Genome assembly and annotation of aDrosophila simulansstrain from Madagascar

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

Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations ofDrosophila melanogaster

(2013) Martin Kapun et al.   MOLECULAR ECOLOGY

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

(2013) Ram Vinay Pandey et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

(2012) Darren J. Obbard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in Drososphila pseudoobscura

(2012) Nicola Palmieri et al.   PLoS One

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

(2012) Russell B. Corbett-Detig et al.   PLoS Genetics

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Robert Kofler et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY