Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes

(2016) Nuria Rius et al.   BMC GENOMICS

DrosophilaFemales Undergo Genome Expansion after Interspecific Hybridization

(2016) Valèria Romero-Soriano et al.   Genome Biology and Evolution

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

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

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

(2016) Valèria Romero-Soriano et al.   PLoS One

PIWI-Interacting RNA: Its Biogenesis and Functions

(2015) Yuka W. Iwasaki et al.   Annual Review of Biochemistry

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data

(2015) Laurent Modolo et al.   BMC BIOINFORMATICS

tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription

(2015) A. Molla-Herman et al.   EMBO JOURNAL

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper

(2015) Alexandre Webster et al.   MOLECULAR CELL

Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline

(2015) Kaoru Sato et al.   MOLECULAR CELL

Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms

(2015) Wei Wang et al.   MOLECULAR CELL

Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae

(2015) Maria Pilar García Guerreiro   MOLECULAR GENETICS AND GENOMICS

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation

(2015) N. Senerchia et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis

(2015) F. Mohn et al.   SCIENCE

piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production

(2015) B. W. Han et al.   SCIENCE

Panoramix enforces piRNA-dependent cotranscriptional silencing

(2015) Y. Yu et al.   SCIENCE

MicroRNA-Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells

(2015) Bruno Mugat et al.   PLoS Genetics

Genomics of Ecological Adaptation in Cactophilic Drosophila

(2015) Yolanda Guillén et al.   Genome Biology and Evolution

Fly piRNA biogenesis: tap dancing with Tej

(2014) Zhaolin Yang et al.   BMC BIOLOGY

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

Transcriptional properties and splicing of the flamenco piRNA cluster

(2014) C. Goriaux et al.   EMBO REPORTS

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

(2014) Laurent Modolo et al.   Genome Biology and Evolution

Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

(2014) Elias A.G. Carnelossi et al.   Genome Biology and Evolution

RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species

(2014) Anne-Marie Dion-Côté et al.   MOLECULAR BIOLOGY AND EVOLUTION

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers

(2014) S. Renaut et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Genome-Wide Survey of Genetic Instability by Transposition in Drosophila Hybrids

(2014) Doris Vela et al.   PLoS One

Variable expression levels detected in the Drosophila effectors of piRNA biogenesis

(2013) Marie Fablet et al.   GENE

Multiple roles for Piwi in silencing Drosophila transposons

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

Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family

(2013) Peter D. Keightley et al.   GENETICS

The Genetic Makeup of the Drosophila piRNA Pathway

(2013) Dominik Handler et al.   MOLECULAR CELL

A Transcriptome-wide RNAi Screen in the Drosophila Ovary Reveals Factors of the Germline piRNA Pathway

(2013) Benjamin Czech et al.   MOLECULAR CELL

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

piRNA-mediated transgenerational inheritance of an acquired trait

(2012) T. Grentzinger et al.   GENOME RESEARCH

Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

(2012) Deodoro C.S.G. Oliveira et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Drosophila Interspecific Hybrids Phenocopy piRNA-Pathway Mutants

(2012) Erin S. Kelleher et al.   PLOS BIOLOGY

piRNA Production Requires Heterochromatin Formation in Drosophila

(2011) Prashanth Rangan et al.   CURRENT BIOLOGY

A systematic analysis ofDrosophilaTUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors

(2011) Dominik Handler et al.   EMBO JOURNAL

Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons

(2011) Takeshi Kawakami et al.   Genome Biology and Evolution

What makes transposable elements move in the Drosophila genome?

(2011) M P García Guerreiro   HEREDITY

Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3 Ligase and Tudor Domains

(2011) Zhao Zhang et al.   MOLECULAR CELL

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster

(2011) Hang Yin et al.   PLoS Genetics

Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia

(2010) Ningning Wang et al.   BMC PLANT BIOLOGY

Small RNA-Mediated Quiescence of Transposable Elements in Animals

(2010) Kuniaki Saito et al.   DEVELOPMENTAL CELL

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

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Intra- and interspecific divergence in the nuclear sequences of the clock gene period in species of the Drosophila buzzatii cluster

(2010) Fernando Faria Franco et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis

(2010) A. Nagao et al.   RNA

piRNA-mediated silencing in Drosophila germlines

(2010) Mikiko C. Siomi et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The piRNA pathway: a fly's perspective on the guardian of the genome

(2010) Kirsten-André Senti et al.   TRENDS IN GENETICS

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

Epigenetic, transposon and small RNA determinants of hybrid dysfunctions

(2008) P Michalak   HEREDITY

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

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

The evolution of RNAi as a defence against viruses and transposable elements

(2008) D. J Obbard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline

(2008) S. Chambeyron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

(2008) J. Brennecke et al.   SCIENCE

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE