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

PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans

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

The evolutionary journey of Argonaute proteins

(2014) Daan C Swarts et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2014) Matt Simon et al.   Cell Reports

Functional diversification of Argonautes in nematodes: an expanding universe: Figure 1

(2013) Amy H. Buck et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda

(2013) Philipp H Schiffer et al.   BMC GENOMICS

Molecular Timetrees Reveal a Cambrian Colonization of Land and a New Scenario for Ecdysozoan Evolution

(2013) Omar Rota-Stabelli et al.   CURRENT BIOLOGY

The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle

(2013) J. Srinivasan et al.   GENETICS

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

(2013) Z. Shi et al.   GENOME RESEARCH

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

(2012) Alan D Winter et al.   BMC GENOMICS

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence

(2012) Yuval Tabach et al.   NATURE

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

Transposable element small RNAs as regulators of gene expression

(2012) Andrea D. McCue et al.   TRENDS IN GENETICS

The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs

(2012) Allison C. Billi et al.   PLoS Genetics

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

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

Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans

(2012) Leonie M. Kamminga et al.   PLoS Genetics

Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

(2012) Fei Gao et al.   GENOME BIOLOGY

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles

(2011) J. Wang et al.   GENOME RESEARCH

PIWI-interacting small RNAs: the vanguard of genome defence

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Initiation by a Eukaryotic RNA-dependent RNA Polymerase Requires Looping of the Template End and Is Influenced by the Template-tailing Activity of an Associated Uridyltransferase

(2010) Kristin Benjamin Talsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Distinct Phases of siRNA Synthesis in an Endogenous RNAi Pathway in C. elegans Soma

(2010) Jonathan I. Gent et al.   MOLECULAR CELL

Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway

(2010) Jessica J. Vasale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

The microRNAs of Caenorhabditis elegans

(2010) Ethan J. Kaufman et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

(2009) Jie Zong et al.   GENE

Repertoire and evolution of miRNA genes in four divergent nematode species

(2009) E. de Wit et al.   GENOME RESEARCH

Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematodeGlobodera pallida

(2009) JOHN T. JONES et al.   MOLECULAR PLANT PATHOLOGY

MEME SUITE: tools for motif discovery and searching

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

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans

(2009) T. Han 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

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