIOINFORMATICS

Sex-specific differences in desiccation resistance and the use of energy metabolites as osmolytes in Drosophila melanogaster flies acclimated to dehydration stress

(2013) Ravi Parkash et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments

(2013) Ray Tobler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

(2013) Subhash Rajpurohit et al.   MOLECULAR ECOLOGY

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

(2013) Simon Boitard et al.   Molecular Ecology Resources

Population genomics of rapid adaptation by soft selective sweeps

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

Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies

(2012) R. Kofler et al.   BIOINFORMATICS

GENOMIC BASIS OF AGING AND LIFE-HISTORY EVOLUTION INDROSOPHILA MELANOGASTER

(2012) Silvia C. Remolina et al.   EVOLUTION

Investigating Natural Variation in Drosophila Courtship Song by the Evolve and Resequence Approach

(2012) T. L. Turner et al.   GENETICS

Selective Sweeps in Multilocus Models of Quantitative Traits

(2012) P. Pavlidis et al.   GENETICS

Estimating the Strength of Selective Sweeps from Deep Population Diversity Data

(2012) P. W. Messer et al.   GENETICS

Parallel Genetic Changes and Nonparallel Gene-Environment Interactions Characterize the Evolution of Drug Resistance in Yeast

(2012) A. C. Gerstein et al.   GENETICS

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

(2012) Benjamin M. Peter et al.   PLoS Genetics

Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

(2012) John E. Pool et al.   PLoS Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Experimental selection of hypoxia-tolerant Drosophila melanogaster

(2011) D. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

(2011) Thomas L. Turner et al.   PLoS Genetics

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Understanding Adaptation in Large Populations

(2010) Nick Barton   PLoS Genetics

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

Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags

(2009) Bishwo N Adhikari et al.   BMC GENOMICS

Transcriptional Regulation of Metabolism Associated With the Increased Desiccation Resistance of the Cactophilic Drosophila mojavensis

(2009) Luciano M. Matzkin et al.   GENETICS

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

(2009) Jeffrey E. Barrick et al.   NATURE

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

(2008) Luis-Miguel Chevin et al.   GENETICS

A Potential Role for Drosophila Mucins in Development and Physiology

(2008) Zulfeqhar A. Syed et al.   PLoS One