Bioinformatic tools for microRNA dissection

miR2GO: comparative functional analysis for microRNAs: Fig. 1.

(2015) Anindya Bhattacharya et al.   BIOINFORMATICS

DIANA-miRPath v3.0: deciphering microRNA function with experimental support

(2015) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs

(2014) Dongfang Wang et al.   BIOINFORMATICS

MicroRNAs in Allergy and Asthma

(2014) Ana Rebane et al.   CURRENT ALLERGY AND ASTHMA REPORTS

Development of microRNA therapeutics is coming of age

(2014) E. van Rooij et al.   EMBO Molecular Medicine

MicroRNA and gynecological reproductive diseases

(2014) Xavier Santamaria et al.   FERTILITY AND STERILITY

Admission levels of circulating miR-499-5p and risk of death in elderly patients after acute non-ST elevation myocardial infarction

(2014) Fabiola Olivieri et al.   INTERNATIONAL JOURNAL OF CARDIOLOGY

The effects of environmental chemical carcinogens on the microRNA machinery

(2014) A. Izzotti et al.   INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH

microRNAs in Cardiovascular Diseases

(2014) Gianluigi Condorelli et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Therapeutic targeting of microRNAs: current status and future challenges

(2014) Zhonghan Li et al.   NATURE REVIEWS DRUG DISCOVERY

STarMir: a web server for prediction of microRNA binding sites

(2014) William Rennie et al.   NUCLEIC ACIDS RESEARCH

ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context

(2014) Chao Wu et al.   NUCLEIC ACIDS RESEARCH

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

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

miRDB: an online resource for microRNA target prediction and functional annotations

(2014) Nathan Wong et al.   NUCLEIC ACIDS RESEARCH

Upregulation of miR-21 in Cisplatin Resistant Ovarian Cancer via JNK-1/c-Jun Pathway

(2014) Ileabett M. Echevarría-Vargas et al.   PLoS One

miRror-Suite: decoding coordinated regulation by microRNAs

(2014) Y. Friedman et al.   Database-The Journal of Biological Databases and Curation

Friend or foe: the role of microRNA in chemotherapy resistance

(2013) Haoran Li et al.   ACTA PHARMACOLOGICA SINICA

MicroRNAs linking inflamm-aging, cellular senescence and cancer

(2013) Fabiola Olivieri et al.   AGEING RESEARCH REVIEWS

miRCancer: a microRNA-cancer association database constructed by text mining on literature

(2013) B. Xie et al.   BIOINFORMATICS

The Long and Short of MicroRNA

(2013) Luke A. Yates et al.   CELL

Circulating microRNAs as novel biomarkers for diabetes mellitus

(2013) Claudiane Guay et al.   Nature Reviews Endocrinology

Analysis of microRNA-target interactions across diverse cancer types

(2013) Anders Jacobsen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CLIP-based prediction of mammalian microRNA binding sites

(2013) Chaochun Liu et al.   NUCLEIC ACIDS RESEARCH

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

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

miRmap web: comprehensive microRNA target prediction online

(2013) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

(2013) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

HMDD v2.0: a database for experimentally supported human microRNA and disease associations

(2013) Yang Li et al.   NUCLEIC ACIDS RESEARCH

ComiR: combinatorial microRNA target prediction tool

(2013) Claudia Coronnello et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

(2013) Anindya Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Sequencing of microRNAs in Peripheral Blood Mononuclear Cells: Identification of Potential Weight Loss Biomarkers

(2013) Fermín I. Milagro et al.   PLoS One

mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data

(2013) Peng Wang et al.   PLoS One

miReader: Discovering Novel miRNAs in Species without Sequenced Genome

(2013) Ashwani Jha et al.   PLoS One

Interactive exploration of RNA22 microRNA target predictions

(2012) Phillipe Loher et al.   BIOINFORMATICS

Functional microRNA targets in protein coding sequences

(2012) Martin Reczko et al.   BIOINFORMATICS

miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

(2012) Andrew E Bruno et al.   BMC GENOMICS

MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs

(2012) Chenxing Liu et al.   BMC GENOMICS

Clinical Applications for microRNAs in Cancer

(2012) S P Nana-Sinkam et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Identification of microRNA-regulated gene networks by expression analysis of target genes

(2012) Vincenzo Alessandro Gennarino et al.   GENOME RESEARCH

HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens

(2012) Hamed Ahmadi et al.   GENOMICS

SomamiR: a database for somatic mutations impacting microRNA function in cancer

(2012) Anindya Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting

(2012) Sooyoung Cho et al.   NUCLEIC ACIDS RESEARCH

DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways

(2012) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

miRmap: Comprehensive prediction of microRNA target repression strength

(2012) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

Prediction of Disease-Related Interactions between MicroRNAs and Environmental Factors Based on a Semi-Supervised Classifier

(2012) Xing Chen et al.   PLoS One

miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets

(2012) Tzu-Pin Lu et al.   PLoS One

Integrative Analysis of Somatic Mutations Altering MicroRNA Targeting in Cancer Genomes

(2012) Jesse D. Ziebarth et al.   PLoS One

miRandola: Extracellular Circulating MicroRNAs Database

(2012) Francesco Russo et al.   PLoS One

miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes

(2011) Qingqing Yang et al.   BIOINFORMATICS

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model

(2011) Antony Le Béchec et al.   BMC BIOINFORMATICS

miRTar: an integrated system for identifying miRNA-target interactions in human

(2011) Justin Hsu et al.   BMC BIOINFORMATICS

MicroRNA-21: A novel therapeutic target in human cancer

(2011) Xuan Pan et al.   CANCER BIOLOGY & THERAPY

The Influence of 3′UTRs on MicroRNA Function Inferred from Human SNP Data

(2011) Zihua Hu et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

MicroRNA therapeutics in cardiovascular medicine

(2011) Thomas Thum   EMBO Molecular Medicine

Developing therapeutic microRNAs for cancer

(2011) A G Bader et al.   GENE THERAPY

miRWalk – Database: Prediction of possible miRNA binding sites by “walking” the genes of three genomes

(2011) Harsh Dweep et al.   JOURNAL OF BIOMEDICAL INFORMATICS

MicroRNAs as mediators and therapeutic targets in chronic kidney disease

(2011) Johan M. Lorenzen et al.   Nature Reviews Nephrology

mirConnX: condition-specific mRNA-microRNA network integrator

(2011) G. T. Huang et al.   NUCLEIC ACIDS RESEARCH

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

Inferring causative variants in microRNA target sites

(2011) Laurent F. Thomas et al.   NUCLEIC ACIDS RESEARCH

PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits

(2011) J. D. Ziebarth 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

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

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

Experimental strategies for microRNA target identification

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

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Circulating Plasma MiR-141 Is a Novel Biomarker for Metastatic Colon Cancer and Predicts Poor Prognosis

(2011) Hanyin Cheng et al.   PLoS One

NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs

(2011) Elize A. Shirdel et al.   PLoS One

miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs

(2011) A. Kowarsch et al.   RNA

Diabetes mellitus, a microRNA-related disease?

(2011) Claudiane Guay et al.   Translational Research

MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets

(2010) Y. Friedman et al.   BIOINFORMATICS

MiRonTop: mining microRNAs targets across large scale gene expression studies

(2010) K. Le Brigand et al.   BIOINFORMATICS

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

(2010) Sanghamitra Bandyopadhyay et al.   BMC BIOINFORMATICS

Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

(2010) Sumeet Agarwal et al.   BMC BIOINFORMATICS

Gene bi-targeting by viral and human miRNAs

(2010) Isana Veksler-Lublinsky et al.   BMC BIOINFORMATICS

CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse

(2010) Olivier Friard et al.   BMC BIOINFORMATICS

miR-328 Functions as an RNA Decoy to Modulate hnRNP E2 Regulation of mRNA Translation in Leukemic Blasts

(2010) Anna M. Eiring et al.   CELL

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

(2010) Markus Hafner et al.   CELL

MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

(2010) Maxim Barenboim et al.   HUMAN MUTATION

The discovery approaches and detection methods of microRNAs

(2010) Yong Huang et al.   MOLECULAR BIOLOGY REPORTS

Posttranscriptional Regulation of MicroRNA Biogenesis in Animals

(2010) Haruhiko Siomi et al.   MOLECULAR CELL

Targeting microRNAs in cancer: rationale, strategies and challenges

(2010) Ramiro Garzon et al.   NATURE REVIEWS DRUG DISCOVERY

Environmental causes of cancer: endocrine disruptors as carcinogens

(2010) Ana M. Soto et al.   Nature Reviews Endocrinology

mESAdb: microRNA Expression and Sequence Analysis Database

(2010) Koray D. Kaya et al.   NUCLEIC ACIDS RESEARCH

RepTar: a database of predicted cellular targets of host and viral miRNAs

(2010) Naama Elefant et al.   NUCLEIC ACIDS RESEARCH

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu 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

MAGIA, a web-based tool for miRNA and Genes Integrated Analysis

(2010) G. Sales et al.   NUCLEIC ACIDS RESEARCH

The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function

(2010) Panagiotis Alexiou et al.   PLoS One

MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors

(2010) Katerina Gkirtzou et al.   PLoS One

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

(2010) Andreas Ruepp et al.   GENOME BIOLOGY

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

The interplay between transcription factors and microRNAs in genome-scale regulatory networks

(2009) Natalia J. Martinez et al.   BIOESSAYS

DIANA-mirPath: Integrating human and mouse microRNAs in pathways

(2009) G. L. Papadopoulos et al.   BIOINFORMATICS

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

(2009) Sabah Kadri et al.   BMC BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

MicroRNAs: Potential biomarkers for cancer diagnosis, prognosis and targets for therapy

(2009) William C.S. Cho   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Computational approaches for microRNA studies: a review

(2009) Li Li et al.   MAMMALIAN GENOME

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach

(2009) Anastasis Oulas et al.   NUCLEIC ACIDS RESEARCH

Current tools for the identification of miRNA genes and their targets

(2009) N. D. Mendes et al.   NUCLEIC ACIDS RESEARCH

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

DIANA-microT web server: elucidating microRNA functions through target prediction

(2009) M. Maragkakis 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

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

(2009) Samuel Hiard et al.   NUCLEIC ACIDS RESEARCH

miR-221 overexpression contributes to liver tumorigenesis

(2009) P. Pineau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small-Molecule Inhibitors of MicroRNA miR-21 Function

(2008) Kiranmai Gumireddy et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma

(2008) Charles H. Lawrie et al.   BRITISH JOURNAL OF HAEMATOLOGY

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts

(2008) Thomas Thum et al.   NATURE

Endogenous human microRNAs that suppress breast cancer metastasis

(2008) Sohail F. Tavazoie et al.   NATURE

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs

(2008) Xueping Yu et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

MicroRNA-directed transcriptional gene silencing in mammalian cells

(2008) D. H. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRDB: A microRNA target prediction and functional annotation database with a wiki interface

(2008) X. Wang   RNA

MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries

(2008) Merav Bar et al.   STEM CELLS

Adverse cardiovascular effects of air pollution

(2008) Nicholas L Mills et al.   Nature clinical practice. Cardiovascular medicine