Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

The search for loci under selection: trends, biases and progress

(2018) Collin W. Ahrens et al.   MOLECULAR ECOLOGY

Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations

(2018) Lidia Mateo et al.   Scientific Reports

Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster

(2018) Sara Guirao-Rico et al.   Current Opinion in Insect Science

Is diapause an ancient adaptation in Drosophila ?

(2017) Valeria Zonato et al.   JOURNAL OF INSECT PHYSIOLOGY

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster

(2017) Hung Le Manh et al.   Scientific Reports

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Human adaptation and evolution by segmental duplication

(2016) Megan Y Dennis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

(2016) Martin Kapun et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

(2016) Justin B. Lack et al.   MOLECULAR BIOLOGY AND EVOLUTION

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation inDrosophila melanogaster

(2016) Alan O. Bergland et al.   MOLECULAR ECOLOGY

Controlling false discoveries in genome scans for selection

(2016) Olivier François et al.   MOLECULAR ECOLOGY

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Going global by adapting local: A review of recent human adaptation

(2016) S. Fan et al.   SCIENCE

Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

(2016) Miriam Merenciano et al.   PLoS Genetics

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Indy gene variation in natural populations confers fitness advantage and life span extension through transposon insertion

(2016) Chen-Tseh Zhu et al.   Aging-US

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

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

The Release 6 reference sequence of theDrosophila melanogastergenome

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

Adaptive Evolution Is Substantially Impeded by Hill–Robertson Interference inDrosophila

(2015) David Castellano et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring the Phenotypic Space and the Evolutionary History of a Natural Mutation inDrosophila melanogaster

(2015) Anna Ullastres et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unique transposon landscapes are pervasive acrossDrosophila melanogastergenomes

(2015) Reazur Rahman et al.   NUCLEIC ACIDS RESEARCH

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

(2015) Helen Attrill et al.   NUCLEIC ACIDS RESEARCH

Genetic basis of transcriptome diversity inDrosophila melanogaster

(2015) Wen Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards the identification of the loci of adaptive evolution

(2015) Carolina Pardo-Diaz et al.   Methods in Ecology and Evolution

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Global Diversity Lines–A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains

(2015) Jennifer K. Grenier et al.   G3-Genes Genomes Genetics

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

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

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

Population Genomics of Transposable Elements inDrosophila

(2014) Maite G. Barrón et al.   Annual Review of Genetics

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

(2014) Seung Park et al.   BMC GENOMICS

Adaptations to local environments in modern human populations

(2014) Choongwon Jeong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Resources for Functional Genomics Studies in Drosophila melanogaster

(2014) Stephanie E. Mohr et al.   GENETICS

Parallel Geographic Variation in Drosophila melanogaster

(2014) Josie A. Reinhardt et al.   GENETICS

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure

(2014) Anna Ferrer-Admetlla et al.   MOLECULAR BIOLOGY AND EVOLUTION

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

The transposable elementBari-Jhehmediates oxidative stress response in Drosophila

(2014) Lain Guio et al.   MOLECULAR ECOLOGY

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

(2014) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome

(2014) A. Kuhn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

(2014) Lidia Mateo et al.   PLoS Genetics

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

An Age-of-Allele Test of Neutrality for Transposable Element Insertions

(2013) J. P. Blumenstiel et al.   GENETICS

Whole-genome sequencing of two North AmericanDrosophila melanogasterpopulations reveals genetic differentiation and positive selection

(2013) D. Campo et al.   MOLECULAR ECOLOGY

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster

(2013) Héloïse Bastide et al.   PLoS Genetics

Using the Köppen classification to quantify climate variation and change: An example for 1901–2010

(2013) Deliang Chen et al.   Environmental Development

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

The Drosophila melanogaster Genetic Reference Panel

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

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron 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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The struggle for life of the genome's selfish architects

(2011) Aurélie Hua-Van et al.   Biology Direct

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Heterozygote advantage as a natural consequence of adaptation in diploids

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

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Drosophila melanogaster recombination rate calculator

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

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster

(2010) B. Kolaczkowski et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop 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

Population Genomics of Transposable Elements in Drosophila melanogaster

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

Adaptation – not by sweeps alone

(2010) Jonathan K. Pritchard et al.   NATURE REVIEWS GENETICS

Mutations and quantitative genetic variation: lessons from Drosophila

(2010) T. F. C. Mackay   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

(2010) Josefa González et al.   PLoS Genetics

Copy Number Variation and Transposable Elements Feature in Recent, Ongoing Adaptation at the Cyp6g1 Locus

(2010) Joshua M. Schmidt et al.   PLoS Genetics

A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster

(2009) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

(2008) Josefa González et al.   PLOS BIOLOGY

Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes

(2008) Hsiao-Pei Yang et al.   GENOME BIOLOGY