Rewired RNAi-mediated genome surveillance in house dust mites

Gene silencing by RNA interference in Sarcoptes scabiei: a molecular tool to identify novel therapeutic targets

(2017) Deepani D. Fernando et al.   Parasites & Vectors

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

(2017) Samuel H. Lewis et al.   Nature Ecology & Evolution

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

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

PIWI-Interacting RNA: Its Biogenesis and Functions

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

Maternal piRNAs Are Essential for Germline Development following De Novo Establishment of Endo-siRNAs in Caenorhabditis elegans

(2015) Bruno F.M. de Albuquerque et al.   DEVELOPMENTAL CELL

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

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

Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery

(2015) Grzegorz Sienski et al.   GENES & DEVELOPMENT

The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens

(2015) Ting-Fung Chan et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Gene silencing by RNA interference in the house dust mite, Dermatophagoides pteronyssinus

(2015) Edward J. Marr et al.   MOLECULAR AND CELLULAR PROBES

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

(2015) Wei Wang et al.   MOLECULAR CELL

Draft genome of the scabies mite

(2015) S. Dean Rider et al.   Parasites & Vectors

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

Somatic Primary piRNA Biogenesis Driven by cis-Acting RNA Elements and trans-Acting Yb

(2015) Hirotsugu Ishizu et al.   Cell Reports

Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages

(2015) Peter Sarkies et al.   PLOS BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

piRNAs: from biogenesis to function

(2014) E.-M. Weick et al.   DEVELOPMENT

Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain

(2014) R. Fukunaga et al.   EMBO JOURNAL

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

(2014) J. Wen et al.   GENOME RESEARCH

AGO3 Slicer activity regulates mitochondria–nuage localization of Armitage and piRNA amplification

(2014) Haidong Huang et al.   JOURNAL OF CELL BIOLOGY

Antiviral immunity via RIG-I-mediated recognition of RNA bearing 5′-diphosphates

(2014) Delphine Goubau et al.   NATURE

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Analysis of the Endoribonuclease Dicer Family

(2014) Zeqian Gao et al.   PLoS One

RNAi Dynamics in Juvenile Fasciola spp. Liver Flukes Reveals the Persistence of Gene Silencing In Vitro

(2014) Paul McVeigh et al.   PLoS Neglected Tropical Diseases

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes

(2013) Kathrin K Geyer et al.   BMC GENOMICS

Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline

(2013) James H. Crichton et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

(2013) Z. Shi et al.   GENOME RESEARCH

The genomes of four tapeworm species reveal adaptations to parasitism

(2013) Isheng J. Tsai et al.   NATURE

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Evolution of parasitism along convergent lines: from ecology to genomics

(2013) ROBERT POULIN et al.   PARASITOLOGY

Is Permanent Parasitism Reversible?—Critical Evidence from Early Evolution of House Dust Mites

(2013) Pavel B. Klimov et al.   SYSTEMATIC BIOLOGY

A Conserved Upstream Motif Orchestrates Autonomous, Germline-Enriched Expression of Caenorhabditis elegans piRNAs

(2013) Allison C. Billi et al.   PLoS Genetics

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

PIWI Associated siRNAs and piRNAs Specifically Require the Caenorhabditis elegans HEN1 Ortholog henn-1

(2012) Taiowa A. Montgomery et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

RNA-dependent RNA polymerases in RNA silencing

(2011) Yoshiko Maida et al.   BIOLOGICAL CHEMISTRY

Host-parasite relationships in the genome

(2011) John FY Brookfield   BMC BIOLOGY

Dicer recognizes the 5′ end of RNA for efficient and accurate processing

(2011) Jong-Eun Park et al.   NATURE

The genome of Tetranychus urticae reveals herbivorous pest adaptations

(2011) Miodrag Grbić et al.   NATURE

PIWI-interacting small RNAs: the vanguard of genome defence

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

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila

(2009) Sebastian Kurscheid et al.   BMC MOLECULAR BIOLOGY

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

(2009) Colin D. Malone et al.   CELL

Common themes in siRNA-mediated epigenetic silencing pathways

(2009) Andre Verdel et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

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

The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila

(2009) Delphine Fagegaltier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster

(2008) Katsutomo Okamura et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium

(2008) Yoshinori Tomoyasu et al.   GENOME BIOLOGY