Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation

The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster

(2020) Shiqi Luo et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans

(2020) Deniz M. Özata et al.   Nature Ecology & Evolution

GenMap: ultra-fast computation of genome mappability

(2020) Christopher Pockrandt et al.   BIOINFORMATICS

The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility

(2020) Pei-Hsuan Wu et al.   NATURE GENETICS

Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation

(2019) Daniel Gebert et al.   Genome Biology and Evolution

Adenine Methylation in Drosophila Is Associated with the Tissue-Specific Expression of Developmental and Regulatory Genes

(2019) Kinnary Shah et al.   G3-Genes Genomes Genetics

Female Meiosis: Synapsis, Recombination, and Segregation inDrosophila melanogaster

(2018) Stacie E. Hughes et al.   GENETICS

Female Meiosis: Synapsis, Recombination, and Segregation inDrosophila melanogaster

(2018) Stacie E. Hughes et al.   GENETICS

piRNA-Guided Genome Defense: From Biogenesis to Silencing

(2018) Benjamin Czech et al.   Annual Review of Genetics

A Robust Transposon-Endogenizing Response from Germline Stem Cells

(2018) Sungjin Moon et al.   DEVELOPMENTAL CELL

Deep experimental profiling of microRNA diversity, deployment, and evolution across theDrosophilagenus

(2017) Jaaved Mohammed et al.   GENOME RESEARCH

A heterochromatin-dependent transcription machinery drives piRNA expression

(2017) Peter Refsing Andersen et al.   NATURE

Coevolution between transposable elements and recombination

(2017) Tyler V. Kent et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

(2015) Kirsten-André Senti et al.   GENES & DEVELOPMENT

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

Drosophila germ granules are structured and contain homotypic mRNA clusters

(2015) Tatjana Trcek et al.   Nature Communications

Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo

(2015) Bridlin Barckmann et al.   Cell Reports

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals

(2015) Gung-wei Chirn et al.   PLoS Genetics

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

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

(2014) Fabio Mohn et al.   CELL

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway

(2013) Robyn S.M. Lim et al.   DEVELOPMENTAL BIOLOGY

Multiple roles for Piwi in silencing Drosophila transposons

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

Analysis of piRNA-Mediated Silencing of Active TEs in Drosophila melanogaster Suggests Limits on the Evolution of Host Genome Defense

(2013) Erin S. Kelleher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing de novo silencing of an active plant retrotransposon

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

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

(2012) David Rosenkranz et al.   BMC BIOINFORMATICS

RECURRENT AND RECENT SELECTIVE SWEEPS IN THE piRNA PATHWAY

(2012) Alfred Simkin et al.   EVOLUTION

Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory

(2012) Marta Farré et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Cochaperone Shutdown Defines a Group of Biogenesis Factors Essential for All piRNA Populations in Drosophila

(2012) Daniel Olivieri et al.   MOLECULAR CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

(2012) Russell B. Corbett-Detig et al.   PLoS Genetics

Learning to Protect Your Genome on the Fly

(2011) Mia T. Levine et al.   CELL

Adaptation to P Element Transposon Invasion in Drosophila melanogaster

(2011) Jaspreet S. Khurana et al.   CELL

TheDrosophilaGene Disruption Project: Progress Using Transposons With Distinctive Site Specificities

(2011) Hugo J. Bellen et al.   GENETICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line

(2011) S. H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A New Resource for Characterizing X-Linked Genes in Drosophila melanogaster: Systematic Coverage and Subdivision of the X Chromosome With Nested, Y-Linked Duplications

(2010) R. K. Cook et al.   GENETICS

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

Population Genomics of Transposable Elements in Drosophila melanogaster

(2010) D. A. Petrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

miRBase: integrating microRNA annotation and deep-sequencing data

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

(2009) Colin D. Malone et al.   CELL

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

(2009) Chengjian Li et al.   CELL

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters

(2009) Carla Klattenhoff et al.   CELL

Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution

(2009) R. Assis 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

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

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

Invasion of the Arabidopsis Genome by the Tobacco Retrotransposon Tnt1 Is Controlled by Reversible Transcriptional Gene Silencing

(2008) J. Perez-Hormaeche et al.   PLANT PHYSIOLOGY