Protease-mediated processing of Argonaute proteins controls small RNA association

Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants

(2020) Giorgia Barucci et al.   NATURE CELL BIOLOGY

A Family of Argonaute-Interacting Proteins Gates Nuclear RNAi

(2020) Alexandra Lewis et al.   MOLECULAR CELL

Structural insights into Fe–S protein biogenesis by the CIA targeting complex

(2020) Susanne A. Kassube et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Physiology and Pharmacology of DPP-4 in Glucose Homeostasis and the Treatment of Type 2 Diabetes

(2019) Carolyn F. Deacon   Frontiers in Endocrinology

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways

(2019) Miguel Vasconcelos Almeida et al.   PLoS Genetics

Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression

(2019) Jan Padeken et al.   GENES & DEVELOPMENT

ALFA: annotation landscape for aligned reads

(2019) Mathieu Bahin et al.   BMC GENOMICS

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

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

(2018) En-Zhi Shen et al.   CELL

Differential Expression of Histone H3.3 Genes and Their Role in Modulating Temperature Stress Response inCaenorhabditis elegans

(2018) Kamila Delaney et al.   GENETICS

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

A Cytoplasmic Argonaute Protein Promotes the Inheritance of RNAi

(2018) Fei Xu et al.   Cell Reports

Differential Expression of Histone H3.3 Genes and Their Role in Modulating Temperature Stress Response inCaenorhabditis elegans

(2018) Kamila Delaney et al.   GENETICS

The P Granules of C. elegans: A Genetic Model for the Study of RNA–Protein Condensates

(2018) Geraldine Seydoux   JOURNAL OF MOLECULAR BIOLOGY

Spatiotemporal regulation of liquid-like condensates in epigenetic inheritance

(2018) Gang Wan et al.   NATURE

Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes

(2018) Veronika Ostapcuk et al.   NATURE

The RNAi Inheritance Machinery of Caenorhabditis elegans

(2017) George Spracklin et al.   GENETICS

TrackMate: An open and extensible platform for single-particle tracking

(2017) Jean-Yves Tinevez et al.   METHODS

LIN41 Post-transcriptionally Silences mRNAs by Two Distinct and Position-Dependent Mechanisms

(2017) Florian Aeschimann et al.   MOLECULAR CELL

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

Reliable CRISPR/Cas9 Genome Engineering in Caenorhabditis elegans Using a Single Efficient sgRNA and an Easily Recognizable Phenotype

(2017) Sonia El Mouridi et al.   G3-Genes Genomes Genetics

The RNAi Inheritance Machinery of Caenorhabditis elegans

(2017) George Spracklin et al.   GENETICS

Dipeptidyl peptidase 9 substrates and their discovery: current progress and the application of mass spectrometry-based approaches

(2016) Claire H. Wilson et al.   BIOLOGICAL CHEMISTRY

Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability

(2016) Peter Zeller et al.   NATURE GENETICS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans

(2016) Takashi S. Miki et al.   PLoS Genetics

DPP9 is a novel component of the N-end rule pathway targeting the tyrosine kinase Syk

(2016) Daniela Justa-Schuch et al.   eLife

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

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

CRISPR/Cas9 Genome Editing in Caenorhabditis elegans : Evaluation of Templates for Homology-Mediated Repair and Knock-Ins by Homology-Independent DNA Repair

(2015) Iskra Katic et al.   G3-Genes Genomes Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Efficient Marker-Free Recovery of Custom Genetic Modifications with CRISPR/Cas9 in Caenorhabditis elegans

(2014) J. A. Arribere et al.   GENETICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations

(2014) A. Sakaguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From early lessons to new frontiers: the worm as a treasure trove of small RNA biology

(2014) Elaine M. Youngman et al.   Frontiers in Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Argonautes Promote Male Fertility and Provide a Paternal Memory of Germline Gene Expression in C. elegans

(2013) Colin C. Conine et al.   CELL

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

Advances in Understanding the Expression and Function of Dipeptidyl Peptidase 8 and 9

(2013) H. Zhang et al.   MOLECULAR CANCER RESEARCH

Homeostatic control of Argonaute stability by microRNA availability

(2013) Peter Smibert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Turning catalytically inactive human Argonaute proteins into active slicer enzymes

(2013) Judith Hauptmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

Improved Mos1-mediated transgenesis in C. elegans

(2012) Christian Frøkjær-Jensen et al.   NATURE METHODS

The N domain of Argonaute drives duplex unwinding during RISC assembly

(2012) Pieter Bas Kwak et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neuropeptide Y, B-type natriuretic peptide, substance P and peptide YY are novel substrates of fibroblast activation protein-α

(2011) Fiona M. Keane et al.   FEBS Journal

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Protein N-Terminal Processing: Substrate Specificity ofEscherichia coliand Human Methionine Aminopeptidases

(2010) Qing Xiao et al.   BIOCHEMISTRY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

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

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

Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans

(2010) Colin C. Conine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Biochemistry, pharmacokinetics, and toxicology of a potent and selective DPP8/9 inhibitor

(2009) Jia-Jing Wu et al.   BIOCHEMICAL PHARMACOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock 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

The genetics and cell biology of spermatogenesis in the nematode C. elegans

(2009) Steven W. L’Hernault   MOLECULAR AND CELLULAR ENDOCRINOLOGY

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

(2009) Weifeng Gu et al.   MOLECULAR CELL

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Adverse effects of dipeptidyl peptidases 8 and 9 inhibition in rodents revisited

(2008) B. F. Burkey et al.   DIABETES OBESITY & METABOLISM

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

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH