Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci inDrosophila melanogaster

(2017) Daniel E. Khost et al.   GENOME RESEARCH

Genetic conflicts: the usual suspects and beyond

(2017) Richard N. McLaughlin et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Human Y-chromosome variation in the genome-sequencing era

(2017) Mark A. Jobling et al.   NATURE REVIEWS GENETICS

Dissecting evolution and disease using comparative vertebrate genomics

(2017) Jennifer R. S. Meadows et al.   NATURE REVIEWS GENETICS

Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

(2017) Yibo Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Did sex chromosome turnover promote divergence of the major mammal groups?

(2016) Jennifer A. M. Graves   BIOESSAYS

Multicopy gene family evolution on primate Y chromosomes

(2016) Ana-Hermina Ghenu et al.   BMC GENOMICS

Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages

(2016) Matthew T. Oetjens et al.   Genome Biology and Evolution

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal

(2016) Pille Hallast et al.   GENOME RESEARCH

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

(2016) Marta Tomaszkiewicz et al.   GENOME RESEARCH

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

(2016) G David Poznik et al.   NATURE GENETICS

The Biology and Evolution of Mammalian Y Chromosomes

(2015) Jennifer F. Hughes et al.   Annual Review of Genetics

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   BIOPRESERVATION AND BIOBANKING

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

(2015) Gang Li et al.   GENOME RESEARCH

The pig X and Y Chromosomes: structure, sequence, and evolution

(2015) Benjamin M. Skinner et al.   GENOME RESEARCH

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

(2015) Monika Karmin et al.   GENOME RESEARCH

Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models

(2015) Brian W. Davis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   Biopreservation and Biobanking

Who's behind that mask and cape? The Asian leopard cat'sAgouti(ASIP) allele likely affects coat colour phenotype in the Bengal cat breed

(2014) L. C. Gershony et al.   ANIMAL GENETICS

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes

(2014) Y.Q. Shirleen Soh et al.   CELL

X–Y Interactions Underlie Sperm Head Abnormality in Hybrid Male House Mice

(2014) Polly Campbell et al.   GENETICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

(2014) Daniel W. Bellott et al.   NATURE

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

(2014) Michael J. Montague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Sex Chromosome Drive

(2014) Quentin Helleu et al.   Cold Spring Harbor Perspectives in Biology

Consed: a graphical editor for next-generation sequencing

(2013) David Gordon et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

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

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

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

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

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

(2013) Magali Soumillon et al.   Cell Reports

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The Contribution of the Y Chromosome to Hybrid Male Sterility in House Mice

(2012) P. Campbell et al.   GENETICS

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

(2012) Jennifer F. Hughes et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The Conflict within and the Escalating War between the Sex Chromosomes

(2012) Jeffrey M. Good   PLoS Genetics

A Genetic Basis for a Postmeiotic X Versus Y Chromosome Intragenomic Conflict in the Mouse

(2012) Julie Cocquet et al.   PLoS Genetics

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

A Gene Catalogue of the Euchromatic Male-Specific Region of the Horse Y Chromosome: Comparison with Human and Other Mammals

(2011) Nandina Paria et al.   PLoS One

Selfish genetic elements, genetic conflict, and evolutionary innovation

(2011) J. H. Werren   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences

(2010) Eduardo Eizirik et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2010) Jennifer F. Hughes et al.   NATURE

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genetic conflict and sex chromosome evolution

(2009) Colin D. Meiklejohn et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Temporal Dynamics of Processes Underlying Y Chromosome Degeneration

(2008) D. Bachtrog   GENETICS

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

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols