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

MLSeq: Machine learning interface for RNA-sequencing data

(2019) Dincer Goksuluk et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Evo–Devo: The Double Identity of Insect Wings

(2018) Yoshinori Tomoyasu   CURRENT BIOLOGY

Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes

(2018) Cong Liang et al.   Genome Biology and Evolution

A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle

(2018) Yonggang Hu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Review of the Genus Cladonota Stål (Hemiptera: Membracidae: Membracinae: Hypsoprorini) with Keys, Illustrations of Adults, and Known Nymphs, and Description of a New Species from Costa Rica. I. Introduction and Subgenus Falculifera McKamey

(2018) Dawn J. Flynn   PROCEEDINGS OF THE ENTOMOLOGICAL SOCIETY OF WASHINGTON

Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis

(2017) Meng Mao et al.   Genome Biology and Evolution

A comprehensive simulation study on classification of RNA-Seq data

(2017) Gökmen Zararsız et al.   PLoS One

Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development

(2016) Heidi Connahs et al.   BMC GENOMICS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

A phylogeny of the treehopper subfamily Heteronotinae reveals convergent pronotal traits (Hemiptera: Auchenorrhyncha: Membracidae)

(2016) OLIVIA EVANGELISTA et al.   SYSTEMATIC ENTOMOLOGY

Exploring the origin of insect wings from an evo-devo perspective

(2016) Courtney M Clark-Hachtel et al.   Current Opinion in Insect Science

Tergal and pleural structures contribute to the formation of ectopic prothoracic wings in cockroaches

(2016) Moysés Elias-Neto et al.   Royal Society Open Science

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

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Origin and diversification of wings: Insights from a neopteran insect

(2015) Victor Medved et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wing patterning genes of Nilaparvata lugens identification by transcriptome analysis, and their differential expression profile in wing pads between brachypterous and macropterous morphs

(2015) Kai-yin LI et al.   Journal of Integrative Agriculture

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development

(2014) David Plaza et al.   BMC GENOMICS

Emergence of tissue sensitivity to Hox protein levels underlies the evolution of an adaptive morphological trait

(2014) Peter Nagui Refki et al.   DEVELOPMENTAL BIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Insights into the Development and Evolution of Exaggerated Traits Using De Novo Transcriptomes of Two Species of Horned Scarab Beetles

(2014) Ian A. Warren et al.   PLoS One

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

(2014) Natalie Ward et al.   PLoS One

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

(2014) Arnaud Martin et al.   EvoDevo

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers

(2013) Z. C. Zhou et al.   Molecular Ecology Resources

Insights into insect wing origin provided by functional analysis of vestigial in the red flour beetle, Tribolium castaneum

(2013) C. M. Clark-Hachtel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insect Morphological Diversification Through the Modification of Wing Serial Homologs

(2013) T. Ohde et al.   SCIENCE

Gene regulatory networks reused to build novel traits

(2012) Antónia Monteiro   BIOESSAYS

Using Genetic Networks and Homology to Understand the Evolution of Phenotypic Traits

(2012) Amy R. McCune et al.   CURRENT GENOMICS

On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence

(2012) István Mikó et al.   PLoS One

Function, Developmental Genetics, and Fitness Consequences of a Sexually Antagonistic Trait

(2012) A. Khila et al.   SCIENCE

Classification and clustering of sequencing data using a Poisson model

(2011) Daniela M. Witten   Annals of Applied Statistics

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Body plan innovation in treehoppers through the evolution of an extra wing-like appendage

(2011) Benjamin Prud’homme et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The treehopper's helmet is not homologous with wings (Hemiptera: Membracidae)

(2011) KAZUNORI YOSHIZAWA   SYSTEMATIC ENTOMOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Evolution of insect development: to the hemimetabolous paradigm

(2010) Taro Mito et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Repeated Co-options of Exoskeleton Formation during Wing-to-Elytron Evolution in Beetles

(2009) Yoshinori Tomoyasu et al.   CURRENT BIOLOGY

Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae)

(2009) A. S. Chanderbali et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential recruitment of limb patterning genes during development and diversification of beetle horns

(2009) A. P. Moczek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Sean B. Carroll   CELL

Prepatterning the Drosophila notum: The three genes of the iroquois complex play intrinsically distinct roles

(2008) Aissam Ikmi et al.   DEVELOPMENTAL BIOLOGY