Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans- acting factors in Drosophila melanogaster

Silencing transposable elements in the Drosophila germline

(2016) Fu Yang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Interplay of Temperature and Genotype on Patterns of Alternative Splicing in Drosophila melanogaster

(2016) Ana Marija Jakšić et al.   GENETICS

Transposition burst of mariner-like elements in the sequenced genome of Rhodnius prolixus

(2016) R.D. Fernández-Medina et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

(2016) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing

(2016) Benjamin Czech et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Interplay of Temperature and Genotype on Patterns of Alternative Splicing in Drosophila melanogaster

(2016) Ana Marija Jakšić et al.   GENETICS

A Stress-Activated Transposon in Arabidopsis Induces Transgenerational Abscisic Acid Insensitivity

(2016) Hidetaka Ito et al.   Scientific Reports

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

Temperature-Related Reaction Norms of Gene Expression: Regulatory Architecture and Functional Implications

(2015) Jun Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster

(2015) Jun Chen et al.   PLoS Genetics

Tempo and Mode of Transposable Element Activity in Drosophila

(2015) Robert Kofler et al.   PLoS Genetics

The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster

(2015) Yuh Chwen G. Lee   PLoS Genetics

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

(2014) Concepcion M. Diez et al.   PLoS Genetics

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Multiple roles for Piwi in silencing Drosophila transposons

(2013) N. V. Rozhkov et al.   GENES & DEVELOPMENT

The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression

(2013) C. D. Meiklejohn et al.   GENOME RESEARCH

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Intra-Specific Regulatory Variation in Drosophila pseudoobscura

(2013) Anton Suvorov et al.   PLoS One

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Transposable elements domesticated and neofunctionalized by eukaryotic genomes

(2012) Ahmed M. Alzohairy et al.   PLASMID

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

(2012) Robert Kofler et al.   PLoS Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

piRNAs, transposon silencing, andDrosophilagermline development

(2010) Jaspreet S. Khurana et al.   JOURNAL OF CELL BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

(2009) Florian Maumus et al.   BMC GENOMICS

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

(2009) Marc Deloger et al.   GENE

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

(2008) G. Servant et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS