title: BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.
abstract: BACKGROUND
  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-mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise.
  
  
  RESULTS
  The objective of this study was to modify our widely recognized Web server for the integrated mRNA-miRNA 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.
  
  
  METHODS
  http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/.
authors.affiliation: Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, School of Computer Science and Engineering, Seoul National University, Seoul, Korea and Indiana University School of Medicine, Indianapolis, IN 46202, USA.
authors.forename: Heejoon
authors.initials: H
authors.lastname: Chae
authors.affiliation: Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, School of Computer Science and Engineering, Seoul National University, Seoul, Korea and Indiana University School of Medicine, Indianapolis, IN 46202, USA.
authors.forename: Sungmin
authors.initials: S
authors.lastname: Rhee
authors.affiliation: Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, School of Computer Science and Engineering, Seoul National University, Seoul, Korea and Indiana University School of Medicine, Indianapolis, IN 46202, USA.
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Nephew
authors.affiliation: Department of Computer Science, School of Informatics and Computing, Indiana University Bloomington, IN 47404, USA, School of Computer Science and Engineering, Seoul National University, Seoul, Korea and Indiana University School of Medicine, Indianapolis, IN 46202, USA.
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D012313:RNA / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D012313:RNA