Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

Antagonistic Roles of Dmrt1 and Foxl2 in Sex Differentiation via Estrogen Production in Tilapia as Demonstrated by TALENs

(2013) Ming-Hui Li et al.   ENDOCRINOLOGY

Evolutionary Dynamics of Sex-Biased Genes in a Hermaphrodite Fungus

(2013) Carrie A. Whittle 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

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

(2013) B. Vicoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq

(2013) BingXin Lu et al.   Science China-Life Sciences

Masculinization of Gene Expression Is Associated with Exaggeration of Male Sexual Dimorphism

(2013) Marie A. Pointer et al.   PLoS Genetics

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

(2012) Limin Fu et al.   BIOINFORMATICS

Disentangling the relationship between sex-biased gene expression and X-linkage

(2012) R. P. Meisel et al.   GENOME RESEARCH

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

(2011) Bonnie A Fraser et al.   BMC GENOMICS

Extracellular matrix molecules, their receptors, and secreted proteases in synaptic plasticity

(2011) Jakub Wlodarczyk et al.   Developmental Neurobiology

Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems

(2011) H. Ellegren   GENOME RESEARCH

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Forkhead transcription factors in ovarian function

(2011) Nina Henriette Uhlenhaut et al.   REPRODUCTION

Female-Biased Expression on the X Chromosome as a Key Step in Sex Chromosome Evolution in Threespine Sticklebacks

(2010) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ontogenetic Complexity of Sexual Dimorphism and Sex-Specific Selection

(2010) J. E. Mank et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

(2010) EVA-MARIA WILLING et al.   MOLECULAR ECOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Are sex-biased genes more dispensable?

(2009) J. E. Mank et al.   Biology Letters

A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: Evidence for masculinization of the transcriptome

(2009) Clayton M Small et al.   BMC GENOMICS

Females Battle to Suppress Their Inner Male

(2009) Andrew Sinclair et al.   CELL

Linkage Analysis Reveals the Independent Origin of Poeciliid Sex Chromosomes and a Case of Atypical Sex Inheritance in the Guppy (Poecilia reticulata)

(2009) N. Tripathi et al.   GENETICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Sex Chromosomes and the Evolution of Sexual Dimorphism: Lessons from the Genome

(2008) Judith E. Mank   AMERICAN NATURALIST

The unique genomic properties of sex-biased genes: Insights from avian microarray data

(2008) Judith E Mank et al.   BMC GENOMICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

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

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

Sexual Dimorphic Expression of Genes in Gonads During Early Differentiation of a Teleost Fish, the Nile Tilapia Oreochromis niloticus1

(2007) Shigeho Ijiri et al.   BIOLOGY OF REPRODUCTION