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

CPSS: a computational platform for the analysis of small RNA deep sequencing data

(2012) Yuanwei Zhang et al.   BIOINFORMATICS

shortran: a pipeline for small RNA-seq data analysis

(2012) Vikas Gupta et al.   BIOINFORMATICS

ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data

(2012) Chong-Jian Chen et al.   BIOINFORMATICS

Roles for MicroRNAs in Conferring Robustness to Biological Processes

(2012) Margaret S. Ebert et al.   CELL

A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity

(2012) Priyamvada Rajasethupathy et al.   CELL

A new member of the family

(2012) Rachel David   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2012) Yue Li et al.   NUCLEIC ACIDS RESEARCH

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data

(2012) Chikako Ragan et al.   NUCLEIC ACIDS RESEARCH

YM500: a small RNA sequencing (smRNA-seq) database for microRNA research

(2012) Wei-Chung Cheng et al.   NUCLEIC ACIDS RESEARCH

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

(2012) Marek Zywicki et al.   NUCLEIC ACIDS RESEARCH

Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms

(2011) Celina Juliano et al.   Annual Review of Genetics

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome

(2011) Lorena Pantano et al.   BIOINFORMATICS

A k-mer scheme to predict piRNAs and characterize locust piRNAs

(2011) Yi Zhang et al.   BIOINFORMATICS

Small RNA transcriptome investigation based on next-generation sequencing technology

(2011) Linglin Zhou et al.   Journal of Genetics and Genomics

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

(2011) Mario Fasold 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

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

miRNAkey: a software for microRNA deep sequencing analysis

(2010) Roy Ronen et al.   BIOINFORMATICS

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

(2010) Anthony Mathelier et al.   BIOINFORMATICS

DSAP: deep-sequencing small RNA analysis pipeline

(2010) Po-Jung Huang et al.   NUCLEIC ACIDS RESEARCH

mirTools: microRNA profiling and discovery based on high-throughput sequencing

(2010) Erle Zhu et al.   NUCLEIC ACIDS RESEARCH

Spliceosomal snRNA modifications and their function

(2010) John Karijolich et al.   RNA Biology

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

(2010) David Hendrix et al.   GENOME BIOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

(2009) Wei-Chi Wang et al.   BMC BIOINFORMATICS

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa 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

smyRNA: A Novel Ab Initio ncRNA Gene Finder

(2009) Raheleh Salari et al.   PLoS One

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

Mireval: a web tool for simple microRNA prediction in genome sequences

(2008) W. Ritchie et al.   BIOINFORMATICS

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH