Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila

Numerous Transitions of Sex Chromosomes in Diptera

(2015) Beatriz Vicoso et al.   PLOS BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

(2014) Kohta Yoshida et al.   PLoS Genetics

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

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

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

(2013) Daniel R. Schrider et al.   GENETICS

Reversal of an ancient sex chromosome to an autosome in Drosophila

(2013) Beatriz Vicoso et al.   NATURE

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

Dosage Compensation of the Sex Chromosomes

(2012) Christine M. Disteche   Annual Review of Genetics

Chromosome-Wide Gene Silencing Initiates Y Degeneration in Drosophila

(2012) Qi Zhou et al.   CURRENT BIOLOGY

Molecular Evolution in Nonrecombining Regions of the Drosophila melanogaster Genome

(2012) José L. Campos et al.   Genome Biology and Evolution

POF Regulates the Expression of Genes on the Fourth Chromosome in Drosophila melanogaster by Binding to Nascent RNA

(2012) A.-M. Johansson et al.   MOLECULAR AND CELLULAR BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription

(2012) Thomas Conrad et al.   NATURE REVIEWS GENETICS

Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters

(2012) T. Conrad et al.   SCIENCE

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain

(2012) Nicole C. Riddle et al.   PLoS Genetics

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Buffering and the evolution of chromosome-wide gene regulation

(2011) Per Stenberg et al.   CHROMOSOMA

Nonrandom Gene Loss from the Drosophila miranda Neo-Y Chromosome

(2011) Vera B. Kaiser et al.   Genome Biology and Evolution

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis

(2010) W. Leung et al.   GENETICS

A supermatrix-based molecular phylogeny of the family Drosophilidae

(2010) KIM VAN DER LINDE et al.   Genetics Research

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Nonrecombining Genes in a Recombination Environment: The Drosophila "Dot" Chromosome

(2010) J. R. Powell et al.   MOLECULAR BIOLOGY AND EVOLUTION

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley 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

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

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Recombination Yet Inefficient Selection along the Drosophila melanogaster Subgroup's Fourth Chromosome

(2009) J. Roman Arguello et al.   MOLECULAR BIOLOGY AND EVOLUTION

Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation

(2009) Marnie E Gelbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide Analysis Reveals MOF as a Key Regulator of Dosage Compensation and Gene Expression in Drosophila

(2008) Jop Kind et al.   CELL

A Sequence Motif within Chromatin Entry Sites Directs MSL Establishment on the Drosophila X Chromosome

(2008) Artyom A. Alekseyenko et al.   CELL

Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia

(2008) Gabriel A.B. Marais et al.   CURRENT BIOLOGY

Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes

(2008) A. Bhutkar et al.   GENETICS

The Temporal Dynamics of Processes Underlying Y Chromosome Degeneration

(2008) D. Bachtrog   GENETICS

DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya

(2008) W. Zhang et al.   GENOME RESEARCH

The effects of deleterious mutations on evolution in non-recombining genomes

(2008) Vera B. Kaiser et al.   TRENDS IN GENETICS

SU(VAR)3-7 Links Heterochromatin and Dosage Compensation in Drosophila

(2008) Anne Spierer et al.   PLoS Genetics

Genomic degradation of a young Y chromosome in Drosophila miranda

(2008) Doris Bachtrog et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY