A New Genome-Wide Method to Track Horizontally Transferred Sequences: Application to Drosophila

Horizontal transfer of OC1 transposons in the Tasmanian devil

(2013) Clement Gilbert et al.   BMC GENOMICS

Horizontal Transfer and Evolution of Prokaryote Transposable Elements in Eukaryotes

(2013) Clément Gilbert et al.   Genome Biology and Evolution

A Selective Sweep across Species Boundaries in Drosophila

(2013) Cara L. Brand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates

(2012) Jerzy Jurka et al.   Biology Direct

Integrating Prior Knowledge in Multiple Testing under Dependence with Applications to Detecting Differential DNA Methylation

(2012) Pei Fen Kuan et al.   BIOMETRICS

Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

(2012) Elaine Dias et al.   BMC EVOLUTIONARY BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Methods for detection of horizontal transfer of transposable elements in complete genomes

(2012) Marcos Oliveira de Carvalho et al.   GENETICS AND MOLECULAR BIOLOGY

Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives

(2012) Gabriel Luz Wallau et al.   Genome Biology and Evolution

Reconstructing the Evolutionary History of Transposable Elements

(2012) Arnaud Le Rouzic et al.   Genome Biology and Evolution

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

(2012) T. T. Hu et al.   GENOME RESEARCH

FlyBase: improvements to the bibliography

(2012) Steven J. Marygold et al.   NUCLEIC ACIDS RESEARCH

Lateral gene transfer as a support for the tree of life

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

Quantifying introgression risk with realistic population genetics

(2012) A. Ghosh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Families of transposable elements, population structure and the origin of species

(2011) Jerzy Jurka et al.   Biology Direct

Models, algorithms and programs for phylogeny reconciliation

(2011) J.-P. Doyon et al.   BRIEFINGS IN BIOINFORMATICS

Transfer of a chromosomal Maverick to endogenous bracovirus in a parasitoid wasp

(2011) C. Dupuy et al.   GENETICA

What makes transposable elements move in the Drosophila genome?

(2011) M P García Guerreiro   HEREDITY

Vertical inheritance and bursts of transposition have shaped the evolution of the BS non-LTR retrotransposon in Drosophila

(2011) Adriana Granzotto et al.   MOLECULAR GENETICS AND GENOMICS

Towards more robust methods of alien gene detection

(2011) Rajeev K. Azad et al.   NUCLEIC ACIDS RESEARCH

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes

(2010) Emmanuelle Lerat et al.   GENE

Ninety Years of Drosophila melanogaster Hybrids

(2010) Daniel A. Barbash   GENETICS

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

Multiple testing in genome-wide association studies via hidden Markov models

(2009) Zhi Wei et al.   BIOINFORMATICS

Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

(2009) Nicole de la Chaux et al.   BMC EVOLUTIONARY BIOLOGY

Transpositionally active episomal hAT elements

(2009) David A O'Brochta et al.   BMC MOLECULAR BIOLOGY

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally

(2009) L. A. Weinert et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

(2009) Carolina Bartolomé et al.   GENOME BIOLOGY

African Drosophila melanogaster and D. simulans Populations Have Similar Levels of Sequence Variability, Suggesting Comparable Effective Population Sizes

(2008) Viola Nolte et al.   GENETICS

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus

(2008) D. A. Ray et al.   GENOME RESEARCH

Revisiting horizontal transfer of transposable elements in Drosophila

(2008) E L S Loreto et al.   HEREDITY

Multiple invasions of Errantivirus in the genus Drosophila

(2008) A. Ludwig et al.   INSECT MOLECULAR BIOLOGY

Large-scale multiple testing under dependence

(2008) Wenguang Sun et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Calibrating the avian molecular clock

(2008) J. T. WEIR et al.   MOLECULAR ECOLOGY

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

A new SPIN on horizontal transfer

(2008) D. Lisch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods

(2008) J. K. Pace et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA