{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T16:09:23Z","timestamp":1784563763900,"version":"3.55.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.<\/jats:p>\n               <jats:p>Results: Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3\u2032-untranslated regions (3\u2032-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3\u2032-UTR target sites. Further analysis indicates that genes with shorter 3\u2032-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3\u2032-UTR.<\/jats:p>\n               <jats:p>Availability: The results of DIANA-microT-CDS are available at www.microrna.gr\/microT-CDS<\/jats:p>\n               <jats:p>Contact: \u00a0hatzigeorgiou@fleming.gr; reczko@fleming.gr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts043","type":"journal-article","created":{"date-parts":[[2012,1,28]],"date-time":"2012-01-28T05:35:03Z","timestamp":1327728903000},"page":"771-776","source":"Crossref","is-referenced-by-count":447,"title":["Functional microRNA targets in protein coding sequences"],"prefix":"10.1093","volume":"28","author":[{"given":"Martin","family":"Reczko","sequence":"first","affiliation":[{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"},{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manolis","family":"Maragkakis","sequence":"additional","affiliation":[{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"},{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"},{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panagiotis","family":"Alexiou","sequence":"additional","affiliation":[{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"},{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo","family":"Grosse","sequence":"additional","affiliation":[{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander Fleming\u2019, Vari, Greece, 2Synaptic Ltd, Heraklion, Greece, 3Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany and 4Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 19104 Philadelphia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artemis G.","family":"Hatzigeorgiou","sequence":"additional","affiliation":[{"name":"1 Institute of Molecular Oncology, Biomedical Sciences Research Center \u2018Alexander 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