Computational Approaches and Related Tools to Identify MicroRNAs in a Species: A Bird’s Eye View

No abstract is available for this paper.

• Publication year

  2018

• Venue

  Interdisciplinary Sciences Computational Life Sciences

• Publication date

  2018-09-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1007/s12539-017-0223-xPMID 28361256
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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

  2016cited by this paper
• Predicting effective microRNA target sites in mammalian mRNAs

  2015cited by this paper
• miR2GO: comparative functional analysis for microRNAs

  2015cited by this paper
• Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

  2015cited by this paper
• miRBoost: boosting support vector machines for microRNA precursor classification

  2015cited by this paper
• OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs

  2014cited by this paper
• miRDB: an online resource for microRNA target prediction and functional annotations

  2014cited by this paper
• DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

  2014cited by this paper
• Computational prediction of microRNA genes.

  2014cited by this paper
• miR-34 cooperates with p53 in suppression of prostate cancer by joint regulation of stem cell compartment.

  2014cited by this paper
• A detailed analysis of next generation sequencing reads of microRNA expression in Barrett’s Esophagus: absolute versus relative quantification

  2014cited by this paper
• Development of microRNA therapeutics is coming of age

  2014cited by this paper
• miRCancer: a microRNA-cancer association database constructed by text mining on literature

  2013cited by this paper
• HMDD v2.0: a database for experimentally supported human microRNA and disease associations

  2013cited by this paper
• Mechanism of miRNA-mediated repression of mRNA translation.

  2013cited by this paper
• miRBase: annotating high confidence microRNAs using deep sequencing data

  2013cited by this paper
• DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

  2013cited by this paper
• PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

  2013cited by this paper
• MicroRNA: function, detection, and bioanalysis.

  2013cited by this paper
• A Review of Computational Tools in microRNA Discovery

  2013cited by this paper
• miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

  2012cited by this paper
• Genome‐wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis

  2012cited by this paper
• A fast ab-initio method for predicting miRNA precursors in genomes

  2012cited by this paper
• MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs

  2012cited by this paper
• Identification of microRNA-regulated gene networks by expression analysis of target genes

  2012cited by this paper
• SomamiR: a database for somatic mutations impacting microRNA function in cancer

  2012cited by this paper
• MiRmat: Mature microRNA Sequence Prediction

  2012cited by this paper
• MicroRNA Prediction Using a Fixed-Order Markov Model Based on the Secondary Structure Pattern

  2012cited by this paper
• PsRobot: a web-based plant small RNA meta-analysis toolbox

  2012cited by this paper
• miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting

  2012cited by this paper
• Interactive exploration of RNA22 microRNA target predictions

  2012cited by this paper
• miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets

  2012cited by this paper
• mirConnX: condition-specific mRNA-microRNA network integrator

  2011cited by this paper
• MaturePred: Efficient Identification of MicroRNAs within Novel Plant Pre-miRNAs

  2011cited by this paper
• miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs.

  2011cited by this paper
• Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis

  2011cited by this paper
• miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes

  2011cited by this paper
• Employing machine learning for reliable miRNA target identification in plants

  2011cited by this paper
• Inferring causative variants in microRNA target sites

  2011cited by this paper
• miRTour: Plant miRNA and target prediction tool

  2011cited by this paper
• MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

  2011influential reference
• miRTar: an integrated system for identifying miRNA-target interactions in human

  2011cited by this paper
• psRNATarget: a plant small RNA target analysis server

  2011cited by this paper
• MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

  2010cited by this paper
• The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function

  2010cited by this paper
• mESAdb: microRNA Expression and Sequence Analysis Database

  2010cited by this paper
• MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors

  2010influential reference
• miRTarBase: a database curates experimentally validated microRNA–target interactions

  2010cited by this paper
• MicroRNA: Biogenesis, Function and Role in Cancer

  2010cited by this paper
• MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

  2010cited by this paper
• Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

  2010cited by this paper
• MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features

  2010cited by this paper
• TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

  2010cited by this paper
• PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

  2010cited by this paper
• MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

  2010cited by this paper
• microPred: effective classification of pre-miRNAs for human miRNA gene prediction

  2009cited by this paper
• DIANA-mirPath: Integrating human and mouse microRNAs in pathways

  2009cited by this paper
• Origin, biogenesis, and activity of plant microRNAs.

  2009cited by this paper
• miRò: a miRNA knowledge base

  2009cited by this paper
• Current tools for the identification of miRNA genes and their targets

  2009cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• A Brief Review on the Mechanisms of miRNA Regulation

  2009cited by this paper
• Review of Current Methodological Approaches for Characterizing MicroRNAs in Plants

  2009cited by this paper
• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

  2009cited by this paper
• Connexins: a myriad of functions extending beyond assembly of gap junction channels

  2009cited by this paper
• MicroRNAs in embryonic stem cells

  2009cited by this paper
• miRecords: an integrated resource for microRNA–target interactions

  2008cited by this paper
• UNAFold: software for nucleic acid folding and hybridization.

  2008cited by this paper
• Small non-coding RNAs in animal development

  2008cited by this paper
• miR2Disease: a manually curated database for microRNA deregulation in human disease

  2008cited by this paper
• Discovering microRNAs from deep sequencing data using miRDeep

  2008cited by this paper
• Deep Sequencing of Chicken microRNAs

  2008cited by this paper
• MicroRNA prediction with a novel ranking algorithm based on random walks

  2008cited by this paper
• miRiad roles for the miR-17-92 cluster in development and disease.

  2008cited by this paper
• The role of microRNAs (miRNA) in circadian rhythmicity

  2008cited by this paper
• Designing multiple degenerate primers via consecutive pairwise alignments

  2008cited by this paper
• Phylogenetic shadowing: sequence comparisons of multiple primate species.

  2008cited by this paper
• miREval 2.0: a web tool for simple microRNA prediction in genome sequences

  2008cited by this paper
• let-7 microRNAs in development, stem cells and cancer.

  2008cited by this paper
• CID-miRNA: a web server for prediction of novel miRNA precursors in human genome.

  2008cited by this paper
• High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families

  2008cited by this paper
• Mireval: a web tool for simple microRNA prediction in genome sequences

  2008cited by this paper
• miRNApath: a database of miRNAs, target genes and metabolic pathways.

  2007cited by this paper
• miRBase: tools for microRNA genomics

  2007cited by this paper
• RNA stem-loops: to be or not to be cleaved by RNAse III.

  2007cited by this paper
• The let-7 microRNA represses cell proliferation pathways in human cells.

  2007cited by this paper
• MicroRNAs regulate synthesis of the neurotransmitter substance P in human mesenchymal stem cell-derived neuronal cells

  2007cited by this paper
• Fine‐tuning of the innate immune response by microRNAs

  2007cited by this paper
• MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features

  2007cited by this paper
• A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors.

  2007cited by this paper
• Host Immune System Gene Targeting by a Viral miRNA

  2007cited by this paper
• High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

  2007cited by this paper
• A generic motif discovery algorithm for sequential data

  2006cited by this paper
• RNAhybrid: microRNA target prediction easy, fast and flexible

  2006cited by this paper
• Bioinformatic discovery of microRNA precursors from human ESTs and introns

  2006cited by this paper
• Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

  2006cited by this paper
• Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data

  2006cited by this paper
• Non-coding RNA.

  2006cited by this paper
• MicroRNAS and their regulatory roles in plants.

  2006cited by this paper
• A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors.

  2006cited by this paper

• Noncoding RNAs and the phytochemical economy: Molecular regulators of secondary metabolism in medicinal plants

  2026cites this paper
• The epigenetic landscape of circulating tumour cells.

  2021cites this paper
• Identification of Novel miRNAs in the F8 Gene Via Bioinformatics Tools

  2021cites this paper
• Expression levels and clinical values of miR-92b-3p in breast cancer

  2021cites this paper
• Clinical significance of miR-139-5p and FGF2 in ovarian cancer.

  2021cites this paper
• Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

  2020cites this paper
• Interaction of a photosensitizer methylene blue with various structural forms (cruciform, bulge duplex and hairpin) of designed DNA sequences.

  2020cites this paper
• Popular Computational Tools Used for miRNA Prediction and Their Future Development Prospects

  2020influential citation
• MicroRNAs in rheumatoid arthritis: what is the latest with regards to diagnostics?

  2019cites this paper
• Discovery and functional annotation of novel microRNAs in the porcine genome by using a semi-supervised transductive learning approach.

  2019cites this paper
• A survey of software tools for microRNA discovery and characterization using RNA-seq

  2019cites this paper
• Prediction and Characterization of miRNA/Target Pairs in Non‐Model Plants Using RNA‐seq

  2019cites this paper
• An Overview of miRNA and miRNA Target Analysis Tools.

  2019cites this paper
• rs61991156 in miR-379 is associated with low capability of glycolysis of gastric cancer by enhanced regulation of PKM2

  2018cites this paper
• ExtendAlign: a computational algorithm for delivering multiple, local end-to-end alignments

  2018cites this paper