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

Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

(2015) Damien Formey et al.   BMC GENOMICS

Identification of novel and salt-responsive miRNAs to explore miRNA-mediated regulatory network of salt stress response in radish (Raphanus sativus L.)

(2015) Xiaochuan Sun et al.   BMC GENOMICS

Construction of regulatory networks mediated by small RNAs responsive to abiotic stresses in rice (Oryza sativa)

(2015) Jingping Qin et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing

(2015) Min Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MicroRNAs expression patterns in the response of poplar woody root to bending stress

(2015) Miriam Rossi et al.   PLANTA

ROS-mediated abiotic stress-induced programmed cell death in plants

(2015) Veselin Petrov et al.   Frontiers in Plant Science

Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

(2015) Maria Barciszewska-Pacak et al.   Frontiers in Plant Science

Profiling the expression domains of a rice-specific microRNA under stress

(2015) Neha Sharma et al.   Frontiers in Plant Science

Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis

(2015) Xue Cao et al.   BMC GENOMICS

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

(2014) Jiyuan An et al.   BMC BIOINFORMATICS

Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

(2014) Hongjun Liu et al.   BMC GENOMICS

Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton

(2014) Fuliang Xie et al.   JOURNAL OF EXPERIMENTAL BOTANY

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Differential expression of microRNAs and other small RNAs in barley between water and drought conditions

(2014) Michael Hackenberg et al.   PLANT BIOTECHNOLOGY JOURNAL

Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database

(2014) Yusuf Khan et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Transcriptome-Wide Characterization of Novel and Heat-Stress-Responsive microRNAs in Radish (Raphanus Sativus L.) Using Next-Generation Sequencing

(2014) Ronghua Wang et al.   PLANT MOLECULAR BIOLOGY REPORTER

The Art of Being Flexible: How to Escape from Shade, Salt, and Drought

(2014) Ronald Pierik et al.   PLANT PHYSIOLOGY

Identification of the Conserved and Novel miRNAs in Mulberry by High-Throughput Sequencing

(2014) Ling Jia et al.   PLoS One

Abiotic stress responses in plant roots: a proteomics perspective

(2014) Dipanjana Ghosh et al.   Frontiers in Plant Science

PMTED: a plant microRNA target expression database

(2013) Xiuli Sun et al.   BMC BIOINFORMATICS

High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves

(2013) Anna Lukasik et al.   BMC GENOMICS

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

(2013) Elena A Vidal et al.   BMC GENOMICS

PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress

(2013) Shihua Zhang et al.   BMC PLANT BIOLOGY

isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets

(2013) Gaurav Sablok et al.   FEBS LETTERS

Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa)

(2013) Tapan Kumar Mondal et al.   GENE

Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants

(2013) Mirza Hasanuzzaman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ST105 Deep sequencing reveals abundant Pol III retroviral microRNA cluster in Bovine Leukemia Virus-induced leukemia

(2013) Nicolas Rosewick et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Identification of tissue-preferential expression patterns of rice miRNAs

(2013) Deepti Mittal et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Micro-regulators of auxin action

(2013) Neeti Sanan-Mishra et al.   PLANT CELL REPORTS

Heat stress induction ofmiR398triggers a regulatory loop that is critical for thermotolerance in Arabidopsis

(2013) Qingmei Guan et al.   PLANT JOURNAL

Global identification of miRNAs and targets in Populus euphratica under salt stress

(2013) Bosheng Li et al.   PLANT MOLECULAR BIOLOGY

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

Cellular Localization and Processing of Primary Transcripts of Exonic MicroRNAs

(2013) Izabella Slezak-Prochazka et al.   PLoS One

CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts

(2013) S. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CoLIde

(2013) Irina Mohorianu et al.   RNA Biology

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

(2013) Jinyu Wu et al.   RNA Biology

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

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

(2012) Somrak Numnark et al.   BMC GENOMICS

Effects of abiotic stress on plants: a systems biology perspective

(2012) Grant R Cramer et al.   BMC PLANT BIOLOGY

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

(2012) Pablo A. Manavella et al.   CELL

Molecular Identification and Analysis of Arsenite Stress-Responsive miRNAs in Rice

(2012) Qingpo Liu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Biogenesis, functions and fate of plant microRNAs

(2012) Afsar Raza Naqvi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge 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

Semirna: Searching for Plant miRNAs Using Target Sequences

(2012) Antonio Muñoz-Mérida et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

MiR-128 Inhibits Tumor Growth and Angiogenesis by Targeting p70S6K1

(2012) Zhu-mei Shi et al.   PLoS One

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis

(2012) G. Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis

(2012) X. Zhan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

IsomiRs – the overlooked repertoire in the dynamic microRNAome

(2012) Corine T. Neilsen et al.   TRENDS IN GENETICS

Environmental control of plant nuclear gene expression by chloroplast redox signals

(2012) Jeannette Pfalz et al.   Frontiers in Plant Science

Finding MicroRNA Targets in Plants: Current Status and Perspectives

(2012) Jiandong Ding et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

Identification of novel soybean microRNAs involved in abiotic and biotic stresses

(2011) Franceli R Kulcheski et al.   BMC GENOMICS

Exploring plant transcriptomes using ultra high-throughput sequencing

(2011) L. Wang et al.   Briefings in Functional Genomics

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

(2011) Yun Ju Kim et al.   EMBO JOURNAL

Sensitivity of flowering plant gametophytes to temperature fluctuations

(2011) Afif Hedhly   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Aluminum triggers broad changes in microRNA expression in rice roots

(2011) J.C. Lima et al.   GENETICS AND MOLECULAR RESEARCH

The putative tumour suppressor microRNA-124 modulates hepatocellular carcinoma cell aggressiveness by repressing ROCK2 and EZH2

(2011) Fang Zheng et al.   GUT

Regulation of root water uptake under abiotic stress conditions

(2011) R. Aroca et al.   JOURNAL OF EXPERIMENTAL BOTANY

Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa)

(2011) Yanfei Ding et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE

(2011) Yanping Zhang et al.   MOLECULAR BIOLOGY REPORTS

Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity

(2011) Zujun Yin et al.   MOLECULAR BIOLOGY REPORTS

Plants and flooding stress

(2011) Pierdomenico Perata et al.   NEW PHYTOLOGIST

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

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

Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE

(2011) Satoru Machida et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Regulation of miR319 during cold stress in sugarcane

(2011) FLÁVIA THIEBAUT et al.   PLANT CELL AND ENVIRONMENT

Predicting the decline in daily maximum transpiration rate of two pine stands during drought based on constant minimum leaf water potential and plant hydraulic conductance

(2011) R. A. Duursma et al.   TREE PHYSIOLOGY

MicroRNA networks and developmental plasticity in plants

(2011) Ignacio Rubio-Somoza et al.   TRENDS IN PLANT SCIENCE

Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens

(2011) Ping Wan et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Structure and RNA Interactions of the Plant MicroRNA Processing-Associated Protein HYL1

(2010) Rodolfo M. Rasia et al.   BIOCHEMISTRY

MicroRNAs: Synthesis, mechanism, function, and recent clinical trials

(2010) Fazli Wahid et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

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

(2010) Eric Bonnet et al.   BIOINFORMATICS

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

(2010) Changnian Song et al.   BMC GENOMICS

Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development

(2010) Guru Jagadeeswaran et al.   BMC GENOMICS

Regulation of barley miRNAs upon dehydration stress correlated with target gene expression

(2010) Melda Kantar et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Profiling of cold-stress-responsive miRNAs in rice by microarrays

(2010) De-Kang Lv et al.   GENE

Origins and Evolution of MicroRNA Genes in Drosophila Species

(2010) Masafumi Nozawa et al.   Genome Biology and Evolution

Temperature stress and plant sexual reproduction: uncovering the weakest links

(2010) K. E. Zinn et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

(2010) Liguo Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

microRNA expression alteration after arsenic trioxide treatment in HepG-2 cells

(2010) Xian-Zhi Meng et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Enhanced production of melatonin by ectopic overexpression of human serotonin N-acetyltransferase plays a role in cold resistance in transgenic rice seedlings

(2010) Kiyoon Kang et al.   JOURNAL OF PINEAL RESEARCH

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

PmiRKB: a plant microRNA knowledge base

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

Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica)

(2010) Tian Li et al.   NUCLEIC ACIDS RESEARCH

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

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

miRNA expression patterns of Triticum dicoccoides in response to shock drought stress

(2010) Melda Kantar et al.   PLANTA

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

(2010) H.-M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction

(2010) H. Qin et al.   RNA

Structure of Arabidopsis HYPONASTIC LEAVES1 and Its Molecular Implications for miRNA Processing

(2010) Seong Wook Yang et al.   STRUCTURE

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

(2010) David Hendrix et al.   GENOME BIOLOGY

Next Generation Sequencing of miRNAs – Strategies, Resources and Methods

(2010) Susanne Motameny et al.   Genes

Small RNAs and Their Roles in Plant Development

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

Novel gene clusters involved in arsenite oxidation and resistance in two arsenite oxidizers: Achromobacter sp. SY8 and Pseudomonas sp. TS44

(2009) Lin Cai et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2009) Sabah Kadri et al.   BMC BIOINFORMATICS

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

(2009) Jingyu Zhang et al.   BMC GENOMICS

Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor

(2009) Botao Zhao et al.   BMC MOLECULAR BIOLOGY

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Cold stress effects on reproductive development in grain crops: An overview

(2009) Prince Thakur et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling

(2009) Qing Liu et al.   FEBS LETTERS

Genomic organization of microRNAs

(2009) Abigail F. Olena et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses

(2009) Neeti Sanan-Mishra et al.   MOLECULAR GENETICS AND GENOMICS

PMRD: plant microRNA database

(2009) Zhenhai Zhang et al.   NUCLEIC ACIDS RESEARCH

Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

(2009) E. Lanet et al.   PLANT CELL

Post-transcriptional gene regulation of salinity and drought responses by plant microRNAs

(2009) ALEJANDRA A. COVARRUBIAS et al.   PLANT CELL AND ENVIRONMENT

Cloning and characterization of small non-coding RNAs from grape

(2009) Andrea Carra et al.   PLANT JOURNAL

Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana

(2009) Xiaoyun Jia et al.   PLANT MOLECULAR BIOLOGY

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress

(2009) Catalina Arenas-Huertero et al.   PLANT MOLECULAR BIOLOGY

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula

(2009) Inês Trindade et al.   PLANTA

A Genome-Wide Characterization of MicroRNA Genes in Maize

(2009) Lifang Zhang et al.   PLoS Genetics

Differential expression of miRNAs in response to salt stress in maize roots

(2008) Dong Ding et al.   ANNALS OF BOTANY

Flooding Stress: Acclimations and Genetic Diversity

(2008) J. Bailey-Serres et al.   Annual Review of Plant Biology

Identification of cold-inducible microRNAs in plants by transcriptome analysis

(2008) X ZHOU et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

Enhanced tolerance to drought stress in transgenic tobacco plants overexpressing VTE1 for increased tocopherol production from Arabidopsis thaliana

(2008) Xiaoli Liu et al.   BIOTECHNOLOGY LETTERS

In silico identification of conserved microRNAs in large number of diverse plant species

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

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

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill

(2008) Jianguang Zhang et al.   GENE

Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum)

(2008) Zujun Yin et al.   GENE

Identification and verification of microRNA in wheat (Triticum aestivum)

(2008) Weibo Jin et al.   JOURNAL OF PLANT RESEARCH

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Two Cap-Binding Proteins CBP20 and CBP80 are Involved in Processing Primary MicroRNAs

(2008) S. Kim et al.   PLANT AND CELL PHYSIOLOGY

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance

(2008) W.-X. Li et al.   PLANT CELL

Criteria for Annotation of Plant MicroRNAs

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

Stress-responsive microRNAs inPopulus

(2008) Shanfa Lu et al.   PLANT JOURNAL

Identification of soybean microRNAs and their targets

(2008) Baohong Zhang et al.   PLANTA

The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis

(2008) B. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1

(2008) Z. Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana

(2008) H.-H. Liu et al.   RNA

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Evolution of plant microRNAs and their targets

(2008) Michael J. Axtell et al.   TRENDS IN PLANT SCIENCE