Detecting selected haplotype blocks in evolve and resequence experiments

Modifying the Chi-square and the CMH test for population genetic inference: Adapting to overdispersion

(2020) Kerstin Spitzer et al.   Annals of Applied Statistics

Distinct patterns of selective sweep and polygenic adaptation in evolve and re-sequence studies

(2020) Neda Barghi et al.   Genome Biology and Evolution

Genetic redundancy fuels polygenic adaptation in Drosophila

(2019) Neda Barghi et al.   PLOS BIOLOGY

Shifting the paradigm in Evolve and Resequence studies: From analysis of single nucleotide polymorphisms to selected haplotype blocks

(2019) Neda Barghi et al.   MOLECULAR ECOLOGY

DNA Motifs Are Not General Predictors of Recombination in Two Drosophila Sister Species

(2019) James M Howie et al.   Genome Biology and Evolution

MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies

(2018) Christos Vlachos et al.   PLoS Computational Biology

Replicability of Introgression Under Linked, Polygenic Selection

(2018) Himani Sachdeva et al.   GENETICS

Experimental Evolution withCaenorhabditisNematodes

(2017) Henrique Teotónio et al.   GENETICS

Quantifying Selection with Pool-Seq Time Series Data

(2017) Thomas Taus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Drosophila simulans : A Species with Improved Resolution in Evolve and Resequence Studies

(2017) Neda Barghi et al.   G3-Genes Genomes Genetics

Experimental Evolution withCaenorhabditisNematodes

(2017) Henrique Teotónio et al.   GENETICS

Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

(2016) A. Jonas et al.   GENETICS

Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines

(2016) Philippa C. Griffin et al.   GENETICS

Uncovering the genetic signature of quantitative trait evolution with replicated time series data

(2016) S U Franssen et al.   HEREDITY

Reconstruction of Haplotype-Blocks Selected during Experimental Evolution

(2016) Susanne U. Franssen et al.   MOLECULAR BIOLOGY AND EVOLUTION

High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium

(2016) Marek Bukowicki et al.   Molecular Ecology Resources

Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines

(2016) Philippa C. Griffin 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

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing

(2014) Chang-Chang Cao et al.   BIOINFORMATICS

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

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

The Power to Detect Quantitative Trait Loci Using Resequenced, Experimentally Evolved Populations of Diploid, Sexual Organisms

(2014) James G. Baldwin-Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae

(2014) Molly K. Burke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Promises and limitations of hitchhiking mapping

(2013) Sergey V Nuzhdin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

(2013) Francisco A. Cubillos et al.   GENETICS

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data

(2013) D. Kessner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Combining Genome-Wide Methods to Investigate the Genetic Complexity of Courtship Song Variation in Drosophila melanogaster

(2013) Thomas L. Turner et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Guide for the Design of Evolve and Resequencing Studies

(2013) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

GENOMIC BASIS OF AGING AND LIFE-HISTORY EVOLUTION INDROSOPHILA MELANOGASTER

(2012) Silvia C. Remolina et al.   EVOLUTION

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

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

Improved whole-chromosome phasing for disease and population genetic studies

(2012) Olivier Delaneau et al.   NATURE METHODS

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Limits to the Rate of Adaptive Substitution in Sexual Populations

(2012) Daniel B. Weissman et al.   PLoS Genetics

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

(2011) R. Kofler et al.   BIOINFORMATICS

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo

(2011) Charles H. Langley et al.   GENETICS

PoolHap: Inferring Haplotype Frequencies from Pooled Samples by Next Generation Sequencing

(2011) Quan Long et al.   PLoS One

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

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

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

(2010) Molly K. Burke et al.   NATURE