Contemporary evolution of a Lepidopteran species, Heliothis virescens , in response to modern agricultural practices

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

(2017) Julian M. Catchen et al.   Molecular Ecology Resources

Application of a dense genetic map for assessment of genomic responses to selection and inbreeding inHeliothis virescens

(2016) M. L. Fritz et al.   INSECT MOLECULAR BIOLOGY

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Host plant specialization in the generalist moth Heliothis virescens and the role of egg imprinting

(2014) Anne Karpinski et al.   EVOLUTIONARY ECOLOGY

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

A role for migration-linked genes and genomic islands in divergence of a songbird

(2014) Kristen Ruegg et al.   MOLECULAR ECOLOGY

Genome-wide single-generation signatures of local selection in the panmictic European eel

(2014) J. M. Pujolar et al.   MOLECULAR ECOLOGY

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Insect resistance to Bt crops: lessons from the first billion acres

(2013) Bruce E Tabashnik et al.   NATURE BIOTECHNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Diversity and convergence of sodium channel mutations involved in resistance to pyrethroids

(2013) Frank D. Rinkevich et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Role of cytochrome P450s in insecticide resistance: impact on the control of mosquito-borne diseases and use of insecticides on Earth

(2013) J.-P. David et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Assessing the Effects of Aedes aegypti kdr Mutations on Pyrethroid Resistance and Its Fitness Cost

(2013) Luiz Paulo Brito et al.   PLoS One

THE GENETIC ARCHITECTURE OF A COMPLEX ECOLOGICAL TRAIT: HOST PLANT USE IN THE SPECIALIST MOTH,HELIOTHIS SUBFLEXA

(2012) Sara J. Oppenheim et al.   EVOLUTION

LARGE-SCALE CANDIDATE GENE SCAN REVEALS THE ROLE OF CHEMORECEPTOR GENES IN HOST PLANT SPECIALIZATION AND SPECIATION IN THE PEA APHID

(2012) Carole M. Smadja et al.   EVOLUTION

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fitness costs associated with insecticide resistance

(2012) Adi Kliot et al.   PEST MANAGEMENT SCIENCE

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Impacts of genetically engineered crops on pesticide use in the U.S. -- the first sixteen years

(2012) Charles M Benbrook   Environmental Sciences Europe

Heliothis virescens and Bt cotton in the United States

(2012) Carlos A. Blanco   GM Crops & Food-Biotechnology in Agriculture and the Food Chain

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Genetic differentiation across North America in the generalist moth Heliothis virescens and the specialist H. subflexa

(2011) A. T. GROOT et al.   MOLECULAR ECOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Expression responses of nine cytochrome P450 genes to xenobiotics in the cotton bollworm Helicoverpa armigera

(2010) Xiaojie Zhou et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic Changes Accompanying the Evolution of Host Specialization in Drosophila sechellia

(2008) I. Dworkin et al.   GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY