Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

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

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

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

(2013) Qi Zhou et al.   PLOS BIOLOGY

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

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

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

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

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

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Vincent J Lynch et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Galih Kunarso et al.   NATURE GENETICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

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

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

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

(2008) Artyom A. Alekseyenko et al.   CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes

(2008) Hsiao-Pei Yang et al.   GENOME BIOLOGY