Recent trends and advances in identification and functional characterization of plant miRNAs

PmiRDiscVali: an integrated pipeline for plant microRNA discovery and validation

(2019) Dongliang Yu et al.   BMC GENOMICS

Identification and characterization of drought responsive miRNAs in a drought tolerant upland rice cultivar KMJ 1-12-3

(2019) Jay Prakash Awasthi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

The Elaboration of miRNA Regulation and Gene Regulatory Networks in Plant–Microbe Interactions

(2019) de Vries et al.   Genes

The genome-wide impact of cadmium on microRNA and mRNA expression in contrasting Cd responsive wheat genotypes

(2019) Min Zhou et al.   BMC GENOMICS

Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants

(2019) Sara Cimini et al.   Frontiers in Plant Science

Trends in the development of miRNA bioinformatics tools

(2018) Liang Chen et al.   BRIEFINGS IN BIOINFORMATICS

A comprehensive review of web-based resources of non-coding RNAs for plant science research

(2018) Peiran Liao et al.   International Journal of Biological Sciences

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update

(2018) Jia Ye et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Small but powerful: function of microRNAs in plant development

(2018) Haiping Liu et al.   PLANT CELL REPORTS

Plant small RNAs: advancement in the understanding of biogenesis and role in plant development

(2018) Archita Singh et al.   PLANTA

Expression profiling across wild and cultivated tomatoes supports the relevance of early miR482/2118 suppression for Phytophthora resistance

(2018) Sophie de Vries et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination

(2018) Shabari Sarkar Das et al.   Scientific Reports

ARMOUR – A Rice miRNA: mRNA Interaction Resource

(2018) Neeti Sanan-Mishra et al.   Frontiers in Plant Science

Plant Small Non-coding RNAs and Their Roles in Biotic Stresses

(2018) Eleanor J. Brant et al.   Frontiers in Plant Science

Function identification of miR482b, a negative regulator during tomato resistance to Phytophthora infestans

(2018) Ning Jiang et al.   Horticulture Research

Biological significance, computational analysis, and applications of plant microRNAs

(2018) Maria Szwacka et al.   ACTA PHYSIOLOGIAE PLANTARUM

Regulation of microRNA biogenesis and its crosstalk with other cellular pathways

(2018) Thomas Treiber et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants

(2018) Zheng Kuang et al.   BIOINFORMATICS

Identification and validation of plant miRNA from NGS data—an experimental approach

(2018) Kamalakshi Devi et al.   Briefings in Functional Genomics

An emerging technique for reducing the response time in plant miRNA identification

(2018) Somrak Numnark et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Exploring miRNAs for developing climate-resilient crops: A perspective review

(2018) Jin Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Insights into the miRNA-mediated response of maize leaf to arsenate stress

(2017) Supriya Ghosh et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

MicroRNAs in model and complex organisms

(2017) Hikmet Budak et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Small RNA profiling reveals important roles for miRNAs in Arabidopsis response to Bacillus velezensis FZB42

(2017) Shanshan Xie et al.   GENE

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

(2017) Rolf Backofen et al.   JOURNAL OF BIOTECHNOLOGY

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

(2017) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance

(2017) Vinay Kumar et al.   PLANT CELL REPORTS

Small RNAs: Big Impact on Plant Development

(2017) Marco D’Ario et al.   TRENDS IN PLANT SCIENCE

Identification and analysis of brown planthopper-responsive microRNAs in resistant and susceptible rice plants

(2017) Yan Wu et al.   Scientific Reports

Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors

(2017) J. Miskiewicz et al.   Biomed Research International

An Optimized Transient Dual Luciferase Assay for Quantifying MicroRNA Directed Repression of Targeted Sequences

(2017) Richard L. Moyle et al.   Frontiers in Plant Science

Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

(2017) Arnaud T. Djami-Tchatchou et al.   Frontiers in Plant Science

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

(2016) Marc Sturm et al.   BMC BIOINFORMATICS

miRNAFold: a web server for fast miRNA precursor prediction in genomes

(2016) Christophe Tav et al.   NUCLEIC ACIDS RESEARCH

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

(2016) Aditya Banerjee et al.   Plant Biotechnology Reports

SorghumFDB: sorghum functional genomics database with multidimensional network analysis

(2016) Tian Tian et al.   Database-The Journal of Biological Databases and Curation

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

(2016) Varsha Shriram et al.   Frontiers in Plant Science

Hexaploid wheat (Triticum aestivum) root miRNome analysis in response to salt stress

(2015) H. Eren et al.   ANNALS OF APPLIED BIOLOGY

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

Optimization of miRNA-seq data preprocessing

(2015) S. Tam et al.   BRIEFINGS IN BIOINFORMATICS

Principles of miRNA–mRNA interactions: beyond sequence complementarity

(2015) Fabian Afonso-Grunz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae

(2015) Sophie de Vries et al.   Genome Biology and Evolution

MicroRNAs in Control of Plant Development

(2015) Chao Li et al.   JOURNAL OF CELLULAR PHYSIOLOGY

To Bloom or Not to Bloom: Role of MicroRNAs in Plant Flowering

(2015) Sachin Teotia et al.   Molecular Plant

Bioinformatic tools for microRNA dissection

(2015) Most Mauluda Akhtar et al.   NUCLEIC ACIDS RESEARCH

Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

(2015) Wen-Chi Lee et al.   RNA Biology

The use of high-throughput sequencing methods for plant microRNA research

(2015) Xiaoxia Ma et al.   RNA Biology

miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

(2015) T. Desvignes et al.   TRENDS IN GENETICS

Challenges in Using Circulating miRNAs as Cancer Biomarkers

(2015) Paola Tiberio et al.   Biomed Research International

Identification of cold-inducible microRNAs in grapevine

(2015) Xiaoming Sun et al.   Frontiers in Plant Science

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution

(2015) Anita Tripathi et al.   Frontiers in Physiology

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

(2015) Pingchuan Deng et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

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

Identification of miRNAs involved in pear fruit development and quality

(2014) Jun Wu et al.   BMC GENOMICS

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

(2014) Atul Kakrana et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Genome-wide fungal stress responsive miRNA expression in wheat

(2014) Behçet Inal et al.   PLANTA

MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to Fusarium oxysporum

(2014) Shouqiang Ouyang et al.   PLoS Pathogens

Common features of microRNA target prediction tools

(2014) Sarah M. Peterson et al.   Frontiers in Genetics

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

Multiple RNA recognition patterns during microRNA biogenesis in plants

(2013) N. G. Bologna et al.   GENOME RESEARCH

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

(2013) Dimitrios Kleftogiannis et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

miRNEST 2.0: a database of plant and animal microRNAs

(2013) Michał W. Szcześniak et al.   NUCLEIC ACIDS RESEARCH

PlantGSEA: a gene set enrichment analysis toolkit for plant community

(2013) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Identification of Conserved and Novel Cold-Responsive MicroRNAs in Trifoliate Orange (Poncirus trifoliata (L.) Raf.) Using High-Throughput Sequencing

(2013) Xiao-Na Zhang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Genome organization and characteristics of soybean microRNAs

(2012) Marie Turner et al.   BMC GENOMICS

C-mii: a tool for plant miRNA and target identification

(2012) Somrak Numnark et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa

(2012) Lei Chen et al.   GENE

Genome-wide identification of miRNA targets by PAR-CLIP

(2012) Markus Hafner et al.   METHODS

Computational Identification of MicroRNAs and Their Targets in Cassava (Manihot esculenta Crantz.)

(2012) Onsaya Patanun et al.   MOLECULAR BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

(2012) Jiyuan An et al.   NUCLEIC ACIDS RESEARCH

A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and Other mRNAs

(2012) P. V. Shivaprasad et al.   PLANT CELL

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

(2012) Feng Li et al.   PLANT JOURNAL

Cloning and Characterization of Maize miRNAs Involved in Responses to Nitrogen Deficiency

(2012) Meng Zhao et al.   PLoS One

Identification of Soybean MicroRNAs Involved in Soybean Cyst Nematode Infection by Deep Sequencing

(2012) Xiaoyan Li et al.   PLoS One

Evaluation of normalization methods in mammalian microRNA-Seq data

(2012) L. X. Garmire et al.   RNA

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science

(2012) Sebastian Klie et al.   Frontiers in Genetics

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

(2011) Tianzuo Wang et al.   BMC GENOMICS

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa

(2011) Xiang Yu et al.   JOURNAL OF EXPERIMENTAL BOTANY

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

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

MicroRNAs and their diverse functions in plants

(2011) Guiling Sun   PLANT MOLECULAR BIOLOGY

MicroRNAs as regulators of root development and architecture

(2011) Ghazanfar A. Khan et al.   PLANT MOLECULAR BIOLOGY

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

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

(2011) Ping Xuan et al.   PLoS One

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

MicroRNA-mediated signaling involved in plant root development

(2010) Yijun Meng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

Computational analysis of miRNA targets in plants: current status and challenges

(2010) X. Dai et al.   BRIEFINGS IN BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

MicroRNA Processing: Battle of the Bulge

(2010) Blake C. Meyers et al.   CURRENT BIOLOGY

Biological functions of microRNAs: a review

(2010) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

(2010) Annelie Carlsbecker et al.   NATURE

MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity

(2010) Oswaldo Valdés-López et al.   NEW PHYTOLOGIST

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

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

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo

(2010) Elisabeth M. Mahen et al.   PLOS BIOLOGY

Next Generation Sequencing of miRNAs – Strategies, Resources and Methods

(2010) Susanne Motameny et al.   Genes

Computational Identification of miRNAs and Their Target Genes from Expressed Sequence Tags of Tea (Camellia sinensis)

(2010) G.R. Prabu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Small RNAs and Their Roles in Plant Development

(2009) Xuemei Chen   Annual Review of Cell and Developmental Biology

Short-Read Sequencing Technologies for Transcriptional Analyses

(2009) Stacey A. Simon et al.   Annual Review of Plant Biology

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Identification of MicroRNA Processing Determinants by Random Mutagenesis of Arabidopsis MIR172a Precursor

(2009) Julieta L. Mateos et al.   CURRENT BIOLOGY

Structure Determinants for Accurate Processing of miR172a in Arabidopsis thaliana

(2009) Schallum Werner et al.   CURRENT BIOLOGY

Survey of Computational Algorithms for MicroRNA Target Prediction

(2009) Dong Yue et al.   CURRENT GENOMICS

UV-B-responsive microRNAs in Populus tremula

(2009) Xiaoyun Jia et al.   JOURNAL OF PLANT PHYSIOLOGY

Computational approaches for microRNA studies: a review

(2009) Li Li et al.   MAMMALIAN GENOME

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

PMRD: plant microRNA database

(2009) Zhenhai Zhang et al.   NUCLEIC ACIDS RESEARCH

Computational and analytical framework for small RNA profiling by high-throughput sequencing

(2009) N. Fahlgren et al.   RNA

Functional genetic variation of human miRNAs and phenotypic consequences

(2008) Christelle Borel et al.   MAMMALIAN GENOME

Criteria for Annotation of Plant MicroRNAs

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

Reconstituting plant miRNA biogenesis

(2008) J.-K. Zhu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Profiling microRNA expression with microarrays

(2008) James Q. Yin et al.   TRENDS IN BIOTECHNOLOGY