The molecular genetic basis of herbivory between butterflies and their host plants

Arabidopsis glucosinolates trigger a contrasting transcriptomic response in a generalist and a specialist herbivore

(2017) Fabian Schweizer et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic basis of octanoic acid resistance inDrosophila sechellia: functional analysis of a fine-mapped region

(2017) J. M. Andrade López et al.   MOLECULAR ECOLOGY

The Layers of Plant Responses to Insect Herbivores

(2016) Meredith C. Schuman et al.   Annual Review of Entomology

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Glutathione S-transferase SlGSTE1 in Spodoptera litura may be associated with feeding adaptation of host plants

(2016) Xiaopeng Zou et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

The transcriptome response ofHeliconius melpomenelarvae to a novel host plant

(2016) Quan-You Yu et al.   MOLECULAR ECOLOGY

Arabidopsis MYC Transcription Factors Are the Target of Hormonal Salicylic Acid/Jasmonic Acid Cross Talk in Response toPieris brassicaeEgg Extract

(2016) André Schmiesing et al.   PLANT PHYSIOLOGY

Recurrent specialization on a toxic fruit in an islandDrosophilapopulation

(2016) Amir Yassin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Drosophila to study the evolution of herbivory and diet specialization

(2016) Simon C Groen et al.   Current Opinion in Insect Science

Plant Responses to Insect Egg Deposition

(2015) Monika Hilker et al.   Annual Review of Entomology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Control of Synaptic Connectivity by a Network of Drosophila IgSF Cell Surface Proteins

(2015) Robert A. Carrillo et al.   CELL

Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions

(2015) Camille Meslin et al.   MOLECULAR BIOLOGY AND EVOLUTION

A new cyanogenic metabolite in Arabidopsis required for inducible pathogen defence

(2015) Jakub Rajniak et al.   NATURE

Transcriptional networks in plant immunity

(2015) Kenichi Tsuda et al.   NEW PHYTOLOGIST

Indole Glucosinolate Biosynthesis Limits Phenylpropanoid Accumulation inArabidopsis thaliana

(2015) Jeong Im Kim et al.   PLANT CELL

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coselected genes determine adaptive variation in herbivore resistance throughout the native range ofArabidopsis thaliana

(2015) Benjamin Brachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Evolution in an Ancient Detoxification Pathway Is Coupled with a Transition to Herbivory in the Drosophilidae

(2014) Andrew D. Gloss et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

(2014) Marcus Lechner et al.   PLoS One

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

STEPWISE EVOLUTION OF RESISTANCE TO TOXIC CARDENOLIDES VIA GENETIC SUBSTITUTIONS IN THE NA+/K+-ATPASE OF MILKWEED BUTTERFLIES (LEPIDOPTERA: DANAINI)

(2013) Georg Petschenka et al.   EVOLUTION

A Locus in Drosophila sechellia Affecting Tolerance of a Host Plant Toxin

(2013) Eric A. Hungate et al.   GENETICS

The family of Peps and their precursors in Arabidopsis: differential expression and localization but similar induction of pattern-triggered immune responses

(2013) S. Bartels et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly

(2012) Noah K. Whiteman et al.   Genome Biology and Evolution

Signalling of Arabidopsis thaliana response to Pieris brassicae eggs shares similarities with PAMP-triggered immunity

(2012) Caroline Gouhier-Darimont et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

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

Evolution of a Large, Conserved, and Syntenic Gene Family in Insects

(2012) Neethu Shah et al.   G3-Genes Genomes Genetics

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Cretaceous origin and repeated tertiary diversification of the redefined butterflies

(2011) M. Heikkila et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Differential Effects of Indole and Aliphatic Glucosinolates on Lepidopteran Herbivores

(2010) René Müller et al.   JOURNAL OF CHEMICAL ECOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Myo-inositol abolishes salicylic acid-dependent cell death and pathogen defence responses triggered by peroxisomal hydrogen peroxide

(2010) Sejir Chaouch et al.   NEW PHYTOLOGIST

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunity and other defenses in pea aphids, Acyrthosiphon pisum

(2010) Nicole M Gerardo et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

H2O2-Activated Up-Regulation of Glutathione in Arabidopsis Involves Induction of Genes Encoding Enzymes Involved in Cysteine Synthesis in the Chloroplast

(2009) Guillaume Queval et al.   Molecular Plant

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

(2009) Da Wei Huang et al.   Nature Protocols

Macroevolution and the biological diversity of plants and herbivores

(2009) D. J. Futuyma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Glucosinolates in Insect-Plant Relationships and Multitrophic Interactions

(2008) Richard J. Hopkins et al.   Annual Review of Entomology

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms

(2008) Xiaoyi Gao et al.   GENETIC EPIDEMIOLOGY

The glutathione-deficient mutantpad2-1accumulates lower amounts of glucosinolates and is more susceptible to the insect herbivoreSpodoptera littoralis

(2008) Klaus Schlaeppi et al.   PLANT JOURNAL

Plant Immunity to Insect Herbivores

(2007) Gregg A. Howe et al.   Annual Review of Plant Biology