A cure for the blues: opsin duplication and subfunctionalization for short-wavelength sensitivity in jewel beetles (Coleoptera: Buprestidae)

Variation in opsin genes correlates with signalling ecology in North American fireflies

(2015) S. E. Sander et al.   MOLECULAR ECOLOGY

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Review of the firefly visual system (Coleoptera: Lampyridae) and evolution of the opsin genes underlying color vision

(2015) Gavin J. Martin et al.   ORGANISMS DIVERSITY & EVOLUTION

A study of common scorpionfly (Mecoptera: Panorpidae) visual systems reveals the expression of a single opsin

(2015) Katie F. Manwaring et al.   ORGANISMS DIVERSITY & EVOLUTION

Extraordinary diversity of visual opsin genes in dragonflies

(2015) Ryo Futahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches

(2015) S. M. Tierney et al.   Royal Society Open Science

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms

(2014) Daniel I Speiser et al.   BMC BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Attraction to Different Wavelength Light Emitting Diodes (LEDs), the Compound Eye Structure, and opsin Genes in Nilaparvata lugens

(2014) Yukiko Matsumoto et al.   JAPANESE JOURNAL OF APPLIED ENTOMOLOGY AND ZOOLOGY

Physiological basis of phototaxis to near-infrared light in Nephotettix cincticeps

(2014) Motohiro Wakakuwa et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY A-NEUROETHOLOGY SENSORY NEURAL AND BEHAVIORAL PHYSIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

(2013) Jianyi Yang et al.   BIOINFORMATICS

Identification of G protein-coupled receptors in the pea aphid, Acyrthosiphon pisum

(2013) Chengjun Li et al.   GENOMICS

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Preservation of RNA and DNA from mammal samples under field conditions

(2013) Miguel Camacho-Sanchez et al.   Molecular Ecology Resources

Correction: Temporal Expression of Pelp1 during Proliferation and Osteogenic Differentiation of Rat Bone Marrow Mesenchymal Stem Cells

(2013) Jing Wang et al.   PLoS One

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

(2012) Jia-Ming Chang et al.   BMC BIOINFORMATICS

Opsin evolution and expression in Arthropod compound Eyes and Ocelli: Insights from the cricket Gryllus bimaculatus

(2012) Miriam J Henze et al.   BMC EVOLUTIONARY BIOLOGY

Evidence of red sensitive photoreceptors in Pygopleurus israelitus (Glaphyridae: Coleoptera) and its implications for beetle pollination in the southeast Mediterranean

(2012) J. Martínez-Harms et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY A-NEUROETHOLOGY SENSORY NEURAL AND BEHAVIORAL PHYSIOLOGY

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

UV Photoreceptors and UV-Yellow Wing Pigments in Heliconius Butterflies Allow a Color Signal to Serve both Mimicry and Intraspecific Communication

(2011) Seth M. Bybee et al.   AMERICAN NATURALIST

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Spectral sensitivity of the principal eyes of sunburst diving beetle, Thermonectus marmoratus (Coleoptera: Dytiscidae), larvae

(2011) S. Maksimovic et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Shedding new light on opsin evolution

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

Optimization of Trap Color for Emerald Ash Borer (Coleoptera: Buprestidae)

(2010) Joseph A. Francese et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Evolution and Mechanism of Spectral Tuning of Blue-Absorbing Visual Pigments in Butterflies

(2010) Motohiro Wakakuwa et al.   PLoS One

Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies

(2010) Adriana D. Briscoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Green-absorbingDrosophilaRh6 Visual Pigment Contains a Blue-shifting Amino Acid Substitution That Is Conserved in Vertebrates

(2009) Ernesto Salcedo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Laboratory and Field Response of the Emerald Ash Borer (Coleoptera: Buprestidae), to Selected Regions of the Electromagnetic Spectrum

(2009) Damon J. Crook et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

Spatial distribution of opsin-encoding mRNAs in the tiered larval retinas of the sunburst diving beetle Thermonectus marmoratus (Coleoptera: Dytiscidae)

(2009) S. Maksimovic et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A contact sex pheromone component of the emerald ash borer Agrilus planipennis Fairmaire (Coleoptera: Buprestidae)

(2009) Peter J. Silk et al.   NATURWISSENSCHAFTEN

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum

(2009) Hee Shin Kim et al.   NUCLEIC ACIDS RESEARCH

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites

(2008) Matthew N Ward et al.   BMC EVOLUTIONARY BIOLOGY

Crystal structure of squid rhodopsin

(2008) Midori Murakami et al.   NATURE

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

BLOSUM62 miscalculations improve search performance

(2008) Mark P Styczynski et al.   NATURE BIOTECHNOLOGY