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

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

(2014) Todd H Oakley et al.   BMC BIOINFORMATICS

Ocular and Extraocular Expression of Opsins in the Rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa)

(2014) Jan Bielecki et al.   PLoS One

A Different Form of Color Vision in Mantis Shrimp

(2014) H. H. Thoen et al.   SCIENCE

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

(2013)   JOURNAL OF HEREDITY

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

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

The Drosophila Visual Cycle and De Novo Chromophore Synthesis Depends on rdhB

(2012) X. Wang et al.   JOURNAL OF NEUROSCIENCE

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Transcriptome Analysis of the Planarian Eye Identifies ovo as a Specific Regulator of Eye Regeneration

(2012) Sylvain W. Lapan et al.   Cell Reports

iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

(2011) Yi Zheng et al.   BMC BIOINFORMATICS

Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

(2011) Luke D Gardner et al.   BMC GENOMICS

Mesopelagic Cephalopods Switch between Transparency and Pigmentation to Optimize Camouflage in the Deep

(2011) Sarah Zylinski et al.   CURRENT BIOLOGY

Box Jellyfish Use Terrestrial Visual Cues for Navigation

(2011) Anders Garm et al.   CURRENT BIOLOGY

Phototransduction and clock gene expression in the troglobiont beetle Ptomaphagus hirtus of Mammoth cave

(2011) M. Friedrich et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A highly distributed Bragg stack with unique geometry provides effective camouflage for Loliginid squid eyes

(2011) A. L. Holt et al.   Journal of the Royal Society Interface

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Evidence for distributed light sensing in the skin of cuttlefish, Sepia officinalis

(2010) L. M. Mathger et al.   Biology Letters

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

(2010) Ajna S Rivera et al.   BMC EVOLUTIONARY BIOLOGY

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

Phototransduction and the Evolution of Photoreceptors

(2010) Gordon L. Fain et al.   CURRENT BIOLOGY

Requirement for an Enzymatic Visual Cycle in Drosophila

(2010) Xiaoyue Wang et al.   CURRENT BIOLOGY

The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway

(2010) D. C. Plachetzki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Ontogeny of sexual dimorphism via tissue duplication in an ostracod (Crustacea)

(2009) Ajna S. Rivera et al.   EVOLUTION & DEVELOPMENT

Structural colours create a flashing cue for sexual recognition and male quality in a Neotropical giant damselfly

(2009) Tom D. Schultz et al.   FUNCTIONAL ECOLOGY

Structure and optics of the eyes of the box jellyfish Chiropsella bronzie

(2009) Megan O’Connor et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY A-NEUROETHOLOGY SENSORY NEURAL AND BEHAVIORAL PHYSIOLOGY

Parallel Evolution of Nacre Building Gene Sets in Molluscs

(2009) Daniel J. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Eye evolution: common use and independent recruitment of genetic components

(2009) P. Vopalensky et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evidence for light perception in a bioluminescent organ

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

Recent developments in the MAFFT multiple sequence alignment program

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

Eye Evolution: The Blurry Beginning

(2008) Dan-E. Nilsson et al.   CURRENT BIOLOGY

Circular Polarization Vision in a Stomatopod Crustacean

(2008) Tsyr-Huei Chiou et al.   CURRENT BIOLOGY

Swim pacemakers in box jellyfish are modulated by the visual input

(2008) A. Garm et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY A-NEUROETHOLOGY SENSORY NEURAL AND BEHAVIORAL PHYSIOLOGY

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

Assembly of the cnidarian camera-type eye from vertebrate-like components

(2008) Zbynek Kozmik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Jellyfish vision starts with cAMP signaling mediated by opsin-Gs cascade

(2008) M. Koyanagi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY