Discovering MicroRNAs and Their Targets in Plants

miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data

(2014) Jikai Lei et al.   BIOINFORMATICS

miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data

(2014) Jiyuan An et al.   BMC BIOINFORMATICS

Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data

(2014) Cheng-Yu Hou et al.   BMC GENOMICS

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction

(2014) Prashant K Srivastava et al.   BMC GENOMICS

Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay

(2014) Q. Liu et al.   PLANT CELL

Evolutionary history of plant microRNAs

(2014) Richard S. Taylor et al.   TRENDS IN PLANT SCIENCE

HuntMi: an efficient and taxon-specific approach in pre-miRNA identification

(2013) Adam Gudyś et al.   BMC BIOINFORMATICS

PMTED: a plant microRNA target expression database

(2013) Xiuli Sun et al.   BMC BIOINFORMATICS

Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis

(2013) Xiyan Yang et al.   JOURNAL OF EXPERIMENTAL BOTANY

miRspring: a compact standalone research tool for analyzing miRNA-seq data

(2013) David T. Humphreys et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide analysis of dynamic variations in regulation modes of grapevine microRNAs on their target genes during grapevine development

(2013) Chen Wang et al.   PLANT MOLECULAR BIOLOGY

Comprehensive Investigation of MicroRNAs Enhanced by Analysis of Sequence Variants, Expression Patterns, ARGONAUTE Loading, and Target Cleavage

(2013) D.-H. Jeong et al.   PLANT PHYSIOLOGY

Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

(2013) Runxuan Zhang et al.   PLoS One

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Identification of Cassava MicroRNAs under Abiotic Stress

(2013) Carolina Ballén-Taborda et al.   International Journal of Genomics

Genome-Wide Analysis of MicroRNAs in Sacred Lotus, Nelumbo nucifera (Gaertn)

(2013) Yun Zheng et al.   Tropical Plant Biology

A Review of Computational Tools in microRNA Discovery

(2013) Clarissa P. C. Gomes et al.   Frontiers in Genetics

Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis

(2012) Miao Y Xu et al.   BMC GENOMICS

Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

(2012) Pablo Pelaez et al.   BMC GENOMICS

Characterization of microRNAs expression during maize seed development

(2012) Mingming Kang et al.   BMC GENOMICS

Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium

(2012) Zhao Sheng Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

(2012) Leighton Folkes et al.   NUCLEIC ACIDS RESEARCH

SoMART: a web server for plant miRNA, tasiRNA and target gene analysis

(2012) Feng Li et al.   PLANT JOURNAL

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

(2012) Fuliang Xie et al.   PLANT MOLECULAR BIOLOGY

A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber

(2012) Weihua Mao et al.   PLoS One

Identification and Characterization of MicroRNAs in Asiatic Cotton (Gossypium arboreum L.)

(2012) Min Wang et al.   PLoS One

Plant secondary siRNA production determined by microRNA-duplex structure

(2012) P. A. Manavella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are all the miRBase-registered microRNAs true?

(2012) Yijun Meng et al.   RNA Biology

PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs

(2011) Ping Xuan et al.   BIOINFORMATICS

Employing machine learning for reliable miRNA target identification in plants

(2011) Ashwani Jha et al.   BMC GENOMICS

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

(2011) Qing-Xin Song et al.   BMC PLANT BIOLOGY

Identification of novel maize miRNAs by measuring the precision of precursor processing

(2011) Yinping Jiao et al.   BMC PLANT BIOLOGY

The role of Mediator in small and long noncoding RNA production inArabidopsis thaliana

(2011) Yun Ju Kim et al.   EMBO JOURNAL

Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica

(2011) Bosheng Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393∗-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12

(2011) Xiaoming Zhang et al.   MOLECULAR CELL

miRNEST database: an integrative approach in microRNA search and annotation

(2011) Michał Wojciech Szcześniak et al.   NUCLEIC ACIDS RESEARCH

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

(2011) Yun Zheng 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

Experimental strategies for microRNA target identification

(2011) D. W. Thomson et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Small RNA Profiling in Two Brassica napus Cultivars Identifies MicroRNAs with Oil Production- and Development-Correlated Expression and New Small RNA Classes

(2011) Y.-T. Zhao et al.   PLANT PHYSIOLOGY

Computational Prediction of Intronic microRNA Targets using Host Gene Expression Reveals Novel Regulatory Mechanisms

(2011) M. Hossein Radfar et al.   PLoS One

MaturePred: Efficient Identification of MicroRNAs within Novel Plant Pre-miRNAs

(2011) Ping Xuan et al.   PLoS One

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

A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.)

(2010) Moreno Colaiacovo et al.   BMC GENOMICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Got target?: computational methods for microRNA target prediction and their extension

(2010) Hyeyoung Min et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum)

(2010) Fuliang Xie et al.   GENE

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

(2010) H. R. Chiang et al.   GENES & DEVELOPMENT

The discovery approaches and detection methods of microRNAs

(2010) Yong Huang et al.   MOLECULAR BIOLOGY REPORTS

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Antitumor activity of apoptotic nuclease TBN1 from L. esculentum.

(2010) J. Matousek et al.   NEOPLASMA

PmiRKB: a plant microRNA knowledge base

(2010) Y. Meng et al.   NUCLEIC ACIDS RESEARCH

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

(2010) Z. Fei et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

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

The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci

(2010) E. R. Havecker et al.   PLANT CELL

Transcriptome-wide identification of microRNA targets in rice

(2010) Yong-Fang Li et al.   PLANT JOURNAL

Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)

(2010) Taylor P. Frazier et al.   PLANTA

microPred: effective classification of pre-miRNAs for human miRNA gene prediction

(2009) Rukshan Batuwita et al.   BIOINFORMATICS

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models

(2009) Sabah Kadri et al.   BMC BIOINFORMATICS

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Identification of MicroRNAs in Wild Soybean (Glycine soja)

(2009) Rui Chen et al.   Journal of Integrative Plant Biology

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Current tools for the identification of miRNA genes and their targets

(2009) N. D. Mendes 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

Rice MicroRNA Effector Complexes and Targets

(2009) L. Wu et al.   PLANT CELL

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

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

PatMaN: rapid alignment of short sequences to large databases

(2008) Kay Prüfer et al.   BIOINFORMATICS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Criteria for Annotation of Plant MicroRNAs

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

Computational analysis of small RNA cloning data

(2007) Philipp Berninger et al.   METHODS