{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T14:00:05Z","timestamp":1774792805919,"version":"3.50.1"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,11,24]],"date-time":"2011-11-24T00:00:00Z","timestamp":1322092800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-454","type":"journal-article","created":{"date-parts":[[2011,11,24]],"date-time":"2011-11-24T19:26:07Z","timestamp":1322162767000},"source":"Crossref","is-referenced-by-count":30,"title":["miREE: miRNA recognition elements ensemble"],"prefix":"10.1186","volume":"12","author":[{"given":"Paula H","family":"Reyes-Herrera","sequence":"first","affiliation":[]},{"given":"Elisa","family":"Ficarra","sequence":"additional","affiliation":[]},{"given":"Andrea","family":"Acquaviva","sequence":"additional","affiliation":[]},{"given":"Enrico","family":"Macii","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,11,24]]},"reference":[{"issue":"2","key":"4995_CR1","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","volume":"116","author":"D Bartel","year":"2004","unstructured":"Bartel D: MicroRNAsGenomics, Biogenesis, Mechanism, and Function. Cell 2004, 116(2):281\u2013297. 10.1016\/S0092-8674(04)00045-5","journal-title":"Cell"},{"issue":"2","key":"4995_CR2","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","volume":"136","author":"DP Bartel","year":"2009","unstructured":"Bartel DP: MicroRNAs: Target Recognition and Regulatory Functions. Cell 2009, 136(2):215\u2013233. 10.1016\/j.cell.2009.01.002","journal-title":"Cell"},{"issue":"8","key":"4995_CR3","doi-asserted-by":"publisher","first-page":"2419","DOI":"10.1093\/nar\/gkp145","volume":"37","author":"ND Mendes","year":"2009","unstructured":"Mendes ND, Freitas AT, Sagot MF: Current tools for the identification of miRNA genes and their targets. Nucl Acids Res 2009, 37(8):2419\u20132433. 10.1093\/nar\/gkp145","journal-title":"Nucl Acids Res"},{"issue":"5","key":"4995_CR4","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1089\/dna.2006.0551","volume":"26","author":"M Lindow","year":"2007","unstructured":"Lindow M, Gorodkin J: Principles and limitations of computational microRNA gene and target finding. DNA Cell Biol 2007, 26(5):339\u2013351. 10.1089\/dna.2006.0551","journal-title":"DNA Cell Biol"},{"key":"4995_CR5","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","volume":"120","author":"BP Lewis","year":"2005","unstructured":"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: 15\u201320. 10.1016\/j.cell.2004.12.035","journal-title":"Cell"},{"issue":"11","key":"4995_CR6","doi-asserted-by":"publisher","first-page":"e363+","DOI":"10.1371\/journal.pbio.0020363","volume":"2","author":"B John","year":"2004","unstructured":"John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS: Human MicroRNA Targets. PLoS Biol 2004, 2(11):e363+.","journal-title":"PLoS Biol"},{"key":"4995_CR7","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1101\/gr.082701.108","volume":"19","author":"RC Friedman","year":"2009","unstructured":"Friedman RC, Farh KK, Burge CB, Bartel DP: Most mammalian mRNAs are conserved targets of microRNAs. Genome Research 2009, 19: 92\u2013105.","journal-title":"Genome Research"},{"issue":"5","key":"4995_CR8","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1016\/j.cub.2006.01.050","volume":"16","author":"S Lall","year":"2006","unstructured":"Lall S, Gru\u00fcn D, Krek A, Chen K, Wang YLL, Dewey CNN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HLL, Gunsalus KCC, Pachter L, Piano F, Rajewsky N: A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans. Current Biology 2006, 16(5):460\u2013471. 10.1016\/j.cub.2006.01.050","journal-title":"Current Biology"},{"key":"4995_CR9","volume-title":"Bioinformatics (Oxford, England)","author":"S Yoon","year":"2005","unstructured":"Yoon S, De Micheli G: Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics (Oxford, England) 2005., 21(Suppl 2):"},{"issue":"7","key":"4995_CR10","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1261\/rna.7290705","volume":"11","author":"O Saetrom","year":"2005","unstructured":"Saetrom O, Sn\u00f8ve O, Saetrom P: Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA 2005, 11(7):995\u20131003. 10.1261\/rna.7290705","journal-title":"RNA"},{"key":"4995_CR11","volume-title":"BMC Bioinformatics","author":"Y Yang","year":"2008","unstructured":"Yang Y, Wang YP, Li KB: MiRTif: a support vector machine-based microRNA target interaction filter. BMC Bioinformatics 2008., 9(Suppl 12):"},{"key":"4995_CR12","doi-asserted-by":"publisher","first-page":"411+","DOI":"10.1186\/1471-2105-7-411","volume":"7","author":"SK Kim","year":"2006","unstructured":"Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT: miTarget: microRNA target-gene prediction using a Support Vector Machine. BMC Bioinformatics 2006, 7: 411+. 10.1186\/1471-2105-7-411","journal-title":"BMC Bioinformatics"},{"issue":"22","key":"4995_CR13","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1093\/bioinformatics\/btm484","volume":"23","author":"M Yousef","year":"2007","unstructured":"Yousef M, Jung S, Kossenkov AVV, Showe LCC, Showe MKK: Na\u00efve Bayes for microRNA target predictions-machine learning for microRNA targets. Bioinformatics (Oxford, England) 2007, 23(22):2987\u20132992. 10.1093\/bioinformatics\/btm484","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"20","key":"4995_CR14","doi-asserted-by":"publisher","first-page":"2625","DOI":"10.1093\/bioinformatics\/btp503","volume":"25","author":"S Bandyopadhyay","year":"2009","unstructured":"Bandyopadhyay S, Mitra R: TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 2009, 25(20):2625\u20132631. 10.1093\/bioinformatics\/btp503","journal-title":"Bioinformatics"},{"issue":"8","key":"4995_CR15","doi-asserted-by":"publisher","first-page":"1587","DOI":"10.1016\/j.febslet.2007.03.022","volume":"581","author":"X Yan","year":"2007","unstructured":"Yan X, Chao T, Tu K, Zhang Y, Xie L, Gong Y, Yuan J, Qiang B, Peng X: Improving the prediction of human microRNA target genes by using ensemble algorithm. FEBS Lett 2007, 581(8):1587\u20131593. 10.1016\/j.febslet.2007.03.022","journal-title":"FEBS Lett"},{"key":"4995_CR16","volume-title":"BMC bioinformatics","author":"V Chandra","year":"2010","unstructured":"Chandra V, Girijadevi R, Nair AS, Pillai SS, Pillai RM: MTar: a computational microRNA target prediction architecture for human transcriptome. BMC bioinformatics 2010."},{"issue":"3","key":"4995_CR17","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1093\/bioinformatics\/btm595","volume":"24","author":"X Wang","year":"2008","unstructured":"Wang X, El Naqa IM: Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008, 24(3):325\u2013332. 10.1093\/bioinformatics\/btm595","journal-title":"Bioinformatics"},{"key":"4995_CR18","volume-title":"Nucleic acids research","author":"F Xiao","year":"2009","unstructured":"Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T: miRecords: an integrated resource for microRNA-target interactions. Nucleic acids research 2009, (37 Database):D105\u2013110."},{"key":"4995_CR19","volume-title":"Nucleic acids research","author":"GL Papadopoulos","year":"2009","unstructured":"Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG: The database of experimentally supported targets: a functional update of TarBase. Nucleic acids research 2009., (37 Database):"},{"issue":"7209","key":"4995_CR20","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature07228","volume":"455","author":"M Selbach","year":"2008","unstructured":"Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N: Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455(7209):58\u201363. 10.1038\/nature07228","journal-title":"Nature"},{"key":"4995_CR21","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.cell.2010.03.009","volume":"141","author":"M Hafner","year":"2010","unstructured":"Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T: Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP. Cell 2010, 141: 129\u2013141. 10.1016\/j.cell.2010.03.009","journal-title":"Cell"},{"key":"4995_CR22","volume-title":"Bioinformatics","author":"P Alexiou","year":"2009","unstructured":"Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG: Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 2009."},{"key":"4995_CR23","volume-title":"Evol Comput","author":"H M\u00fchlenbein","year":"1993","unstructured":"M\u00fchlenbein H, Schlierkamp-Voosen D: Predictive models for the breeder genetic algorithm i. continuous parameter optimization. Evol Comput 1993."},{"key":"4995_CR24","volume-title":"LIBSVM: a library for support vector machines","author":"CC Chang","year":"2001","unstructured":"Chang CC, Lin CJ: LIBSVM: a library for support vector machines. 2001."},{"key":"4995_CR25","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.molcel.2007.06.017","volume":"27","author":"A Grimson","year":"2007","unstructured":"Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP: MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Molecular Cell 2007, 27: 91\u2013105. 10.1016\/j.molcel.2007.06.017","journal-title":"Molecular Cell"},{"key":"4995_CR26","unstructured":"Enright AJ: MicroRNA Research Fundamentals, Reviews and Perspectives. The 2008 Collection Booklet"},{"issue":"22","key":"4995_CR27","doi-asserted-by":"publisher","first-page":"7138","DOI":"10.1093\/nar\/gki1012","volume":"33","author":"C Barreau","year":"2005","unstructured":"Barreau C, Paillard L, Osborne BH: AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Research 2005, 33(22):7138\u20137150. 10.1093\/nar\/gki1012","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"4995_CR28","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1038\/ng2135","volume":"39","author":"M Kertesz","year":"2007","unstructured":"Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E: The role of site accessibility in microRNA target recognition. Nature genetics 2007, 39(10):1278\u20131284. 10.1038\/ng2135","journal-title":"Nature genetics"},{"issue":"7048","key":"4995_CR29","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nature03817","volume":"436","author":"Y Zhao","year":"2005","unstructured":"Zhao Y, Samal E, Srivastava D: Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436(7048):214\u2013220. 10.1038\/nature03817","journal-title":"Nature"},{"issue":"7","key":"4995_CR30","doi-asserted-by":"publisher","first-page":"e6473+","DOI":"10.1371\/journal.pone.0006473","volume":"4","author":"T Schmidt","year":"2009","unstructured":"Schmidt T, Mewes HW, Stu\u00fcmpflen V: A Novel Putative miRNA Target Enhancer Signal. PLoS ONE 2009, 4(7):e6473+.","journal-title":"PLoS ONE"},{"key":"4995_CR31","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00818163","volume":"125","author":"IL Hofacker","year":"1994","unstructured":"Hofacker IL, Fontana W, Stadler PF, Bonhoeffer SL, Tacker M, Schuster P: Fast Folding and Comparison of RNA Secondary Structures. Monatsh Chem 1994, 125: 167\u2013188. 10.1007\/BF00818163","journal-title":"Monatsh Chem"},{"key":"4995_CR32","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1007\/978-3-540-35488-8_13","volume-title":"Feature Extraction","author":"YW Chen","year":"2006","unstructured":"Chen YW, Lin CJ: Combining SVMs with Various Feature Selection Strategies. In Feature Extraction. Volume 207. Springer Berlin Heidelberg; 2006:315\u2013324. 10.1007\/978-3-540-35488-8_13"},{"key":"4995_CR33","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1109\/CISIS.2010.129","volume-title":"Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems (CISIS), 15-18 February 2010; Krakow","author":"PH Reyes-Herrera","year":"2010","unstructured":"Reyes-Herrera PH, Acquaviva A, Ficarra E, Macii E: MicroRNA Target Prediction and Exploration through Candidate Binding Sites Generation. Proceedings of the International Conference on Complex, Intelligent and Software Intensive Systems (CISIS), 15\u201318 February 2010; Krakow 2010, 683\u2013688."},{"key":"4995_CR34","volume-title":"Cell","author":"Simon","year":"2008","unstructured":"Simon , David J, Madison , Jon M, Conery , Annie L, Thompson-Peer , Katherine L, Soskis , Michael , Ruvkun , Gary B, Kaplan , Joshua M, Kim , John K: The MicroRNA miR-1 Regulates a MEF-2-Dependent Retrograde Signal at Neuromuscular Junctions. Cell 2008."},{"key":"4995_CR35","doi-asserted-by":"publisher","first-page":"295+","DOI":"10.1186\/1471-2105-10-295","volume":"10","author":"M Maragkakis","year":"2009","unstructured":"Maragkakis M, Alexiou P, Papadopoulos G, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis V, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou A: Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 2009, 10: 295+. 10.1186\/1471-2105-10-295","journal-title":"BMC Bioinformatics"},{"key":"4995_CR36","doi-asserted-by":"publisher","first-page":"69+","DOI":"10.1186\/1471-2105-8-69","volume":"8","author":"D Gaidatzis","year":"2007","unstructured":"Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M: Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics 2007, 8: 69+. 10.1186\/1471-2105-8-69","journal-title":"BMC bioinformatics"},{"issue":"6","key":"4995_CR37","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1016\/j.cell.2006.07.031","volume":"126","author":"KC Miranda","year":"2006","unstructured":"Miranda KC, Huynh T, Tay Y, Ang YSS, Tam WLL, Thomson AM, Lim B, Rigoutsos I: A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 2006, 126(6):1203\u20131217. 10.1016\/j.cell.2006.07.031","journal-title":"Cell"},{"issue":"6","key":"4995_CR38","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/nbt.1543","volume":"27","author":"AA Khan","year":"2009","unstructured":"Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnology 2009, 27(6):549\u2013555.","journal-title":"Nature Biotechnology"},{"key":"4995_CR39","volume-title":"Nucleic Acids Research","author":"DW Thomson","year":"2011","unstructured":"Thomson DW, Bracken CP, Goodall GJ: Experimental strategies for microRNA target identification. Nucleic Acids Research 2011."},{"key":"4995_CR40","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nrg2673","volume":"11","author":"DD Licatalosi","year":"2010","unstructured":"Licatalosi DD, Darnell RB: RNA processing and its regulation: global insights into biological networks. Nature reviews. Genetics 2010, 11: 75\u201387.","journal-title":"Nature reviews. Genetics"},{"issue":"2","key":"4995_CR41","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/j.ydbio.2003.12.003","volume":"267","author":"N Rajewsky","year":"2004","unstructured":"Rajewsky N, Socci ND: Computational identification of microRNA targets. Developmental Biology 2004, 267(2):529\u2013535. 10.1016\/j.ydbio.2003.12.003","journal-title":"Developmental Biology"},{"issue":"suppl_2","key":"4995_CR42","doi-asserted-by":"publisher","first-page":"W451","DOI":"10.1093\/nar\/gkl243","volume":"34","author":"J Kruger","year":"2006","unstructured":"Kruger J, Rehmsmeier M: RNAhybrid: microRNA target prediction easy, fast and flexible. Nucl Acids Res 2006, 34(suppl_2):W451\u2013454.","journal-title":"Nucl Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-454.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-454\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-454.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T10:19:13Z","timestamp":1548238753000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-454"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,24]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4995"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-454","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,11,24]]},"article-number":"454"}}