Hidden genetic variation shapes the structure of functional elements in Drosophila

SweepFinder2: increased sensitivity, robustness and flexibility

(2016) Michael DeGiorgio et al.   BIOINFORMATICS

An Incomplete Understanding of Human Genetic Variation

(2016) J. Huddleston et al.   GENETICS

Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome

(2016) Heath A. MacMillan et al.   Scientific Reports

FinisherSC: a repeat-aware tool for upgradingde novoassembly using long reads

(2015) Ka-Kit Lam et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

Detecting recent selective sweeps while controlling for mutation rate and background selection

(2015) Christian D. Huber et al.   MOLECULAR ECOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

Fine-Mapping Nicotine Resistance Loci in Drosophila Using a Multiparent Advanced Generation Inter-Cross Population

(2014) T. N. Marriage et al.   GENETICS

Using Drosophila melanogaster To Identify Chemotherapy Toxicity Genes

(2014) Elizabeth G. King et al.   GENETICS

Gene Expression Variation in Drosophila melanogaster Due to Rare Transposable Element Insertion Alleles of Large Effect

(2014) J. M. Cridland et al.   GENETICS

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

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

A Drosophila RNAi collection is subject to dominant phenotypic effects

(2014) Edward W Green et al.   NATURE METHODS

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

(2013) Kirk E. Lohmueller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

(2013) Julie M. Cridland et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

(2012) E. G. King et al.   GENOME RESEARCH

Drosophila melanogaster p24 trafficking proteins have vital roles in development and reproduction

(2012) Sehresh Saleem et al.   MECHANISMS OF DEVELOPMENT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Correction: HPRT Deficiency Coordinately Dysregulates Canonical Wnt and Presenilin-1 Signaling: A Neuro-Developmental Regulatory Role for a Housekeeping Gene?

(2011) Tae Hyuk Kang et al.   PLoS One

A Study of CNVs As Trait-Associated Polymorphisms and As Expression Quantitative Trait Loci

(2011) Eric R. Gamazon et al.   PLoS Genetics

Drosophila melanogaster recombination rate calculator

(2010) Anna-Sophie Fiston-Lavier et al.   GENE

Population Genomics of Transposable Elements in Drosophila melanogaster

(2010) D. A. Petrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

The human genome at ten

(2010)   NATURE

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

Intron Delays and Transcriptional Timing during Development

(2008) Ian A. Swinburne et al.   DEVELOPMENTAL CELL

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

(2008) J. J. Emerson et al.   SCIENCE