Complex modular architecture around a simple toolkit of wing pattern genes

Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly

(2016) R. Rebecca Love et al.   BMC GENOMICS

The gene cortex controls mimicry and crypsis in butterflies and moths

(2016) Nicola J. Nadeau et al.   NATURE

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Warning signals are under positive frequency-dependent selection in nature

(2016) Mathieu Chouteau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis -Regulatory Evolution in Lepidoptera

(2016) James J. Lewis et al.   Cell Reports

Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

(2016) John W. Davey et al.   G3-Genes Genomes Genetics

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

(2016) Richard W. R. Wallbank et al.   PLOS BIOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Divergence with gene flow across a speciation continuum of Heliconius butterflies

(2015) Megan A. Supple et al.   BMC EVOLUTIONARY BIOLOGY

The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry

(2015) M. R. Kronforst et al.   GENETICS

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2Recombinant Crosses as an Example

(2015) Pasi Rastas et al.   Genome Biology and Evolution

Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies

(2015) B Huber et al.   HEREDITY

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Blue: correcting sequencing errors using consensus and context

(2014) Paul Greenfield et al.   BIOINFORMATICS

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems

(2014) Arnaud Martin et al.   DEVELOPMENTAL BIOLOGY

StableHeliconiusbutterfly hybrid zones are correlated with a local rainfall peak at the edge of the Amazon basin

(2014) Neil Rosser et al.   EVOLUTION

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

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

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

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

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Ancient homology underlies adaptive mimetic diversity across butterflies

(2014) Jason R. Gallant et al.   Nature Communications

Multiple recent co-options of Optix associated with novel traits in adaptive butterfly wing radiations

(2014) Arnaud Martin et al.   EvoDevo

Transcriptional Control of Steroid Biosynthesis Genes in the Drosophila Prothoracic Gland by Ventral Veins Lacking and Knirps

(2014) E. Thomas Danielsen et al.   PLoS Genetics

Lep-MAP: fast and accurate linkage map construction for large SNP datasets

(2013) Pasi Rastas et al.   BIOINFORMATICS

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

(2013) M. A. Supple et al.   GENOME RESEARCH

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

Multi-Allelic Major Effect Genes Interact with Minor Effect QTLs to Control Adaptive Color Pattern Variation in Heliconius erato

(2013) Riccardo Papa et al.   PLoS One

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

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

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

Partial Complementarity of the Mimetic Yellow Bar Phenotype in Heliconius Butterflies

(2012) Luana S. Maroja et al.   PLoS One

Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand

(2012) A. Martin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

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

(2011) Michael Remmert et al.   NATURE METHODS

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Wing patterning gene redefines the mimetic history of Heliconius butterflies

(2011) H. M. Hines et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Radial Spoke Protein 3 Is a Mammalian Protein Kinase A-anchoring Protein That Binds ERK1/2

(2009) Arif Jivan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Butterfly speciation and the distribution of gene effect sizes fixed during adaptation

(2008) S W Baxter et al.   HEREDITY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY