[1]
Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75(5): 843-54.
[2]
Liu B, Li J, Cairns MJ. Identifying miRNAs, targets and functions. Brief Bioinform 2014; 15(1): 1-19.
[3]
He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004; 5(7): 522-31.
[4]
Yanaihara N, Caplen N, Bowman E, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 2006; 9(3): 189-98.
[5]
Porkka KP, Pfeiffer MJ, Waltering KK, Vessella RL, Tammela TL, Visakorpi T. MicroRNA expression profiling in prostate cancer. Cancer Res 2007; 67(13): 6130-5.
[6]
Yang H, Kong W, He L, et al. MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res 2008; 68(2): 425-33.
[7]
Hébert SS, Horré K, Nicolaï L, et al. MicroRNA regulation of Alzheimer’s Amyloid precursor protein expression. Neurobiol Dis 2009; 33(3): 422-8.
[8]
Beveridge NJ, Gardiner E, Carroll AP, Tooney PA, Cairns MJ. Schizophrenia is associated with an increase in cortical microRNA biogenesis. Mol Psychiatry 2010; 15(12): 1176-89.
[9]
Cox MB, Cairns MJ, Gandhi KS, et al. MicroRNAs miR-17 and miR-20a inhibit T cell activation genes and are under-expressed in MS whole blood. PLoS One 2010; 5(8): e12132.
[10]
Mendes ND, Freitas AT, Sagot MF. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 2009; 37(8): 2419-33.
[11]
Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009; 136(2): 215-33.
[12]
Krek A, Grün D, Poy MN, et al. Combinatorial microRNA target predictions. Nat Genet 2005; 37(5): 495-500.
[13]
Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120(1): 15-20.
[14]
Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005; 123(6): 1133-46.
[15]
Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 2007; 8(1): 69.
[16]
Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 2009; 25(23): 3049-55.
[17]
Fan X, Kurgan L. Comprehensive overview and assessment of computational prediction of microRNA targets in animals. Brief Bioinform 2015; 16(5): 780-94.
[18]
Srivastava PK, Moturu TR, Pandey P, Baldwin IT, Pandey SP. A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. BMC Genomics 2014; 15(1): 348.
[19]
Akhtar MM, Micolucci L, Islam MS, Olivieri F, Procopio AD. Bioinformatic tools for microRNA dissection. Nucleic Acids Res 2016; 44(1): 24-44.
[20]
Peterson SM, Thompson JA, Ufkin ML, Sathyanarayana P, Liaw L, Congdon CB. Common features of microRNA target prediction tools. Front Genet 2014; 5: 23.
[21]
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003; 115(7): 787-98.
[22]
Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005; 3(3): e85.
[23]
Yue D, Liu H, Huang Y. Survey of computational algorithms for MicroRNA target prediction. Curr Genomics 2009; 10(7): 478-92.
[24]
Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19(1): 92-105.
[25]
Doench JG, Sharp PA. Specificity of microRNA target selection in translational repression. Genes Dev 2004; 18(5): 504-11.
[26]
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007; 27(1): 91-105.
[27]
Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 2011; 18(10): 1139-46.
[28]
Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 2010; 11(8): R90.
[29]
Griffiths-Jones S, Grocock RJ, Van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006; 1; 34(Suppl-1): D140-4.
[30]
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008; 36(Database issue): D154-8.
[31]
Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 2006; 12(2): 192-7.
[32]
Vlachos IS, Paraskevopoulou MD, Karagkouni D, et al. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res 2015; 43(Database issue): D153-9.
[33]
Chou CH, Chang NW, Shrestha S, et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res 2016; 44(D1): D239-47.
[34]
Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008; 14(6): 1012-7.
[35]
Wang X, El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008; 24(3): 325-32.
[36]
Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, et al. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res 2006; 34(Suppl. 1): D135-9.
[37]
Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 2005; 102(7): 2454-9.
[38]
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol 2003; 5(1): R1.
[39]
Andrés-León E, González Peña D, Gómez-López G, Pisano DG. miRGate: a curated database of human, mouse and rat miRNAmRNA targets. Database (Oxford) 2015; 2015bav035.
[41]
Krüger J, Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 2006; 34(Suppl. 1): W451-4.
[42]
Thadani R, Tammi MT. MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformatics 2006; 7(Suppl. 5): S20.
[43]
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007; 39(10): 1278-84.
[44]
Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 2014; 42(Database issue): D68-73.
[45]
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009; 37(Database issue): D105-10.
[46]
Vergoulis T, Vlachos IS, Alexiou P, et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 2012; 40(Database issue): D222-9.
[47]
Wang D, Gu J, Wang T, Ding Z. OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. Bioinformatics 2014; 30(15): 2237-8.
[48]
Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008; 36(Suppl. 1): D149-53.
[49]
Coronnello C, Benos PV. ComiR: Combinatorial microRNA target prediction tool. Nucleic Acids Res 2013; 41(Web Server issue): W159-64.
[50]
Paraskevopoulou MD, Georgakilas G, Kostoulas N, et al. DIANAmicroT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 2013; 41(Web Server issue) W169-73.
[51]
Friedman Y, Naamati G, Linial M. MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics 2010; 26(15): 1920-1.
[52]
Lu TP, Lee CY, Tsai MH, et al. miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLoS One 2012; 7(8): e42390.
[53]
Carrington JC, Ambros V. Role of microRNAs in plant and animal development. Science 2003; 301(5631): 336-8.
[54]
Martin G, Schouest K, Kovvuru P, Spillane C. Prediction and validation of microRNA targets in animal genomes. J Biosci 2007; 32(6): 1049-52.
[55]
Guo L, Zhang H, Zhao Y, Yang S, Chen F. In-depth exploration of miRNA: a new approach to study miRNA at the miRNA/isomiR levels. Curr Bioinform 2014; 9(5): 522-30.
[56]
Coronnello C, Hartmaier R, Arora A, et al. Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLOS Comput Biol 2012; 8(12): e1002830.
[57]
Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLOS Comput Biol 2009; 5(12): e1000590.
[58]
Dweep H, Gretz N, Sticht C. miRWalk database for miRNA–target interactions. RNA mapping: methods and protocols 2014; 289-305.
[59]
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004; 2(11): e363.
[60]
Miranda KC, Huynh T, Tay Y, et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 2006; 126(6): 1203-17.
[61]
Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M. MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res 2009; 37(Suppl. 2): W266-72.
[62]
Tsang JS, Ebert MS, van Oudenaarden A. Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell 2010; 38(1): 140-53.
[63]
Vejnar CE, Zdobnov EM. MiRmap: comprehensive prediction of microRNA target repression strength. Nucleic Acids Res 2012; 40(22): 11673-83.
[64]
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010; 20(1): 110-21.
[65]
German MA, Pillay M, Jeong DH, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008; 26(8): 941-6.
[66]
Beauclair L, Yu A, Bouché N. microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J 2010; 62(3): 454-62.
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