ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with Pseudo K-Tuple Nucleotide Compositional Features

Development and use of miRNA-derived SSR markers for the study of genetic diversity, population structure, and characterization of genotypes for breeding heat tolerant wheat varieties

(2021) Sandhya Tyagi et al.   PLoS One

PredCRG: A computational method for recognition of plant circadian genes by employing support vector machine with Laplace kernel

(2021) Prabina Kumar Meher et al.   Plant Methods

Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding

(2021) Pooja Sihag et al.   Frontiers in Genetics

Improved recognition of splice sites in A. thaliana by incorporating secondary structure information into sequence-derived features: a computational study

(2021) Prabina Kumar Meher et al.   3 Biotech

miRNA applications for engineering abiotic stress tolerance in plants

(2020) Shabir Hussain Wani et al.   BIOLOGIA

Differential expression of microRNAs in tomato leaves treated with different light qualities

(2020) Fei Dong et al.   BMC GENOMICS

Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses

(2020) Keyvan Asefpour Vakilian   Scientific Reports

miRNA Targeting: Growing beyond the Seed

(2019) Laura B. Chipman et al.   TRENDS IN GENETICS

HRGPred: Prediction of herbicide resistant genes with k-mer nucleotide compositional features and support vector machine

(2019) Prabina Kumar Meher et al.   Scientific Reports

The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides

(2018) Yifei Yan et al.   NUCLEIC ACIDS RESEARCH

Selection of reference genes for miRNA qRT-PCR under abiotic stress in grapevine

(2018) Meng Luo et al.   Scientific Reports

Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4

(2018) Zhenfei Sun et al.   PLoS Genetics

nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine

(2018) Prabina K. Meher et al.   Frontiers in Microbiology

ir-HSP: Improved Recognition of Heat Shock Proteins, Their Families and Sub-types Based On g-Spaced Di-peptide Features and Support Vector Machine

(2018) Prabina K. Meher et al.   Frontiers in Genetics

Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.)

(2018) Shabir H. Wani et al.   PLANT MOLECULAR BIOLOGY

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Recent Advances in Conotoxin Classification by Using Machine Learning Methods

(2017) Fu-Ying Dao et al.   MOLECULES

Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea

(2017) Indra Singh et al.   Frontiers in Plant Science

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC

(2017) Pengmian Feng et al.   Molecular Therapy-Nucleic Acids

2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function

(2017) Bin Liu et al.   Molecular Therapy-Nucleic Acids

Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L

(2016) Yan Qiao et al.   MOLECULAR GENETICS AND GENOMICS

iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets

(2016) Jianhua Jia et al.   MOLECULES

Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.)

(2016) Vijay Gahlaut et al.   THEORETICAL AND APPLIED GENETICS

A Natural Light/Dark Cycle Regulation of Carbon-Nitrogen Metabolism and Gene Expression in Rice Shoots

(2016) Haixing Li et al.   Frontiers in Plant Science

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

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

Expression of zma-miR169 miRNAs and their target ZmNF-YA genes in response to abiotic stress in maize leaves

(2015) Mingda Luan et al.   GENE

iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach

(2015) Xuan Xiao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

MicroRNA: a new target for improving plant tolerance to abiotic stress

(2015) Baohong Zhang   JOURNAL OF EXPERIMENTAL BOTANY

PlantMirnaT: miRNA and mRNA integrated analysis fully utilizing characteristics of plant sequencing data

(2015) S. Rhee et al.   METHODS

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

(2015) Wei Chen et al.   Molecular BioSystems

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

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

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

Genome-wide identification of microRNAs and their targets in wild type and phyB mutant provides a key link between microRNAs and the phyB-mediated light signaling pathway in rice

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

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

(2015) Anita Tripathi et al.   Frontiers in Physiology

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

adabag: AnRPackage for Classification with Boosting and Bagging

(2015) Esteban Alfaro et al.   Journal of Statistical Software

Molecular characterization of StNAC2 in potato and its overexpression confers drought and salt tolerance

(2014) Qinfen Xu et al.   ACTA PHYSIOLOGIAE PLANTARUM

iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Role of MicroRNAs in Biotic and Abiotic Stress Responses in Crop Plants

(2014) Rajesh Kumar   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

(2014) Shou-Hui Guo et al.   BIOINFORMATICS

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

(2014) Jiyuan An et al.   BMC BIOINFORMATICS

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

Photosynthesis: Response to high temperature stress

(2014) Sonal Mathur et al.   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY

SVM-RFE Based Feature Selection and Taguchi Parameters Optimization for Multiclass SVM Classifier

(2014) Mei-Ling Huang et al.   TheScientificWorldJOURNAL

A survey of the small RNA population during far-red light-induced apical hook opening

(2014) Ying Li et al.   Frontiers in Plant Science

Spectral turbulence measuring as feature extraction method from EEG on affective computing

(2013) A.R. Hidalgo-Muñoz et al.   Biomedical Signal Processing and Control

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

(2013) Shihua Zhang et al.   BMC PLANT BIOLOGY

Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.)

(2013) Min Wang et al.   GENE

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Redox signaling mediates the expression of a sulfate-deprivation-inducible microRNA395 in Arabidopsis

(2013) Guru Jagadeeswaran et al.   PLANT JOURNAL

A support vector machine-recursive feature elimination feature selection method based on artificial contrast variables and mutual information

(2012) Xiaohui Lin et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

iNR-PhysChem: A Sequence-Based Predictor for Identifying Nuclear Receptors and Their Subfamilies via Physical-Chemical Property Matrix

(2012) Xuan Xiao et al.   PLoS One

Genome-Wide Identification of miRNAs Responsive to Drought in Peach (Prunus persica) by High-Throughput Deep Sequencing

(2012) Vahap Eldem et al.   PLoS One

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

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

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments

(2011) Ernesto Picardi et al.   BIOINFORMATICS

Identification of novel soybean microRNAs involved in abiotic and biotic stresses

(2011) Franceli R Kulcheski et al.   BMC GENOMICS

Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes

(2011) Blanca E Barrera-Figueroa et al.   BMC PLANT BIOLOGY

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

Salt and Drought Stresses Induce the Aberrant Expression of microRNA Genes in Tobacco

(2011) Taylor P. Frazier et al.   MOLECULAR BIOTECHNOLOGY

miRNEST database: an integrative approach in microRNA search and annotation

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

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

(2010) Mingming Xin et al.   BMC PLANT BIOLOGY

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

(2010) De-Kang Lv et al.   GENE

Margin-Maximizing Feature Elimination Methods for Linear and Nonlinear Kernel-Based Discriminant Functions

(2010) Yaman Aksu et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS

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

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

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

Genome-wide mapping of the HY5-mediated genenetworks in Arabidopsis that involve both transcriptional and post-transcriptional regulation

(2010) Huiyong Zhang et al.   PLANT JOURNAL

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

(2010) Melda Kantar et al.   PLANTA

MicroRNAs with macro-effects on plant stress responses

(2010) Ramanjulu Sunkar   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

Graft-transmissible induction of potato tuberization by the microRNA miR172

(2009) A. Martin et al.   DEVELOPMENT

PMRD: plant microRNA database

(2009) Zhenhai Zhang et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

(2009) Inês Trindade et al.   PLANTA

Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis

(2009) Guru Jagadeeswaran et al.   PLANTA

Analysis of Metabolomic Data Using Support Vector Machines

(2008) Sankar Mahadevan et al.   ANALYTICAL CHEMISTRY

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

(2008) Dong Ding et al.   ANNALS OF BOTANY

Plant miRNAs and abiotic stress responses

(2008) Xiao-Yan Lu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

MicroRNA expression profiling using microarrays

(2008) Chang-Gong Liu et al.   Nature Protocols

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

(2008) W.-X. Li et al.   PLANT CELL

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

(2008) H.-H. Liu et al.   RNA