A collection of existing miRNA target gene prediction papers and some miRNA related databases.
Those papers were mainly published in Nature, Nature Methods, Nature protocols, NAR, Briefings in Bioinformatics, Bioinformatics, Drug Discovery Today, Genome Research, Genome Biology, PLoS computational biology, JCIM, and JPR.
These papers are sorted by the accepted data (from the most current to oldest) and will be updated monthly.
At the bottom of this page, a table contains all these methods is provided.
[01] Silvia Bottini et al. "Recent computational developments on CLIP-seq data analysis and microRNA targeting implications" Briefings in Bioinformatics. (4 May 2017). [pdf] (ps.) ⭐⭐⭐⭐⭐
[01] Minsik Oh et al. "Literature-based condition-specific miRNA-mRNA target prediction" PLOS One. (2017). [pdf] (ps.) ⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] B Lee, J Baek, S Park and S Yoon. "deepTarget: End-to-end Learning Framework for microRNA Target Prediction using Deep Recurrent Neural Networks" arXiv. (deepTarget: End-to-end Learning Framework for microRNA Target Prediction using Deep Recurrent Neural Networks). [pdf] (deepTarget, RNN.) ⭐⭐⭐⭐⭐
[number] J Ding, X Li, H Hu. "TarPmiR: a new approach for microRNA target site prediction" Bioinformatics. (20 May 2016 ). [pdf] (TarPmiR.) ⭐⭐⭐⭐⭐
[number] Cesaré Ovando-Vázquez, Daniel Lepe-Soltero and Cei Abreu-Goodger. "Improving microRNA target prediction with gene expression profiles" BMC Genomics. (17 May 2016). [pdf] (TargetExpress.) ⭐⭐⭐
[number] Xiaowei Wang. "Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies" Bioinformatics. (6 January 2016). [pdf] (mirtarget.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "Prediction of microRNA target genes using an efficient genetic algorithm-based decision tree" FEBS open bio. (19 October 2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel. "Predicting effective microRNA target sites in mammalian mRNAs" journal. (August 12, 2015). [pdf] (TargetScan.) ⭐⭐⭐⭐⭐
[number] S Cheng, M Guo, C Wang and X Liu. "**MiRTDL: A Deep Learning Approach for miRNA Target Prediction **" IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2015). [pdf] (miRTDL.) ⭐⭐⭐⭐⭐
[number] X Fan, L Kurgan. "Comprehensive overview and assessment of computational prediction of microRNA targets in animals" Briefings in bioinformatics. (13 October 2014). [pdf] (Review. Important) ⭐⭐⭐⭐⭐
[number] Sarah M. Peterson et al. "Common features of microRNA target prediction tools" Frontiers in GENETICS. (2014). [pdf] (review of features.) ⭐⭐⭐⭐⭐
[number] William Rennie et al. "STarMir: a web server for prediction of microRNA binding sites" Nucleic Acids Research. (2014). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] MR Mendoza, GC da Fonseca et al. "RFMirTarget: predicting human microRNA target genes with a random forest classifier" PLOS One. (July 26, 2013). [pdf] (RFMirTarget.) ⭐⭐⭐⭐
[number] C Coronnello, PV Benos. "ComiR: combinatorial microRNA target prediction tool" Nucleic Acids Research. (April 18, 2013). [pdf] (ComiR.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Charles E. Vejnar and Evgeny M. Zdobnov. "MiRmap: comprehensive prediction of microRNA target repression strength" Nucleic acids research. (2 October 2012). [pdf] (MiRmap.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] JBK Hsu, CM Chiu et al. "miRTar: an integrated system for identifying miRNA-target interactions in human" BMC Bioinformatics. (26 July 2011). [pdf] (miRTar.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Martin Sturm, Michael Hackenberg, David Langenberger and Dmitrij Frishman. "TargetSpy: a supervised machine learning approach for microRNA target prediction" BMC Bioinformatics. (28 May 2010). [pdf] (TargetSpy.) ⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Marshall Thomas, Judy Lieberman, Ashish Lal. "Desperately seeking microRNA targets" nature structural & molecular biology. (6 October 2010). [pdf] (Review, Perspective) ⭐⭐⭐⭐⭐
[number] Sanghamitra Bandyopadhyayand Ramkrishna Mitra and Ramkrishna Mitra. "TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples" Bioinformatics. (19 August 200). [pdf] (TargetMiner.) ⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] M Hammell, D Long and V Ambros et al.. "mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts" Nature Method. (17 August 2008). [pdf] (mirWIP.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] X Wang and IM El Naqa. "Prediction of both conserved and nonconserved microRNA targets in animals" Bioinformatics. (November 20 2007). [pdf] (MirTarget2.) ⭐⭐⭐⭐⭐
[number] M Yousef, S Jung, AV Kossenkov, LC Showe and Michael K.. Showe. "Naïve Bayes for microRNA target predictions—machine learning for microRNA targets" Bioinformatics. (September 11 2007). [pdf] (NBmiRTar.) ⭐⭐⭐⭐⭐
[number] M Kertesz, N Iovino, U Unnerstall, U Gaul and E Segal. "The role of site accessibility in microRNA target recognition" Nature Genetics. (23 September 2007). [pdf] (PITA.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Sung-Kyu Kim and Byoung-Tak Zhang et al.. "miTarget: microRNA target gene prediction using a support vector machine" BMC Bioinformatics. (18 September 2006). [pdf] (miTarget.) ⭐⭐⭐⭐⭐
[number] N Rajewsky. "microRNA target predictions in animals" Nature Genetics. (30 May 2006). [pdf] (a detailed review of miRNA target prediction methods before 2006. very important) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] A Krek and N Rajewsky et al.. "Combinatorial microRNA target predictions" Nature. (3 April 2005). [pdf] (PicTar.) ⭐⭐⭐⭐⭐
[number] OLA SaeTrom, OLA SNØVE and PÅL SÆTROM. "Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms" RNA. (April 7, 2005). [pdf] (TargetBoost.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Bino John and Debora S. Marks et al.. "Human MicroRNA Targets" PLOS Biology. (October 5, 2004). [pdf] (miranda.) ⭐⭐⭐⭐⭐
[number] Marianthi Kiriakidou and Artemis Hatzigeorgiou et al.. "A combined computational-experimental approach predicts human microRNA targets" Genes Dev. (April 6, 2004). [pdf] (DIANA-microT.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Alexander Stark, Robert B. Russell, Stephen M. Cohen et al.. "Identification of Drosophila MicroRNA Targets" PLoS Biol. (October 13, 2003). [pdf] (the first target identified by performing bioinformatics screen.) ⭐⭐⭐⭐⭐
[number] Lewis, BP; Shih, IH; Jones-Rhoades, MW; Bartel, DP; Burge, CB. "Prediction of mammalian microRNA targets." CELL. (DEC 26 2003). [pdf] (Review.) ⭐⭐⭐⭐⭐
[number] F Xiao, Z Zuo, G Cai, S Kang, X Gao and T Li. "miRecords: an integrated resource for microRNA–target interactions" Nucleic acids research. (07 November 2008 ). [pdf] (miRecords.) ⭐⭐⭐⭐⭐
[number] A Kozomara, S Griffiths-Jones. "miRBase: annotating high confidence microRNAs using deep sequencing data" Nucleic acids research. (25 November 2013). [pdf] (miRBase.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Chih-Hung Chou, Hsien-Da Huang et. al. . "miRTarBase" Nucleic Acids Res. (20 November 2015). [pdf] (November 12 2014). [pdf]
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Bartel, DP. "MicroRNAs: Genomics, biogenesis, mechanism, and function." CELL. (JAN 23 2004). [pdf] (A good paper for introducing microRNA. Times cited larger than 14000.) ⭐⭐⭐⭐⭐
[number] Bartel, DP. "MicroRNAs: Target Recognition and Regulatory Functions." CELL. (JAN 23 2009). [pdf] (Hot paper. Times cited larget than 7000.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] author. "title" journal. (2015). [pdf] (ps.) ⭐⭐⭐⭐⭐
[number] Stefanie Grosswendt, Andrei Filipchyk, Mark Manzano, Filippos Klironomos, Marcel Schilling, Margareta Herzog, Eva Gottwein and Nikolaus Rajewsky. "Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions" CELL. (26 March 2014). [pdf] (famous CLIP dataset.) ⭐⭐⭐⭐⭐
[number] Aleksandra Helwak, Grzegorz Kudla, Tatiana Dudnakova1 and David Tollervey. "Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding" CELL. (25 April 2013). [pdf] (famous CLASH dataset.) ⭐⭐⭐⭐⭐
[number] Markus Hafner et al.. "Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP" journal. (27 February 2010). [pdf] (Independent test dataset.) ⭐⭐⭐⭐⭐
| Predictor | Year published | Model type | availability |
|---|---|---|---|
| Stark et al. | 2003 | Screening | |
| Targetscan | 2003 | Score | |
| DIANA-microT | 2004 | Score | |
| RNAhybrid | 2004 | Score | |
| miRanda | 2004 | Score | |
| Rajewsky | 2004 | Score | |
| TargetScanS | 2005 | Score | |
| Robins | 2005 | Score | |
| Xie et al. | 2005 | Score | |
| PicTar | 2005 | Score | |
| MovingTarget | 2005 | Screening | |
| Microlnspector | 2005 | Score | |
| TargetBoost | 2005 | GP | |
| Stark et al. | 2005 | Score | |
| miTarget | 2006 | SVM | |
| RNA22 | 2006 | Score | |
| MicroTar | 2006 | Score | |
| EIMMo | 2007 | Bayesian | |
| STarMir | 2007 | Score | |
| PITA | 2007 | Score | |
| TargetRank | 2007 | Score | |
| Ensemble | 2007 | SVM | |
| NBmiRTar | 2007 | Bayesian | |
| MiTarget2 | 2008 | SVM | |
| HuMiTar | 2008 | Score | |
| MiRTif | 2008 | SVM | |
| mirWIP | 2008 | ||
| TargetMiner | 2009 | SVM | |
| TargetSpy | 2010 | DS | |
| Mtar | 2010 | ANN | |
| mirSVR | 2010 | Score | |
| SVMicrO | 2010 | SVM | |
| RepTar | 2010 | Screening | |
| miRror | 2010 | ||
| PACMIT | 2011 | Screening | |
| MultiMiTar | 2011 | SVM | |
| miREE | 2011 | SVM | |
| miRcode | 2012 | Screening | |
| miRmap | 2012 | Regression | |
| HomoTarget | 2012 | ANN | |
| SuperMirtTar | 2013 | Graph | |
| Fujiwara’s | 2013 | Cis-element | |
| MIRZA | 2013 | Bayesian | |
| DIANA-microT-CDS | 2013 | ||
| ComiR | 2013 | ||
| mirMark | 2014 | RF | |
| STarMir | 2014 | ||
| TargetScan v7.0 | 2015 | ||
| MiRTDL | 2015 | ||
| Xiaowei Wang | 2016 | SVM | |
| CIDER | |||
| CHIMIrIC | 2016 | ||
| TargetExpress | 2016 | ||
| TarPmiR | 2016 | ||
| deepTarget | 2016 | ||
| MiRNATIP | 2016 | ||
| miRTar2GO | 2017 |