Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment

(2019) Alexandra Bezler et al.   PLoS Genetics

Germline Maintenance Through the Multifaceted Activities of GLH/Vasa in Caenorhabditis elegans P Granules

(2019) Elisabeth A. Marnik et al.   GENETICS

Visualization and Quantification of Transposon Activity in Caenorhabditis elegans RNAi Pathway Mutants

(2019) Dylan C. Wallis et al.   G3-Genes Genomes Genetics

henn-1/HEN1 Promotes Germline Immortality in Caenorhabditis elegans

(2019) Joshua M. Svendsen et al.   Cell Reports

Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline

(2018) En-Zhi Shen et al.   CELL

The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes

(2018) Donglei Zhang et al.   SCIENCE

The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans

(2018) Meetu Seth et al.   Cell Reports

Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci

(2018) Celja J. Uebel et al.   PLoS Genetics

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

piRTarBase: a database of piRNA targeting sites and their roles in gene regulation

(2018) Wei-Sheng Wu et al.   NUCLEIC ACIDS RESEARCH

Germ Granules Prevent Accumulation of Somatic Transcripts in the AdultCaenorhabditis elegansGermline

(2017) Andrew Kekūpa’a Knutson et al.   GENETICS

ALG-5 is a miRNA-associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline

(2017) Kristen C. Brown et al.   NUCLEIC ACIDS RESEARCH

A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

(2017) Alicia N McMurchy et al.   eLife

Germ Granules Prevent Accumulation of Somatic Transcripts in the AdultCaenorhabditis elegansGermline

(2017) Andrew Kekūpa’a Knutson et al.   GENETICS

The RNase PARN-1 Trims piRNA 3′ Ends to Promote Transcriptome Surveillance in C. elegans

(2016) Wen Tang et al.   CELL

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

(2015) A. C. Campbell et al.   DEVELOPMENT

piRNAs and piRNA-Dependent siRNAs Protect Conserved and Essential C. elegans Genes from Misrouting into the RNAi Pathway

(2015) Carolyn M. Phillips et al.   DEVELOPMENTAL CELL

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Germ-Granule Components Prevent Somatic Development in the C. elegans Germline

(2014) Dustin L. Updike et al.   CURRENT BIOLOGY

MUT-14 and SMUT-1 DEAD Box RNA Helicases Have Overlapping Roles in Germline RNAi and Endogenous siRNA Formation

(2014) Carolyn M. Phillips et al.   CURRENT BIOLOGY

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism

(2014) M. Stoeckius et al.   EMBO JOURNAL

Paternal RNA contributions in the Caenorhabditis elegans zygote

(2014) M. Stoeckius et al.   EMBO JOURNAL

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Reduced Insulin/IGF-1 Signaling Restores Germ Cell Immortality to Caenorhabditis elegans Piwi Mutants

(2014) Matt Simon et al.   Cell Reports

A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans

(2014) M. A. Ortiz et al.   G3-Genes Genomes Genetics

The C. elegans CSR-1 Argonaute Pathway Counteracts Epigenetic Silencing to Promote Germline Gene Expression

(2013) Meetu Seth et al.   DEVELOPMENTAL CELL

Protection of Germline Gene Expression by the C. elegans Argonaute CSR-1

(2013) Christopher J. Wedeles et al.   DEVELOPMENTAL CELL

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

(2013) Daniel J Dickinson et al.   NATURE METHODS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

C. elegans piRNAs Mediate the Genome-wide Surveillance of Germline Transcripts

(2012) Heng-Chi Lee et al.   CELL

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans

(2012) Alyson Ashe et al.   CELL

piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline

(2012) Masaki Shirayama et al.   CELL

Extremely stable Piwi-induced gene silencing inCaenorhabditis elegans

(2012) Maartje J Luteijn et al.   EMBO JOURNAL

CSR-1 RNAi pathway positively regulates histone expression inC. elegans

(2012) Daphne C Avgousti et al.   EMBO JOURNAL

MUT-16 promotes formation of perinuclear Mutator foci required for RNA silencing in the C. elegans germline

(2012) C. M. Phillips et al.   GENES & DEVELOPMENT

Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs

(2012) Germano Cecere et al.   MOLECULAR CELL

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality

(2012) Bethany A. Buckley et al.   NATURE

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

mut-16 and other mutator class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans

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

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

(2011) Sylvia E. J. Fischer et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation

(2009) Julie M. Claycomb et al.   CELL

CDE-1 Affects Chromosome Segregation through Uridylation of CSR-1-Bound siRNAs

(2009) Josien C. van Wolfswinkel et al.   CELL

Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

(2009) Weifeng Gu et al.   MOLECULAR CELL

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Computational and analytical framework for small RNA profiling by high-throughput sequencing

(2009) N. Fahlgren et al.   RNA

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

A C. elegans Piwi, PRG-1, Regulates 21U-RNAs during Spermatogenesis

(2008) Guilin Wang et al.   CURRENT BIOLOGY

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

PRG-1 and 21U-RNAs Interact to Form the piRNA Complex Required for Fertility in C. elegans

(2008) Pedro J. Batista et al.   MOLECULAR CELL

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS

Endogenous small interfering RNAs in animals

(2008) Katsutomo Okamura et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY