The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

(2014) Jason T. Huff et al.   CELL

Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation

(2014) J. Lei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

To be or not to be a piRNA: genomic origin and processing of piRNAs

(2014) Adrien Le Thomas et al.   GENOME BIOLOGY

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

(2013) Guilherme Loss-Morais et al.   Biology Direct

Non-Coding RNAs: Multi-Tasking Molecules in the Cell

(2013) Anita Gomes et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Alternative Splicing Regulates Biogenesis of miRNAs Located across Exon-Intron Junctions

(2013) Ze’ev Melamed et al.   MOLECULAR CELL

Reconstructing de novo silencing of an active plant retrotransposon

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

Large scale chromosomal mapping of human microRNA structural clusters

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus

(2013) Bernard Billoud et al.   NUCLEIC ACIDS RESEARCH

Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions

(2013) Martyna Nowacka et al.   PLANT MOLECULAR BIOLOGY

Evidence for Widespread Exonic Small RNAs in the Glaucophyte Alga Cyanophora paradoxa

(2013) Jeferson Gross et al.   PLoS One

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

A Role for Small RNAs in DNA Double-Strand Break Repair

(2012) Wei Wei et al.   CELL

A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm

(2012) Hongying Peng et al.   CELL RESEARCH

Exploring the molecular basis of responses to light in marine diatoms

(2012) F. A. Depauw et al.   JOURNAL OF EXPERIMENTAL BOTANY

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

(2012) Yue Li et al.   NUCLEIC ACIDS RESEARCH

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

(2012) W. Qian et al.   SCIENCE

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation

(2012) Markus Lommer et al.   GENOME BIOLOGY

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis

(2011) Aiyou Huang et al.   BMC GENOMICS

RNA-Mediated Silencing in Algae: Biological Roles and Tools for Analysis of Gene Function

(2011) Heriberto Cerutti et al.   EUKARYOTIC CELL

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

(2011) Jeremy R. Haag et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

(2011) Trina M. Norden-Krichmar et al.   PLoS One

The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

(2011) Oscar Franzén et al.   PLoS Neglected Tropical Diseases

Transfer RNA-derived fragments: origins, processing, and functions

(2011) Andrew Sobala et al.   Wiley Interdisciplinary Reviews-RNA

Silencing signals in plants: a long journey for small RNAs

(2011) Attila Molnar et al.   GENOME BIOLOGY

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo

(2010) M. T. Couvillion et al.   GENES & DEVELOPMENT

MVH in piRNA processing and gene silencing of retrotransposons

(2010) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Repeat elements and the Arabidopsis DNA methylation landscape

(2010) F K Teixeira et al.   HEREDITY

A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules

(2010) Maria Rosa Garcia-Silva et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

A dicer-independent miRNA biogenesis pathway that requires Ago catalysis

(2010) Sihem Cheloufi et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

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

Identification of miRNA from Porphyra yezoensis by High-Throughput Sequencing and Bioinformatics Analysis

(2010) Chengwei Liang et al.   PLoS One

MicroRNA processing without Dicer

(2010) Anne Dueck et al.   GENOME BIOLOGY

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

(2010) David Hendrix et al.   GENOME BIOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

MicroRazerS: rapid alignment of small RNA reads

(2009) A.-K. Emde et al.   BIOINFORMATICS

Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

(2009) Florian Maumus et al.   BMC GENOMICS

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

The long and the short of noncoding RNAs

(2009) Christopher A Brosnan et al.   CURRENT OPINION IN CELL BIOLOGY

Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity

(2009) Sacha Coesel et al.   EMBO REPORTS

RNA silencing

(2009) Angela K. Eggleston   NATURE

qiRNA is a new type of small interfering RNA induced by DNA damage

(2009) Heng-Chi Lee et al.   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Gene silencing in the marine diatom Phaeodactylum tricornutum

(2009) Valentina De Riso et al.   NUCLEIC ACIDS RESEARCH

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

(2009) C. Cole et al.   RNA

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Small RNA guides for de novo DNA methylation in mammalian germ cells

(2008) A. A. Aravin et al.   GENES & DEVELOPMENT

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs

(2008) J. E. Babiarz et al.   GENES & DEVELOPMENT

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL

Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation

(2008) A. E. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tRNA cleavage is a conserved response to oxidative stress in eukaryotes

(2008) D. M. Thompson et al.   RNA