Massive gene amplification on a recently formed Drosophila Y chromosome

Recurrent gene co-amplification on Drosophila X and Y chromosomes

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The hpRNA/RNAi Pathway Is Essential to Resolve Intragenomic Conflict in the Drosophila Male Germline

(2018) Ching-Jung Lin et al.   DEVELOPMENTAL CELL

Spermatogenesis and the Evolution of Mammalian Sex Chromosomes

(2018) Erica L. Larson et al.   TRENDS IN GENETICS

De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture

(2018) Shivani Mahajan et al.   PLOS BIOLOGY

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

(2018) Wesley A. Brashear et al.   GENOME RESEARCH

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators

(2017) Daniel W Bellott et al.   NATURE GENETICS

Convergent evolution of Y chromosome gene content in flies

(2017) Shivani Mahajan et al.   Nature Communications

Sex Determination, Sex Chromosomes, and Karyotype Evolution in Insects

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Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive

(2016) Quentin Helleu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

(2016) Chong Chu et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Dosage Compensation inDrosophila

(2015) John C. Lucchesi et al.   Cold Spring Harbor Perspectives in Biology

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila

(2013) A. A. Alekseyenko et al.   GENES & DEVELOPMENT

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

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

Independent specialization of the human and mouse X chromosomes for the male germ line

(2013) Jacob L Mueller et al.   NATURE GENETICS

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

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

(2013) C. E. Ellison et al.   SCIENCE

The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation

(2013) Qi Zhou et al.   PLOS BIOLOGY

Sex-Biased Transcriptome Evolution in Drosophila

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

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

(2012) Julie Cocquet et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Are all sex chromosomes created equal?

(2011) Doris Bachtrog et al.   TRENDS IN GENETICS

Sex Chromosome-Specific Regulation in the Drosophila Male Germline But Little Evidence for Chromosomal Dosage Compensation or Meiotic Inactivation

(2011) Colin D. Meiklejohn et al.   PLOS BIOLOGY

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

(2010) Daniel W. Bellott et al.   NATURE

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome

(2010) Miriam K. Konkel et al.   SEMINARS IN CANCER BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

General gene movement off the X chromosome in the Drosophila genus

(2009) M. D. Vibranovski et al.   GENOME RESEARCH

Genetic conflict and sex chromosome evolution

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

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

(2009) Julie Cocquet et al.   PLOS BIOLOGY

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS

A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids

(2008) N. Phadnis et al.   SCIENCE

Genomic degradation of a young Y chromosome in Drosophila miranda

(2008) Doris Bachtrog et al.   GENOME BIOLOGY