Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Two sets of candidate crustacean wing homologues and their implication for the origin of insect wings

(2020) Courtney M. Clark-Hachtel et al.   Nature Ecology & Evolution

Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

(2020) Julian Catchen et al.   G3-Genes Genomes Genetics

Knockout of crustacean leg patterning genes suggests that insect wings and body walls evolved from ancient leg segments

(2020) Heather S. Bruce et al.   Nature Ecology & Evolution

Actors with Multiple Roles: Pleiotropic Enhancers and the Paradigm of Enhancer Modularity

(2019) Gonzalo Sabarís et al.   TRENDS IN GENETICS

Model systems for regeneration: zebrafish

(2019) Ines J. Marques et al.   DEVELOPMENT

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

(2019) Judhajeet Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

(2019) James J. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-option of wing-patterning genes underlies the evolution of the treehopper helmet

(2019) Cera R. Fisher et al.   Nature Ecology & Evolution

Enhancer identification and activity evaluation in the red flour beetle,Tribolium castaneum

(2018) Yi-Ting Lai et al.   DEVELOPMENT

Hyperactive piggyBac transposase improves transformation efficiency in diverse insect species

(2018) Kolja N. Eckermann et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome-Wide Regulatory Adaptation Shapes Population-Level Genomic Landscapes in Heliconius

(2018) James J Lewis et al.   MOLECULAR BIOLOGY AND EVOLUTION

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

(2017) Panayotis Vlastaridis et al.   GigaScience

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Genome editing in butterflies reveals that spalt promotes and Distal-less represses eyespot colour patterns

(2016) Linlin Zhang et al.   Nature Communications

A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes

(2016) Juli D. Uhl et al.   PLoS Genetics

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Co-option of an Ancestral Hox-Regulated Network Underlies a Recently Evolved Morphological Novelty

(2015) William J. Glassford et al.   DEVELOPMENTAL CELL

Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called “species signal”

(2015) Jacob M. Musser et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Distal-LessRegulates Eyespot Patterns and Melanization inBicyclusButterflies

(2013) ANTÓNIA MONTEIRO et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

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

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Bleach gel: A simple agarose gel for analyzing RNA quality

(2012) Patrick S. Aranda et al.   ELECTROPHORESIS

Rethinking Butterfly Eyespots

(2012) Lewis I. Held   Evolutionary Biology

A Single Origin for Nymphalid Butterfly Eyespots Followed by Widespread Loss of Associated Gene Expression

(2012) Jeffrey C. Oliver et al.   PLoS Genetics

Involvement of the conserved Hox gene Antennapedia in the development and evolution of a novel trait

(2011) Suzanne V Saenko et al.   EvoDevo

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

G-TRACE: rapid Gal4-based cell lineage analysis in Drosophila

(2009) Cory J Evans et al.   NATURE METHODS

Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve?

(2009) Antónia Monteiro et al.   PLOS BIOLOGY

A Gene-Based Linkage Map for Bicyclus anynana Butterflies Allows for a Comprehensive Analysis of Synteny with the Lepidopteran Reference Genome

(2009) Patrícia Beldade et al.   PLoS Genetics

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Conserved developmental processes and the formation of evolutionary novelties: examples from butterfly wings

(2008) S. V Saenko et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY