Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata

The OGCleaner: filtering false-positive homology clusters

(2016) M. Stanley Fujimoto et al.   BIOINFORMATICS

Detecting false positive sequence homology: a machine learning approach

(2016) M. Stanley Fujimoto et al.   BMC BIOINFORMATICS

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

(2016) Nathan P. Lord et al.   BMC EVOLUTIONARY BIOLOGY

The Dynamic Evolutionary History of Pancrustacean Eyes and Opsins

(2015) Miriam J. Henze et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

I-TASSER server: new development for protein structure and function predictions

(2015) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

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

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

The Influence of Selection for Protein Stability on dN/dS Estimations

(2014) Pouria Dasmeh et al.   Genome Biology and Evolution

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Spectral Sensitivities and Color Signals in a Polymorphic Damselfly

(2014) Shao-chang Huang et al.   PLoS One

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

(2013) Huiguang Yi et al.   NUCLEIC ACIDS RESEARCH

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability

(2013) Pouria Dasmeh et al.   PLoS Computational Biology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.)

(2012) Joan Ho-Huu et al.   BMC EVOLUTIONARY BIOLOGY

Opsins in Onychophora (Velvet Worms) Suggest a Single Origin and Subsequent Diversification of Visual Pigments in Arthropods

(2012) Lars Hering et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Metazoan opsin evolution reveals a simple route to animal vision

(2012) R. Feuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans

(2011) Kendra J. Lipinski et al.   CURRENT BIOLOGY

Olfaction in dragonflies: Electrophysiological evidence

(2011) Manuela Rebora et al.   JOURNAL OF INSECT PHYSIOLOGY

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

Heterozygote advantage as a natural consequence of adaptation in diploids

(2011) D. Sellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shedding new light on opsin evolution

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

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

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

Contrasting Modes of Evolution of the Visual Pigments in Heliconius Butterflies

(2010) F. Yuan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

(2010) Benjamin Schuster-Böckler et al.   PLoS One

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Adaptive evolution of young gene duplicates in mammals

(2009) M. V. Han et al.   GENOME RESEARCH

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

Evolution of Dim-Light and Color Vision Pigments

(2008) Shozo Yokoyama   Annual Review of Genomics and Human Genetics

Gene Dosage and Gene Duplicability

(2008) W. Qian et al.   GENETICS

Crystal structure of squid rhodopsin

(2008) Midori Murakami et al.   NATURE

Evolution of vertebrate visual pigments

(2008) James K. Bowmaker   VISION RESEARCH

Role of Duplicate Genes in Robustness against Deleterious Human Mutations

(2008) Tzu-Lin Hsiao et al.   PLoS Genetics