sRNAtoolbox: an integrated collection of small RNA research tools

Role of microRNAs in plant drought tolerance

(2015) Jannatul Ferdous et al.   PLANT BIOTECHNOLOGY JOURNAL

Surface analysis of Dicrocoelium dendriticum. The molecular characterization of exosomes reveals the presence of miRNAs

(2014) Dolores Bernal et al.   Journal of Proteomics

Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity

(2014) Amy H. Buck et al.   Nature Communications

Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes

(2014) Danijela Koppers-Lalic et al.   Cell Reports

Classification and Comparison of Small RNAs from Plants

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

High-Throughput miRNA and mRNA Sequencing of Paired Colorectal Normal, Tumor and Metastasis Tissues and Bioinformatic Modeling of miRNA-1 Therapeutic Applications

(2013) Christina Röhr et al.   PLoS One

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

(2013) Jinyu Wu et al.   RNA Biology

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Small RNA-mediated regulation of host–pathogen interactions

(2013) Jennifer F Harris et al.   Virulence

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

(2012) M. B. Stocks et al.   BIOINFORMATICS

A Comprehensive Expression Profile of MicroRNAs and Other Classes of Non-Coding Small RNAs in Barley Under Phosphorous-Deficient and -Sufficient Conditions

(2012) M. Hackenberg et al.   DNA RESEARCH

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

(2012) Esther N. M. Nolte-’t Hoen et al.   NUCLEIC ACIDS RESEARCH

Viral MicroRNA Targetome of KSHV-Infected Primary Effusion Lymphoma Cell Lines

(2011) Eva Gottwein et al.   Cell Host & Microbe

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Angiogenin-Induced tRNA Fragments Inhibit Translation Initiation

(2011) Pavel Ivanov et al.   MOLECULAR CELL

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

(2011) Mario Fasold et al.   NUCLEIC ACIDS RESEARCH

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

(2011) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

RNA in pieces

(2011) Alex C. Tuck et al.   TRENDS IN GENETICS

Viruses, microRNAs, and Host Interactions

(2010) Rebecca L. Skalsky et al.   Annual Review of Microbiology

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

(2010) Eric Bonnet et al.   BIOINFORMATICS

TargetSpy: a supervised machine learning approach for microRNA target prediction

(2010) Martin Sturm et al.   BMC BIOINFORMATICS

Circulating microRNA in body fluid: a new potential biomarker for cancer diagnosis and prognosis

(2010) Nobuyoshi Kosaka et al.   CANCER SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells

(2009) Lorena Pantano et al.   NUCLEIC ACIDS RESEARCH

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments

(2009) Michael Hackenberg et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists

(2008) M. Hackenberg et al.   BIOINFORMATICS

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY