miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs

Target-align: a tool for plant microRNA target identification: Fig. 1.

(2010) Fuliang Xie et al.   BIOINFORMATICS

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

(2010) Eric Bonnet 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

Argonaute proteins at a glance

(2010) C. Ender et al.   JOURNAL OF CELL SCIENCE

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

MiRNA–miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features

(2010) Juan Xu et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum)

(2010) Fuliang Xie et al.   PLANTA

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

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

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

(2009) Michael Hackenberg et al.   NUCLEIC ACIDS RESEARCH

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing

(2009) L.-C. Hsieh et al.   PLANT PHYSIOLOGY

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Identification of novel and candidate miRNAs in rice by high throughput sequencing

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Criteria for Annotation of Plant MicroRNAs

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

Identification of soybean microRNAs and their targets

(2008) Baohong Zhang et al.   PLANTA