Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome

(2018) Emily G. Kaye et al.   Cell Reports

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

(2018) Shivani Mahajan et al.   PLOS BIOLOGY

Contingency and determinism in evolution: Replaying life’s tape

(2018) Zachary D. Blount et al.   SCIENCE

Predicting evolution

(2017) Michael Lässig et al.   Nature Ecology & Evolution

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

(2016) Jeffrey J. Quinn et al.   GENES & DEVELOPMENT

PionX sites mark the X chromosome for dosage compensation

(2016) Raffaella Villa et al.   NATURE

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation

(2016) Guray Kuzu et al.   PLoS Genetics

BFC: correcting Illumina sequencing errors

(2015) Heng Li   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

Numerous Transitions of Sex Chromosomes in Diptera

(2015) Beatriz Vicoso et al.   PLOS BIOLOGY

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

(2015) Qi Zhou et al.   PLoS Genetics

Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

(2015) Christopher E Ellison et al.   eLife

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

The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation

(2013) M. M. L. Soruco et al.   GENES & DEVELOPMENT

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

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

Efficient identification of Y chromosome sequences in the human andDrosophilagenomes

(2013) Antonio Bernardo Carvalho et al.   GENOME RESEARCH

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

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   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

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

(2012) Qi Zhou et al.   BMC GENOMICS

Chromosome-Wide Gene Silencing Initiates Y Degeneration in Drosophila

(2012) Qi Zhou et al.   CURRENT 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

Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution

(2012) N. Frankel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes

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

Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase

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

Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context

(2012) Artyom A. Alekseyenko et al.   PLoS Genetics

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

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

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Progress and prospects toward our understanding of the evolution of dosage compensation

(2009) Beatriz Vicoso et al.   CHROMOSOME RESEARCH

General gene movement off the X chromosome in the Drosophila genus

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

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Independent Origins of New Sex-Linked Chromosomes in the melanica and robusta Species Groups of Drosophila

(2008) Sergio V Flores et al.   BMC EVOLUTIONARY BIOLOGY

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

(2008) Artyom A. Alekseyenko et al.   CELL

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

(2008) S. W. Schaeffer et al.   GENETICS

Evidence for Male-Driven Evolution in Drosophila

(2008) D. Bachtrog   MOLECULAR BIOLOGY AND EVOLUTION

Divergence Times in Caenorhabditis and Drosophila Inferred from Direct Estimates of the Neutral Mutation Rate

(2008) A. D. Cutter   MOLECULAR BIOLOGY AND EVOLUTION

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