Pooled Sequencing and Rare Variant Association Tests for Identifying the Determinants of Emerging Drug Resistance in Malaria Parasites

A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

(2014) T. M. Beissinger et al.   GENETICS

Population-Genetic Inference from Pooled-Sequencing Data

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

Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system

(2014) Mehdi Ghorbal et al.   NATURE BIOTECHNOLOGY

Spread of Artemisinin Resistance in Plasmodium falciparum Malaria

(2014) Elizabeth A. Ashley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts

(2014) Thomas D. Otto et al.   Nature Communications

Sequence Kernel Association Tests for the Combined Effect of Rare and Common Variants

(2013) Iuliana Ionita-Laza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genetic Evaluation of the Performance of Malaria Parasite Clearance Rate Metrics

(2013) Standwell C. Nkhoma et al.   JOURNAL OF INFECTIOUS DISEASES

Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

(2013) Francois Olivier Hebert et al.   MOLECULAR ECOLOGY

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

(2013) Frédéric Ariey et al.   NATURE

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

(2013) Olivo Miotto et al.   NATURE GENETICS

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect

(2013) Kevin R. Thornton et al.   PLoS Genetics

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

(2013) Héloïse Bastide et al.   PLoS Genetics

Malaria Burden and Artemisinin Resistance in the Mobile and Migrant Population on the Thai–Myanmar Border, 1999–2011: An Observational Study

(2013) Verena I. Carrara et al.   PLOS MEDICINE

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Emergence of artemisinin-resistant malaria on the western border of Thailand: a longitudinal study

(2012) Aung Pyae Phyo et al.   LANCET

Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples

(2012) Meera Venkatesan et al.   MALARIA JOURNAL

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

(2012) S. Takala-Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Major Genome Region Underlying Artemisinin Resistance in Malaria

(2012) I. H. Cheeseman et al.   SCIENCE

Standing Genetic Variation and the Evolution of Drug Resistance in HIV

(2012) Pleuni Simone Pennings   PLoS Computational Biology

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

(2011) R. Kofler et al.   BIOINFORMATICS

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

Standardizing the measurement of parasite clearance in falciparum malaria: the parasite clearance estimator

(2011) Jennifer A Flegg et al.   MALARIA JOURNAL

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

High Heritability of Malaria Parasite Clearance Rate Indicates a Genetic Basis for Artemisinin Resistance in Western Cambodia

(2010) Tim J. C. Anderson et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2010) Molly K. Burke et al.   NATURE

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Erratum: Artemisinin resistance: current status and scenarios for containment

(2010) Arjen M. Dondorp et al.   NATURE REVIEWS MICROBIOLOGY

Tracking footprints of artificial selection in the dog genome

(2010) J. M. Akey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes

(2010) D. E. Neafsey et al.   SCIENCE

Genetic Evidence for High-Altitude Adaptation in Tibet

(2010) T. S. Simonson et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION

(2009) Jeffrey L. Feder et al.   EVOLUTION

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Artemisinin-Resistant Malaria in Asia

(2009) Harald Noedl et al.   NEW ENGLAND JOURNAL OF MEDICINE

Artemisinin Resistance inPlasmodium falciparumMalaria

(2009) Arjen M. Dondorp et al.   NEW ENGLAND JOURNAL OF MEDICINE

Adaptive Copy Number Evolution in Malaria Parasites

(2008) Shalini Nair et al.   PLoS Genetics