Evidence of Adaptive Evolution and Relaxed Constraints in Sex-Biased Genes of South American and West Indies Fruit Flies (Diptera: Tephritidae)

Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti)

(2017) Carrie A. Whittle et al.   GENETICS

Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes

(2017) Francesco Papa et al.   GENOME RESEARCH

Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti)

(2017) Carrie A. Whittle et al.   GENETICS

The transcriptional architecture of phenotypic dimorphism

(2017) Judith E. Mank   Nature Ecology & Evolution

Molecular evolution of Odorant-binding proteins gene family in two closely related Anastrepha fruit flies

(2016) Emeline Boni Campanini et al.   BMC EVOLUTIONARY BIOLOGY

The Female Post-Mating Response Requires Genes Expressed in the Secondary Cells of the Male Accessory Gland in Drosophila melanogaster

(2016) J. L. Sitnik et al.   GENETICS

De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical ParthenogeneticDaphnia galeata

(2016) Ann Kathrin Huylmans et al.   Genome Biology and Evolution

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sperm competition shapes gene expression and sequence evolution in the ocellated wrasse

(2016) Rebecca Dean et al.   MOLECULAR ECOLOGY

Resolution of inter and intra-species relationships of the West Indian fruit fly Anastrepha obliqua

(2016) M. Scally et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Toward an Automated Identification of Anastrepha Fruit Flies in the fraterculus group (Diptera, Tephritidae)

(2016) P Perre et al.   NEOTROPICAL ENTOMOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini)

(2015) Philipp Brand et al.   BMC EVOLUTIONARY BIOLOGY

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes

(2015) Jorge A. Hongo et al.   BMC GENOMICS

Pheromone processing in Drosophila

(2015) Johannes Kohl et al.   CURRENT OPINION IN NEUROBIOLOGY

Sexual selection drives evolution and rapid turnover of male gene expression

(2015) Peter W. Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating mating compatibility within fruit fly cryptic species complexes and the potential role of sex pheromones in pre-mating isolation

(2015) M. Teresa Vera et al.   ZooKeys

Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

(2015) Janisete Silva et al.   ZooKeys

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

(2015) Nadezda Kryuchkova-Mostacci et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comprehensive transcriptome analysis of early male and female Bactrocera jarvisi embryos

(2014) Jennifer L Morrow et al.   BMC GENETICS

Accelerated Evolution of Morph-Biased Genes in Pea Aphids

(2014) Swapna R. Purandare et al.   MOLECULAR BIOLOGY AND EVOLUTION

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Ontogeny and Evolution of Sex-Biased Gene Expression in Drosophila melanogaster

(2014) Jennifer C. Perry et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

De Novo Assembly and Transcriptome Analysis of the Mediterranean Fruit Fly Ceratitis capitata Early Embryos

(2014) Marco Salvemini et al.   PLoS One

Is Sexual Conflict an "Engine of Speciation"?

(2014) S. Gavrilets   Cold Spring Harbor Perspectives in Biology

Reduced selection and accumulation of deleterious mutations in genes exclusively expressed in men

(2014) Moran Gershoni et al.   Nature Communications

Dual roles of Hh signaling in the regulation of somatic stem cell self-renewal and germline stem cell maintenance in Drosophila testis

(2013) Zhao Zhang et al.   CELL RESEARCH

Evolution of pre-zygotic and post-zygotic barriers to gene flow among three cryptic species within theAnastrepha fraterculuscomplex

(2013) Juan Rull et al.   ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

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

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

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

(2012) Limin Fu et al.   BIOINFORMATICS

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

(2012) J. A. Andres et al.   GENETICS

Little Evidence for Demasculinization of the Drosophila X Chromosome among Genes Expressed in the Male Germline

(2012) Colin D. Meiklejohn et al.   Genome Biology and Evolution

Sex-Biased Transcriptome Evolution in Drosophila

(2012) Raquel Assis et al.   Genome Biology and Evolution

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Discovery of Genes Related to Insecticide Resistance in Bactrocera dorsalis by Functional Genomic Analysis of a De Novo Assembled Transcriptome

(2012) Ju-Chun Hsu et al.   PLoS One

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

(2011) Peter L Chang et al.   BMC GENOMICS

A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

(2011) Dean A Baker et al.   BMC GENOMICS

Sex-dependent modulation of longevity by two Drosophila homologues of human Apolipoprotein D, GLaz and NLaz

(2011) Mario Ruiz et al.   EXPERIMENTAL GERONTOLOGY

Towards a More Nuanced Understanding of the Relationship between Sex-Biased Gene Expression and Rates of Protein-Coding Sequence Evolution

(2011) R. P. Meisel   MOLECULAR BIOLOGY AND EVOLUTION

Regulation of flagellar motility by the conserved flagellar protein CG34110/Ccdc135/FAP50

(2011) Yong Yang et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

Genomic divergence during speciation: causes and consequences

(2011) P. Nosil et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Drosophila Eggshell Production: Identification of New Genes and Coordination by Pxt

(2011) Tina L. Tootle et al.   PLoS One

Drosophila Dynein Intermediate Chain Gene, Dic61B, Is Required for Spermatogenesis

(2011) Roshan Fatima   PLoS One

The genomic response to courtship song stimulation in female Drosophila melanogaster

(2011) E. Immonen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Selection in the Rapid Evolution of Gamete Recognition Proteins in Marine Invertebrates

(2011) V. D. Vacquier et al.   Cold Spring Harbor Perspectives in Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Contrasts between adaptive coding and noncoding changes during human evolution

(2010) Ralph Haygood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Genetic Signature of Conditional Expression

(2009) J. D. Van Dyken et al.   GENETICS

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Molecular evolution of the major chemosensory gene families in insects

(2009) A Sánchez-Gracia et al.   HEREDITY

The Influence of Demography and Weak Selection on the McDonald-Kreitman Test: An Empirical Study in Drosophila

(2009) J. Parsch et al.   MOLECULAR BIOLOGY AND EVOLUTION

SNMP is a signaling component required for pheromone sensitivity in Drosophila

(2008) X. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pleiotropic Constraint Hampers the Resolution of Sexual Antagonism in Vertebrate Gene Expression

(2007) Judith E. Mank et al.   AMERICAN NATURALIST