{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:23:34Z","timestamp":1764689014288},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence-specific manner, and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA\u2013mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise.<\/jats:p>\n               <jats:p>Results: The objective of this study was to modify our widely recognized Web server for the integrated mRNA\u2013miRNA analysis (MMIA) and its subsequent deployment on the Amazon cloud (BioVLAB-MMIA) to be compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). We developed a new version called the BioVLAB-MMIA-NGS, deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of an miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/epigenomics.snu.ac.kr\/biovlab_mmia_ngs\/<\/jats:p>\n               <jats:p>Contact: \u00a0sunkim.bioinfo@snu.ac.kr , heechae@cs.indiana.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu614","type":"journal-article","created":{"date-parts":[[2014,10,1]],"date-time":"2014-10-01T07:57:30Z","timestamp":1412150250000},"page":"265-267","source":"Crossref","is-referenced-by-count":40,"title":["BioVLAB-MMIA-NGS: microRNA\u2013mRNA integrated analysis using high-throughput sequencing data"],"prefix":"10.1093","volume":"31","author":[{"given":"Heejoon","family":"Chae","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, 2 School of Computer Science and Engineering, Seoul National University, Seoul, Korea and 3 Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sungmin","family":"Rhee","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, 2 School of Computer Science and Engineering, Seoul National University, Seoul, Korea and 3 Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenneth P.","family":"Nephew","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, 2 School of Computer Science and Engineering, Seoul National University, Seoul, Korea and 3 Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sun","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, 2 School of Computer Science and Engineering, Seoul National University, Seoul, Korea and 3 Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,9,29]]},"reference":[{"key":"2023020116160003900_btu614-B1","doi-asserted-by":"crossref","first-page":"e9171","DOI":"10.1371\/journal.pone.0009171","article-title":"The DIANA-mirExTra web server: from gene expression data to microRNA function","volume":"5","author":"Alexiou","year":"2010","journal-title":"PLoS One"},{"key":"2023020116160003900_btu614-B2","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023020116160003900_btu614-B3","doi-asserted-by":"crossref","first-page":"R90","DOI":"10.1186\/gb-2010-11-8-r90","article-title":"Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites","volume":"11","author":"Betel","year":"2010","journal-title":"Genome Biol."},{"key":"2023020116160003900_btu614-B4","doi-asserted-by":"crossref","first-page":"D252","DOI":"10.1093\/nar\/gks1168","article-title":"miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting","volume":"41","author":"Cho","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020116160003900_btu614-B5","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/gkr688","article-title":"miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades","volume":"40","author":"Friedl\u00e4nder","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023020116160003900_btu614-B6","author":"Goff","year":"2012"},{"key":"2023020116160003900_btu614-B7","first-page":"169","article-title":"DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists","volume":"35","author":"Huang","year":"2007","journal-title":"Nat. Protoc."},{"key":"2023020116160003900_btu614-B8","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020116160003900_btu614-B9","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1038\/ng2135","article-title":"The role of site accessibility in microRNA target recognition","volume":"39","author":"Kertesz","year":"2007","journal-title":"Nat. Genet."},{"key":"2023020116160003900_btu614-B10","doi-asserted-by":"crossref","first-page":"D152","DOI":"10.1093\/nar\/gkq1027","article-title":"miRBase: integrating microRNA annotation and deep-sequencing data","volume":"39","author":"Kozomara","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020116160003900_btu614-B11","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","article-title":"Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets","volume":"120","author":"Lewis","year":"2005","journal-title":"Cell"},{"key":"2023020116160003900_btu614-B12","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1939-8433-6-8","article-title":"Introns targeted by plant microRNAs: a possible novel mechanism of gene regulation","volume":"6","author":"Meng","year":"2013","journal-title":"Rice"},{"key":"2023020116160003900_btu614-B13","doi-asserted-by":"crossref","first-page":"W356","DOI":"10.1093\/nar\/gkp294","article-title":"MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression","volume":"37","author":"Nam","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020116160003900_btu614-B14","doi-asserted-by":"crossref","first-page":"W352","DOI":"10.1093\/nar\/gkq423","article-title":"MAGIA, a web-based tool for miRNA and genes integrated analysis","volume":"38","author":"Sales","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020116160003900_btu614-B15","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023020116160003900_btu614-B16","first-page":"397","article-title":"Limma: linear models for microarray data","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor","author":"Smyth","year":"2010"},{"key":"2023020116160003900_btu614-B17","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1186\/1471-2105-14-174","article-title":"PMTED: a plant microRNA target expression database","volume":"14","author":"Sun","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023020116160003900_btu614-B18","first-page":"178","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020116160003900_btu614-B19","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."},{"key":"2023020116160003900_btu614-B20","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1093\/bioinformatics\/btn646","article-title":"Computational analysis of miRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance","volume":"25","author":"Xin","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/2\/265\/49012392\/bioinformatics_31_2_265.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/2\/265\/49012392\/bioinformatics_31_2_265.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:26:17Z","timestamp":1675297577000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/2\/265\/2365530"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,29]]},"references-count":20,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2015,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu614","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,15]]},"published":{"date-parts":[[2014,9,29]]}}}