Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design

(2016) Christoph Mayer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential expression of genes in the alate and apterous morphs of the brown citrus aphid, Toxoptera citricida

(2016) Feng Shang et al.   Scientific Reports

Fast fish face fewer mitochondrial mutations: Patterns of dN/dS across fish mitogenomes

(2015) Jeff H.T. Strohm et al.   GENE

Flight-induced changes in gene expression in the Glanville fritillary butterfly

(2015) Jouni Kvist et al.   MOLECULAR ECOLOGY

Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest

(2015) Christopher M. Jones et al.   MOLECULAR ECOLOGY

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

PANTHER version 10: expanded protein families and functions, and analysis tools

(2015) Huaiyu Mi 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

Gene Expression Profiling in Winged and Wingless Cotton Aphids, Aphis gossypii (Hemiptera: Aphididae)

(2014) Xiaowei Yang et al.   International Journal of Biological Sciences

Adaptive Evolution of Mitochondrial Energy Metabolism Genes Associated with Increased Energy Demand in Flying Insects

(2014) Yunxia Yang et al.   PLoS One

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Parallel evolution ofIDH2gene in cetaceans, primates and bats

(2013) Wei-Ming Ai et al.   FEBS LETTERS

Molecular characterization of the flightin gene in the wing-dimorphic planthopper, Nilaparvata lugens, and its evolution in Pancrustacea

(2013) Jian Xue et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

(2013) Walid H. Gharib 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

Dpp-induced Egfr signaling triggers postembryonic wing development in Drosophila

(2013) L. Paul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins

(2012) Yan-Bo Sun et al.   Genome Biology and Evolution

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mining GO Annotations for Improving Annotation Consistency

(2012) Daniel Faria et al.   PLoS One

Evolutionary Patterns of the Mitochondrial Genome in Metazoa: Exploring the Role of Mutation and Selection in Mitochondrial Protein–Coding Genes

(2011) S. Castellana et al.   Genome Biology and Evolution

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The First Molecular Phylogeny of Strepsiptera (Insecta) Reveals an Early Burst of Molecular Evolution Correlated with the Transition to Endoparasitism

(2011) Dino P. McMahon et al.   PLoS One

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

(2010) Joan Pons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis of the Brown Planthopper Nilaparvata lugens

(2010) Jian Xue et al.   PLoS One

Adaptive evolution of energy metabolism genes and the origin of flight in bats

(2010) Y.-Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

(2010) S. H. Eo et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability

(2009) Y.-Y. Shen et al.   GENOME RESEARCH

The difficulty of avoiding false positives in genome scans for natural selection

(2009) S. Mallick et al.   GENOME RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Genome duplication and gene-family evolution: The case of three OXPHOS gene families

(2008) Anna De Grassi et al.   GENE

Weight and nutrition affect pre-mRNA splicing of a muscle gene associated with performance, energetics and life history

(2008) J. H. Marden et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH