Origins and functional evolution of Y chromosomes across mammals

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Just how conserved is vertebrate sex determination?

(2013) Andrew Cutting et al.   DEVELOPMENTAL DYNAMICS

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

(2013) G. Li et al.   GENOME RESEARCH

Efficient identification of Y chromosome sequences in the human andDrosophilagenomes

(2013) Antonio Bernardo Carvalho et al.   GENOME RESEARCH

Lack of Dosage Compensation Accompanies the Arrested Stage of Sex Chromosome Evolution in Ostriches

(2013) Sofia Adolfsson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development

(2013) T.-C. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

(2013) Katie L Ayers et al.   GENOME BIOLOGY

Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of theDAZ(Deleted in AZoospermia) genes

(2012) Jennifer F. Hughes et al.   BIOESSAYS

Identification of avian W-linked contigs by short-read sequencing

(2012) Nancy Chen et al.   BMC GENOMICS

Identification of mediator complex 26 (Crsp7) gametologs on platypus X1 and Y5 sex chromosomes: a candidate testis-determining gene in monotremes?

(2012) Enkhjargal Tsend-Ayush et al.   CHROMOSOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

(2012) Jennifer F. Hughes et al.   NATURE

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Targeted Ubiquitination and Degradation of G-Protein-Coupled Receptor Kinase 5 by the DDB1-CUL4 Ubiquitin Ligase Complex

(2012) Ziyan Wu et al.   PLoS One

No Evidence for a Second Evolutionary Stratum during the Early Evolution of Mammalian Sex Chromosomes

(2012) Yukako Katsura et al.   PLoS One

W chromosome expression responds to female-specific selection

(2012) H. K. Moghadam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination

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

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Genome analyses substantiate male mutation bias in many species

(2011) Melissa A. Wilson Sayres et al.   BIOESSAYS

Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution

(2011) V. J. Murtagh et al.   GENOME RESEARCH

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Sry: the master switch in mammalian sex determination

(2010) K. Kashimada et al.   DEVELOPMENT

Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome?: A Simulation Study

(2010) G. A. B. Marais et al.   Genome Biology and Evolution

Identification of SOX3 as an XX male sex reversal gene in mice and humans

(2010) Edwina Sutton et al.   JOURNAL OF CLINICAL INVESTIGATION

Strong Purifying Selection at Genes Escaping X Chromosome Inactivation

(2010) C. Park et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

(2010) Jennifer F. Hughes et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

Genomic Analyses of Sex Chromosome Evolution

(2009) Melissa A. Wilson et al.   Annual Review of Genomics and Human Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years

(2009) Claudia Leticia Rodríguez Delgado et al.   CHROMOSOME RESEARCH

Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla, But Not Chimpanzee

(2009) Hiroki Goto et al.   JOURNAL OF MOLECULAR EVOLUTION

The avian Z-linked gene DMRT1 is required for male sex determination in the chicken

(2009) Craig A. Smith et al.   NATURE

Analysis of SINE and LINE repeat content of Y chromosomes in the platypus,Ornithorhynchus anatinus

(2009) R. Daniel Kortschak et al.   REPRODUCTION FERTILITY AND DEVELOPMENT

The Multicopy Gene Sly Represses the Sex Chromosomes in the Male Mouse Germline after Meiosis

(2009) Julie Cocquet et al.   PLOS BIOLOGY

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Evolution and Survival on Eutherian Sex Chromosomes

(2009) Melissa A. Wilson et al.   PLoS Genetics

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

The Chicken (Gallus gallus) Z Chromosome Contains at Least Three Nonlinear Evolutionary Strata

(2008) K. Nam et al.   GENETICS

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes

(2008) F. Veyrunes et al.   GENOME RESEARCH

Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome☆☆Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession No. EU879967-EU879988.

(2008) Alison J. Pearks Wilkerson et al.   GENOMICS

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes

(2008) Lukasz Potrzebowski et al.   PLOS BIOLOGY