Identifying miRNAs, targets and functions
Open accessAbstract
microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology.
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Characterizing non-additive contributions of functional groups helps machine learning-based scoring functions consistently maintain accuracy in binding affinity predictions across a variety of protein-ligand complexes.
“Such a characterization can help machine learning-based SFs consistently maintain their accuracy in binding affinity predictions for a variety of protein–ligand complexes [19–23].”
From Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges (2019) · cites this paper as [19]
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Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890 · see citing works
Bartel (2004) · doi:10.1016/s0092-8674(04)00045-5 · Cited by 34,714 · see citing works
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068 · see citing works
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993) · Cell · doi:10.1016/0092-8674(93)90529-y · Cited by 12,948 · see citing works
Lewis, B. P., Burge, C. B., & Bartel, D. P. (2005) · Cell · doi:10.1016/j.cell.2004.12.035 · Cited by 11,855 · see citing works
MicroRNAs: small RNAs with a big role in gene regulation
He, L., & Hannon, G. J. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1379 · Cited by 5,910 · see citing works
Combinatorial microRNA target predictions
Krek, A., Grün, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1536 · Cited by 4,603 · see citing works
miRBase: tools for microRNA genomics
Griffiths‐Jones, S., Saini, H. K., van Dongen, S., & Enright, A. J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm952 · Cited by 4,349 · see citing works
Prediction of Mammalian MicroRNA Targets
Lewis, B. P., Shih, I.-H., Jones-Rhoades, M. W., Bartel, D. P., & Burge, C. B. (2003) · Cell · doi:10.1016/s0092-8674(03)01018-3 · Cited by 4,333 · see citing works
MicroRNA Gene Expression Deregulation in Human Breast Cancer
Iorio, M. V., Ferracin, M., Liu, C.-G., Veronese, A., Spizzo, R., Sabbioni, S., Magri, E., Pedriali, M., Fabbri, M., Campiglio, M., et al. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-1783 · Cited by 4,053 · see citing works
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., & Marks, D. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020363 · Cited by 3,796 · see citing works
MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
Grimson, A., Farh, K. K.-H., Johnston, W. K., Garrett-Engele, P., Lim, L. P., & Bartel, D. P. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.017 · Cited by 3,766 · see citing works
The impact of microRNAs on protein output
Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P., & Bartel, D. P. (2008) · Nature · doi:10.1038/nature07242 · Cited by 3,592 · see citing works
Widespread changes in protein synthesis induced by microRNAs
Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R., & Rajewsky, N. (2008) · Nature · doi:10.1038/nature07228 · Cited by 3,429 · cited 1× · see citing works
“[55].”
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,042 · see citing works
Unique microRNA molecular profiles in lung cancer diagnosis and prognosis
Yanaihara, N., Caplen, N., Bowman, E., Seike, M., Kumamoto, K., Yi, M., Stephens, R. M., Okamoto, A., Yokota, J., Tanaka, T., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.01.025 · Cited by 3,023 · see citing works
Causes and consequences of microRNA dysregulation in cancer
Croce, C. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2634 · Cited by 3,003 · see citing works
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Friedländer, M. R., Mackowiak, S. D., Li, N., Chen, W., & Rajewsky, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr688 · Cited by 2,962 · see citing works
Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.-C., Munschauer, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.009 · Cited by 2,873 · see citing works
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771 · see citing works
Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
Pasquinelli, A. E., Reinhart, B. J., Slack, F. J., Martindale, M. Q., Kuroda, M. I., Maller, B., Hayward, D. C., Ball, E. E., Degnan, B. M., Müller, P., et al. (2000) · Nature · doi:10.1038/35040556 · Cited by 2,568 · see citing works
Fast and effective prediction of microRNA/target duplexes
REHMSMEIER, M., STEFFEN, P., HÖCHSMANN, M., & GIEGERICH, R. (2004) · RNA · doi:10.1261/rna.5248604 · Cited by 2,560 · see citing works
The role of site accessibility in microRNA target recognition
Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., & Segal, E. (2007) · Nature Genetics · doi:10.1038/ng2135 · Cited by 2,460 · see citing works
Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps
Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B. (2009) · Nature · doi:10.1038/nature08170 · Cited by 1,791 · see citing works
Miranda, K. C., Huynh, T., Tay, Y., Ang, Y.-S., Tam, W.-L., Thomson, A. M., Lim, B., & Rigoutsos, I. (2006) · Cell · doi:10.1016/j.cell.2006.07.031 · Cited by 1,739 · see citing works
Dweep, H., Sticht, C., Pandey, P., & Gretz, N. (2011) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2011.05.002 · Cited by 1,699 · see citing works
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
Betel, D., Koppal, A., Agius, P., Sander, C., & Leslie, C. (2010) · Genome Biology · doi:10.1186/gb-2010-11-8-r90 · Cited by 1,592 · see citing works
Karlin, S., & Altschul, S. F. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.6.2264 · Cited by 1,535 · see citing works
miRecords: an integrated resource for microRNA-target interactions
Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., & Li, T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn851 · Cited by 1,439 · see citing works
Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs
Giraldez, A. J., Mishima, Y., Rihel, J., Grocock, R. J., Van Dongen, S., Inoue, K., Enright, A. J., & Schier, A. F. (2006) · Science · doi:10.1126/science.1122689 · Cited by 1,436 · see citing works
miR2Disease: a manually curated database for microRNA deregulation in human disease
Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G., & Liu, Y. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn714 · Cited by 1,415 · see citing works
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
Tay, Y., Zhang, J., Thomson, A. M., Lim, B., & Rigoutsos, I. (2008) · Nature · doi:10.1038/nature07299 · Cited by 1,385 · see citing works
MicroRNA-373 induces expression of genes with complementary promoter sequences
Place, R. F., Li, L., Pookot, D., Noonan, E. J., & Dahiya, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707594105 · Cited by 1,231 · see citing works
Discovering microRNAs from deep sequencing data using miRDeep
Friedländer, M. R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., & Rajewsky, N. (2008) · Nature Biotechnology · doi:10.1038/nbt1394 · Cited by 1,189 · see citing works
microRNA target predictions in animals
Rajewsky, N. (2006) · Nature Genetics · doi:10.1038/ng1798 · Cited by 1,086 · see citing works
Blei, D. M., & Jordan, M. I. (2003) · International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR) · doi:10.1145/860435.860460 · Cited by 1,078 · see citing works
Yang, H., Kong, W. W., He, L., Zhao, J., O’Donnell, J. D., Wang, J., Wenham, R. M., Coppola, D., Kruk, P. A., Nicosia, S. V., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-2488 · Cited by 1,051 · see citing works
Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B., & Bartel, D. P. (2003) · Science · doi:10.1126/science.1080372 · Cited by 967 · see citing works
MicroRNA Expression Profiling in Prostate Cancer
Porkka, K. P., Pfeiffer, M. J., Waltering, K. K., Vessella, R. L., Tammela, T. L. J., & Visakorpi, T. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-0533 · Cited by 896 · see citing works
Computational identification of DrosophilamicroRNA genes
Lai, E. C., Tomančák, P., Williams, R. W., & Rubin, G. M. (2003) · Genome biology · doi:10.1186/gb-2003-4-7-r42 · Cited by 723 · see citing works
miRDB: A microRNA target prediction and functional annotation database with a wiki interface
Wang, X. (2008) · RNA · doi:10.1261/rna.965408 · Cited by 712 · see citing works
Git, A., Dvinge, H., Salmon-Divon, M., Osborne, M., Kutter, C., Hadfield, J., Bertone, P., & Caldas, C. (2010) · RNA · doi:10.1261/rna.1947110 · Cited by 607 · see citing works
Gaur, A., Jewell, D. A., Liang, Y., Ridzon, D., Moore, J. H., Chen, C., Ambros, V. R., & Israel, M. A. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-2698 · Cited by 593 · see citing works
Probabilistic author-topic models for information discovery
Steyvers, M., Smyth, P., Rosen‐Zvi, M., et al. (2004) · ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/1014052.1014087 · Cited by 580 · see citing works
Sethupathy, P., Megraw, M. S., & Hatzigeorgiou, A. G. (2006) · Nature Methods · doi:10.1038/nmeth954 · Cited by 541 · see citing works
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support
Vergoulis, T., Vlachos, I. S., Alexiou, P., Georgakilas, G. K., Maragkakis, M., Reczko, M., Gerangelos, S., Koziris, N., Dalamagas, T., & Hatzigeorgiou, A. G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1161 · Cited by 537 · see citing works
Prediction of both conserved and nonconserved microRNA targets in animals
Wang, X., & Naqa, I. E. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm595 · Cited by 529 · see citing works
Approaches to microRNA discovery
Berezikov, E., Cuppen, E. P. J. G., & Plasterk, R. H. A. (2006) · Nature Genetics · doi:10.1038/ng1794 · Cited by 456 · see citing works
MicroRNA regulation of Alzheimer's Amyloid precursor protein expression
Hébert, S. S., Horré, K., Nicolaï, L., Bergmans, B., Papadopoulou, A. S., Delacourte, A., & De Strooper, B. (2009) · Neurobiology of Disease · doi:10.1016/j.nbd.2008.11.009 · Cited by 436 · see citing works
Schizophrenia is associated with an increase in cortical microRNA biogenesis
Beveridge, N. J., Gardiner, E. J., Carroll, A. P., Tooney, P. A., & Cairns, M. J. (2009) · Molecular Psychiatry · doi:10.1038/mp.2009.84 · Cited by 431 · see citing works
Self-citationA Genome-Wide Map of Conserved MicroRNA Targets in C. elegans
Lall, S., Grün, D., Krek, A., Chen, K., Wang, Y.-L., Dewey, C. N., Sood, P., Colombo, T., Bray, N., MacMenamin, P., et al. (2006) · Current Biology · doi:10.1016/j.cub.2006.01.050 · Cited by 410 · see citing works
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtiiPreprint
Zhao, T., Li, G., Mi, S., Li, S., Hannon, G. J., Wang, X., & Qi, Y. (2007) · Genes & Development · doi:10.1101/gad.1543507 · Cited by 398 · see citing works
The database of experimentally supported targets: a functional update of TarBase
Papadopoulos, G. L., Reczko, M., Simossis, V. A., Sethupathy, P., & Hatzigeorgiou, A. G. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn809 · Cited by 398 · see citing works
Using expression profiling data to identify human microRNA targets
Huang, J., Babak, T., Corson, T. W., Chua, G., Khan, S., Gallie, B. L., Hughes, T. R., Blencowe, B. J., Frey, B. J., & Morris, Q. (2007) · Nature Methods · doi:10.1038/nmeth1130 · Cited by 394 · see citing works
Prediction and validation of microRNAs and their targets
Bentwich, I. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.09.040 · Cited by 365 · see citing works
Accurate microRNA target prediction correlates with protein repression levels
Maragkakis, M., Alexiou, P., Papadopoulos, G. L., Reczko, M., Dalamagas, T., Giannopoulos, G., Goumas, G., Koukis, E., Kourtis, K., Simossis, V. A., et al. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-295 · Cited by 330 · see citing works
An alternative mode of microRNA target recognition
Chi, S. W., Hannon, G. J., & Darnell, R. B. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2230 · Cited by 328 · see citing works
Nunez-Iglesias, J., Liu, C.-C., Morgan, T. E., Finch, C. E., & Zhou, X. J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008898 · Cited by 320 · see citing works
Inference of miRNA targets using evolutionary conservation and pathway analysis
Gaidatzis, D., van Nimwegen, E., Hausser, J., & Zavolan, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-69 · Cited by 320 · see citing works
Lost in translation: an assessment and perspective for computational microRNA target identification
Alexiou, P., Maragkakis, M., Papadopoulos, G. L., Reczko, M., & Hatzigeorgiou, A. G. (2009) · Computer applications in the biosciences · doi:10.1093/bioinformatics/btp565 · Cited by 319 · see citing works
Subgroup Discovery with CN2-SD
Nada Lavrač, A., Kavšek, B., Flach, P. A., & Todorovski, L. (2004) · Explore Bristol Research · Cited by 308 · see citing works
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
Hackenberg, M., Sturm, M., Langenberger, D., Falcón‐Pérez, J. M., & Aransay, A. M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp347 · Cited by 303 · see citing works
Bar, M., Wyman, S. K., Fritz, B. R., Qi, J., Garg, K. S., Parkin, R. K., Kroh, E. M., Bendoraite, A., Mitchell, P. S., Nelson, A. M., et al. (2008) · Stem Cells · doi:10.1634/stemcells.2008-0356 · Cited by 300 · see citing works
Prediction of microRNA targets
Mazière, P., & Enright, A. J. (2007) · Drug Discovery Today · doi:10.1016/j.drudis.2007.04.002 · Cited by 300 · see citing works
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans
Zisoulis, D. G., Lovci, M., Wilbert, M. L., Hutt, K. R., Liang, T. Y., Pasquinelli, A. E., & Yeo, G. W.-M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1745 · Cited by 290 · see citing works
Zhang, S., Li, Q., Liu, J., & Zhou, X. J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr206 · Cited by 239 · see citing works
Cox, M., Cairns, M. J., Gandhi, K. S., Carroll, A. P., Moscovis, S. M., Stewart, G. J., Broadley, S., Scott, R. J., Booth, D. R., & Lechner‐Scott, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012132 · Cited by 239 · see citing works
Self-citationHandbook of computational molecular biology
(2006) · Choice Reviews Online · doi:10.5860/choice.43-6513 · Cited by 236 · see citing works
Genome: The Autobiography of a Species In 23 Chapters
Ridley, M. (1999) · CERN Document Server (European Organization for Nuclear Research) · Cited by 223 · see citing works
MicroRNA-143 and -145 in Colon Cancer
Akao, Y., Nakagawa, Y., & Naoe, T. (2007) · DNA and Cell Biology · doi:10.1089/dna.2006.0550 · Cited by 220 · see citing works
Computational Methods for MicroRNA Target Prediction
Ekimler, S., & Sahin, K. (2014) · Genes · doi:10.3390/genes5030671 · Cited by 193 · see citing works
Consensus algorithms for the generation of all maximal bicliques
Alexe, G., Alexe, S., Crama, Y., Foldes, S., Hammer, P. L., & Simeone, B. (2004) · Discrete Applied Mathematics · doi:10.1016/j.dam.2003.09.004 · Cited by 190 · see citing works
Got target?: computational methods for microRNA target prediction and their extension
Min, H., & Yoon, S. (2010) · Experimental & Molecular Medicine · doi:10.3858/emm.2010.42.4.032 · Cited by 190 · see citing works
Peng, X., Li, Y., Walters, K., Rosenzweig, E., Lederer, S., Aicher, L. D., Proll, S. C., & Katze, M. G. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-373 · Cited by 186 · see citing works
Predicting microRNA targets and functions: traps for the unwary
Ritchie, W., Flamant, S., & Rasko, J. E. J. (2009) · Nature Methods · doi:10.1038/nmeth0609-397 · Cited by 167 · see citing works
Computational approaches for microRNA studies: a review
Li, L., Xu, J., Yang, D., Tan, X., & Wang, H. (2009) · Mammalian Genome · doi:10.1007/s00335-009-9241-2 · Cited by 167 · see citing works
miRGator: an integrated system for functional annotation of microRNAs
Nam, S., Kim, B. S., Shin, S., & Lee, S. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm829 · Cited by 160 · see citing works
MAGIA, a web-based tool for miRNA and Genes Integrated Analysis
Sales, G., Coppe, A., Bisognin, A., Biasiolo, M., Bortoluzzi, S., & Romualdi, C. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq423 · Cited by 156 · see citing works
WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit
Duncan, D. T., Prodduturi, N., & Zhang, B. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-s4-p10 · Cited by 147 · see citing works
Discovery of microRNA–mRNA modules via population-based probabilistic learning
Joung, J., Hwang, K., Nam, J.-W., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm045 · Cited by 147 · see citing works
Predicting and validating microRNA targets.
Lai, E. C. (2004) · Genome biology · doi:10.1186/gb-2004-5-9-115 · Cited by 141 · see citing works
Prediction of regulatory modules comprising microRNAs and target genes
Yoon, S., & Micheli, G. D. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1116 · Cited by 137 · see citing works
The sufficient minimal set of miRNA seed types
Ellwanger, D. C., Büttner, F. A., Mewes, H.-W., & Stümpflen, V. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr149 · Cited by 112 · see citing works
Computational Methods for MicroRNA Target Prediction
Watanabe, Y., Tomita, M., & Kanai, A. (2007) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(07)27004-1 · Cited by 107 · see citing works
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Shi, G., Zhang, L., & Jiang, T. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-10 · Cited by 105 · see citing works
Laganà, A., Forte, S., Giudice, A., Arena, M. R., Puglisi, P. L., Giugno, R., Pulvirenti, A., Shasha, D. E., & Ferro, A. (2009) · Database · doi:10.1093/database/bap008 · Cited by 105 · see citing works
MicroRNA Detection and Target Prediction: Integration of Computational and Experimental Approaches
Chaudhuri, K., & Chatterjee, R. (2007) · DNA and Cell Biology · doi:10.1089/dna.2006.0549 · Cited by 102 · see citing works
Identifying functional miRNA–mRNA regulatory modules with correspondence latent dirichlet allocation
Liu, B., Liu, L., Tsykin, A., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq576 · Cited by 95 · see citing works
Self-citationAlterations in miRNA processing and expression in pleomorphic adenomas of the salivary gland
Zhang, X., Cairns, M. J., Rose, B. R., O’Brien, C. J., Shannon, K. F., Clark, J. R., Gamble, J. R., & Tran, N. (2009) · International Journal of Cancer · doi:10.1002/ijc.24298 · Cited by 90 · see citing works
Self-citationTowards computational prediction of microRNA function and activity
Ulitsky, I., Laurent, L. C., & Ron Shamir, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq570 · Cited by 87 · see citing works
Finding microRNA regulatory modules in human genome using rule induction
Tran, D. H., Satou, K., & Ho, T. B. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-s12-s5 · Cited by 86 · see citing works
Su, Z., Li, Z., Chen, T., Li, Q., Fang, H., Ding, D., Ge, W., Ning, B., Hong, H., Perkins, R., et al. (2011) · Chemical Research in Toxicology · doi:10.1021/tx200103b · Cited by 85 · see citing works
Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?
Barbato, C., Arisi, I., Frizzo, M. E., Brandi, R., Sacco, L. D., & Masotti, A. (2009) · BioMed Research International · doi:10.1155/2009/803069 · Cited by 85 · see citing works
Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy
Liu, B., Li, J., Tsykin, A., Liu, L., Gaur, A. B., & Goodall, G. J. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-408 · Cited by 84 · see citing works
Self-citationMicroRNA prediction with a novel ranking algorithm based on random walks
Xu, Y., Zhou, X., & Zhang, W. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn175 · Cited by 78 · see citing works
Su, W., Kleinhanz, R. R., & Schadt, E. E. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.23 · Cited by 71 · see citing works
Wang, J., Haubrock, M., Cao, K.-M., Hua, X., Zhang, C., Wingender, E., & Li, J. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-199 · Cited by 65 · see citing works
Self-citationBonnet, É., Tatari, M. N., Joshi, A., Michoel, T., Kathleen Marchal, D., Berx, G., & de Peer, Y. V. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010162 · Cited by 62 · see citing works
The discovery approaches and detection methods of microRNAs
Huang, Y., Zou, Q., Wang, S. P., et al. (2010) · Molecular Biology Reports · doi:10.1007/s11033-010-0532-1 · Cited by 56 · see citing works
Discovery of functional miRNA–mRNA regulatory modules with computational methods
Liu, B., Li, J., & Tsykin, A. (2009) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2009.01.005 · Cited by 53 · see citing works
Self-citationIdentification of microRNA regulatory modules inArabidopsisvia a probabilistic graphical model
Joung, J., & Fei, Z. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn626 · Cited by 44 · see citing works
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data
Huang, J., Morris, Q., & Frey, B. J. (2006) · Lecture notes in computer science · doi:10.1007/11732990_11 · Cited by 31 · see citing works
MIRTFnet: Analysis of miRNA Regulated Transcription Factors
Naeem, H., Küffner, R., & Zimmer, R. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022519 · Cited by 26 · see citing works
miReg: a resource for microRNA regulation
Barh, D., Bhat, D., & Viéro, C. (2010) · PubMed · doi:10.2390/biecoll-jib-2010-144 · Cited by 17 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [54]Miranda KC Huynh T Tay Y A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. 2006 126 6 1203 17 16990141
Cited by
Sorted by citations
Nguyen, D. D., Cang, Z., Wu, K., Wang, M., Cao, Y., & Wei, G.-W. (2019) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-018-0146-6 · Cited by 155 · see citing works
Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode
Agrawal, P., Kurcon, T., Pilobello, K. T., Rakus, J. F., Koppolu, S., Liu, Z., Batista, B. S., Eng, W. S., Hsu, K.-L., Liang, Y., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1321524111 · Cited by 77 · see citing works
- Authors
- Liu, B., Li, J., & Cairns, M. J.
- Affiliations
- University of Newcastle Australia (AU)
- University of South Australia (AU)
- Corresponding author
- Cairns, M. J.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-22
- Volume
- 15
- Issue
- 1
- Pages
- 1-19
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- PMC
- PMC3896928
- OpenAlex
- W2142878546
- Cited by
- 563
- References
- 104
- Citations by year
- 2026: 13 · 2025: 37 · 2024: 53 · 2023: 60 · 2022: 80 · 2021: 83 · 2020: 65 · 2019: 39 · 2018: 35 · 2017: 29 · 2016: 21 · 2015: 18 · 2014: 18 · 2013: 12
- FWCI
- 1.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Briefings in Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by-nc)
- NOVA (University of Newcastle Australia) (submittedVersion)
- Funders
- National Alliance for Research on Schizophrenia and Depression
- Hunter Medical Research Institute
- University of New South Wales
- Medical Research Council
- National Health and Medical Research Council (631057)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- microRNA, microRNA discovery, miRNA target identification, post-transcriptional gene silencing, heterogeneous data integration, computational biology
- MeSH terms
- Algorithms, Animals, Binding Sites, Gene Expression Regulation, Humans, Models, Genetic, Computational Biology, 3' Untranslated Regions, Databases, Nucleic Acid, RNA Interference, MicroRNAs, Molecular Sequence Annotation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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