miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis

The Host Shapes the Gut Microbiota via Fecal MicroRNA

(2016) Shirong Liu et al.   Cell Host & Microbe

Bias in microRNA functional enrichment analysis

(2015) Thomas Bleazard et al.   BIOINFORMATICS

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

(2015) Jianguo Xia et al.   Nature Protocols

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

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

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

Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress

(2015) Ali B. Rodgers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration

(2014) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations

(2014) Yuanbin Ru et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Nathan Wong et al.   NUCLEIC ACIDS RESEARCH

Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity

(2014) Amy H. Buck et al.   Nature Communications

EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications

(2014) Enyu Dai et al.   Database-The Journal of Biological Databases and Curation

INVEX—a web-based tool for integrative visualization of expression data

(2013) Jianguo Xia et al.   BIOINFORMATICS

Pharmaco-miR: linking microRNAs and drug effects

(2013) J. L. Rukov et al.   BRIEFINGS IN BIOINFORMATICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

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

INMEX—a web-based tool for integrative meta-analysis of expression data

(2013) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression

(2012) X. Liu et al.   BIOINFORMATICS

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

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

(2012) Tzu-Pin Lu et al.   PLoS One

N-gram analysis of 970 microbial organisms reveals presence of biological language models

(2011) Hatice Osmanbeyoglu et al.   BMC BIOINFORMATICS

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

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

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

(2010) Markus Hafner et al.   CELL

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

miRBase: integrating microRNA annotation and deep-sequencing data

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

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

(2010) Doron Betel et al.   GENOME BIOLOGY

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R

(2009) H. Dvinge et al.   BIOINFORMATICS

Lost in translation: an assessment and perspective for computational microRNA target identification

(2009) Panagiotis Alexiou et al.   BIOINFORMATICS

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

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

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

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