Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity inDrosophilaovarian cell cultures

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

The capacity of target silencing byDrosophilaPIWI and piRNAs

(2014) Christina Post et al.   RNA

Genetic and Epigenetic Changes Involving (Retro)transposons in Animal Hybrids and Polyploids

(2013) I.R. Arkhipova et al.   CYTOGENETIC AND GENOME RESEARCH

A Major Epigenetic Programming Mechanism Guided by piRNAs

(2013) Xiao A. Huang et al.   DEVELOPMENTAL CELL

Multiple roles for Piwi in silencing Drosophila transposons

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

DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary

(2013) H. Ohtani et al.   GENES & DEVELOPMENT

Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex

(2013) D. Donertas et al.   GENES & DEVELOPMENT

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(2013) A. Le Thomas et al.   GENES & DEVELOPMENT

RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila

(2013) Bertsy Goic et al.   NATURE IMMUNOLOGY

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription

(2013) K. L. Pennington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

“Jump Start and Gain” Model for Dosage Compensation in Drosophila Based on Direct Sequencing of Nascent Transcripts

(2013) Francesco Ferrari et al.   Cell Reports

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

(2012) Grzegorz Sienski et al.   CELL

LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells

(2012) Jun Cho et al.   CELL

Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility

(2012) Danny W-K Ng et al.   CURRENT OPINION IN PLANT BIOLOGY

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis

(2012) Anastassios Vourekas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

(2012) Raquel S. Linheiro et al.   PLoS One

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

(2012) Robert Kofler et al.   PLoS Genetics

Experimental Evolution of Legionella pneumophila in Mouse Macrophages Leads to Strains with Altered Determinants of Environmental Survival

(2012) Alexander W. Ensminger et al.   PLoS Pathogens

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

Adaptation to P Element Transposon Invasion in Drosophila melanogaster

(2011) Jaspreet S. Khurana et al.   CELL

Genome Sequencing of Mouse Induced Pluripotent Stem Cells Reveals Retroelement Stability and Infrequent DNA Rearrangement during Reprogramming

(2011) Aaron R. Quinlan et al.   Cell Stem Cell

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

PIWI-interacting small RNAs: the vanguard of genome defence

(2011) Mikiko C. Siomi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

(2011) Anthony K L Leung et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Drosophila P elements preferentially transpose to replication origins

(2011) A. C. Spradling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila

(2010) Daniel Olivieri et al.   EMBO JOURNAL

Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila

(2010) A. D. Haase et al.   GENES & DEVELOPMENT

Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila

(2010) K. Saito et al.   GENES & DEVELOPMENT

The transcriptional diversity of 25 Drosophila cell lines

(2010) L. Cherbas et al.   GENOME RESEARCH

Small RNAs in the animal gonad: Guarding genomes and guiding development

(2010) Nelson C. Lau   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

The Yb Body, a Major Site for Piwi-associated RNA Biogenesis and a Gateway for Piwi Expression and Transport to the Nucleus in Somatic Cells

(2010) Hongying Qi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells

(2010) Jose L. Garcia-Perez et al.   NATURE

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

(2010) Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies

(2009) Chengjian Li et al.   CELL

A Broadly Conserved Pathway Generates 3′UTR-Directed Primary piRNAs

(2009) Nicolas Robine et al.   CURRENT BIOLOGY

Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line

(2009) N. C. Lau et al.   GENOME RESEARCH

A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila

(2009) Kuniaki Saito et al.   NATURE

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

MEME SUITE: tools for motif discovery and searching

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

Dicing of viral replication intermediates during silencing of latent Drosophila viruses

(2009) A. Flynt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mechanism of Induction and Suppression of Antiviral Immunity Directed by Virus-Derived Small RNAs in Drosophila

(2008) Roghiyh Aliyari et al.   Cell Host & Microbe

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

(2008) Yoshinori Kawamura et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

In Drosophila melanogaster the COM Locus Directs the Somatic Silencing of Two Retrotransposons through both Piwi-Dependent and -Independent Pathways

(2008) Sophie Desset et al.   PLoS One

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology