Genome Diversity and Divergence in Drosophila mauritiana : Multiple Signatures of Faster X Evolution

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Recurrent Turnover of Chromosome-Specific Satellites in Drosophila

(2014) Miguel Gallach   Genome Biology and Evolution

Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans

(2014) Rebekah L. Rogers et al.   MOLECULAR BIOLOGY AND EVOLUTION

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments

(2013) Daniel Garrigan   Evolutionary Bioinformatics

Meiotic Sex Chromosome Inactivation Is Disrupted in Sterile Hybrid Male House Mice

(2013) P. Campbell et al.   GENETICS

Faster-X Adaptive Protein Evolution in House Mice

(2013) Athanasios Kousathanas et al.   GENETICS

The faster-X effect: integrating theory and data

(2013) Richard P. Meisel et al.   TRENDS IN GENETICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

(2012) T. T. Hu et al.   GENOME RESEARCH

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

(2012) V. Nolte et al.   GENOME RESEARCH

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

The Rapid Evolution of X-linked Male-Biased Gene Expression and the Large-X Effect in Drosophila yakuba, D. santomea, and Their Hybrids

(2012) Ana Llopart   MOLECULAR BIOLOGY AND EVOLUTION

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Extensive X-linked adaptive evolution in central chimpanzees

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

Faster-X Evolution of Gene Expression in Drosophila

(2012) Richard P. Meisel et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The 1.688 Repetitive DNA of Drosophila: Concerted Evolution at Different Genomic Scales and Association with Genes

(2011) Gustavo C. S. Kuhn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inter-island divergence within Drosophila mauritiana, a species of the D. simulans complex: Past history and/or speciation in progress?

(2011) D. LEGRAND et al.   MOLECULAR ECOLOGY

Wolbachia-Induced Cytoplasmic Incompatibility Is Associated with Decreased Hira Expression in Male Drosophila

(2011) Ya Zheng et al.   PLoS One

Sex Chromosome-Specific Regulation in the Drosophila Male Germline But Little Evidence for Chromosomal Dosage Compensation or Meiotic Inactivation

(2011) Colin D. Meiklejohn et al.   PLOS BIOLOGY

To Pool, or Not to Pool?

(2010) David J. Cutler et al.   GENETICS

On the Utility of Short Intron Sequences as a Reference for the Detection of Positive and Negative Selection in Drosophila

(2010) J. Parsch et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression

(2010) MARIA D. S. NUNES et al.   MOLECULAR ECOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

EFFECTIVE POPULATION SIZE AND THE FASTER-X EFFECT: AN EXTENDED MODEL

(2009) Beatriz Vicoso et al.   EVOLUTION

Recurrent Selection on the Winters sex-ratio Genes in Drosophila simulans

(2009) S. B. Kingan et al.   GENETICS

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

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

A role for a neo-sex chromosome in stickleback speciation

(2009) Jun Kitano et al.   NATURE

Evolution of the Drosophila Nuclear Pore Complex Results in Multiple Hybrid Incompatibilities

(2009) S. Tang et al.   SCIENCE

Genetic conflict and sex chromosome evolution

(2009) Colin D. Meiklejohn et al.   TRENDS IN ECOLOGY & EVOLUTION

A Complex Genetic Basis to X-Linked Hybrid Male Sterility Between Two Species of House Mice

(2008) J. M. Good et al.   GENETICS

The Impact of Founder Events on Chromosomal Variability in Multiply Mating Species

(2008) J. E. Pool et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Male-Driven Evolution in Drosophila

(2008) D. Bachtrog   MOLECULAR BIOLOGY AND EVOLUTION

Estimation of Isolation Times of the Island Species in the Drosophila simulans Complex from Multilocus DNA Sequence Data

(2008) Shannon R. McDermott et al.   PLoS One

A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids

(2008) N. Phadnis et al.   SCIENCE

Sex chromosomes and speciation in Drosophila

(2008) Daven C. Presgraves   TRENDS IN GENETICS

Contrasting the Efficacy of Selection on the X and Autosomes in Drosophila

(2007) N. D. Singh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers

(2003) Glenn-Peter Saetre et al.   MOLECULAR ECOLOGY