MicroRNA

Recent works have demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding gene.Regulation,Proteomics.

In order to facilitate the investigation of microRNA regulation, we developed several biological databases and computational tools in this important field. Six articles in this filed were published in Nucleic Acids Research (2007 SCI Impact = 6.878). miRNAMap was selected as hot research in 2006 NAR Database Issue. miRNAMap was genomics maps for microRNA genes and their targets in metazoan genomes (Nucl Acids Res, 2006, Nucl Acids Res, 2008). ViTa is a database of host microRNA targets on viruses (Nucl Acids Res, 2007). We also survey the literatures to extract the RNA structural motifs and their functions to construct the RegRNA database (Nucl Acids Res, 2006). The RNAMST web server was developed for searching RNA structural homologs (Nucl Acids Res, 2006). RNALogo is designed as a new approach to display structural RNA alignment (Nucl Acids Res, 2008). These databases and tools were cited more than 100 times during last two years.

Small Regulatory RNAs and microRNAs

  • miRNAMap :Genomic maps of microRNAs in metazoan genomes (Nucl Acids Res, 2006, Nucl Acids Res, 2008)

  • miRTarBase :A database curates experimentally validated miRNA-target interactions.

  • miRStart :A database of human miRNA promoters.

  • miRTar :An integrated web server for identifying miRNA-target interactions.

  • RNAMST :An efficient and flexible search tool for RNA structural homologs (Nucl Acids Res, 2006)

  • RegRNA :A regulatory RNA motifs and elements finder (Nucl Acids Res, 2006)

  • ViTa :genomic maps of microRNAs in metazoan genomes (Nucl Acids Res, 2006, Nucl Acids Res, 2008)

  • RNALogo :A new approach to display structural RNA alignment (Nucl Acids Res, 2008)

  • RiboSW :A effective tool for identifying riboswitches (RNA, 2009)

We coperate with...

  • miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression.

    Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, & Lin NS
    BMC Bioinformatics 10, 328.

    PUBMED: 19821977

  • Computational Identification of Riboswitches Based on RNA Conserved Functional Sequences and Conformations.

    Chang TH, Huang HD, Wu LC, Yeh CT, Liu BJ, & Horng JT
    (2009) RNA 15, 1426-1430.

    PUBMED: 19460868

  • RNALogo: a new approach to display structural RNA alignment.

    Chang TH, Horng JT, & Huang HD
    (2008) Nucleic Acids Res 36, W91-96.

    PUBMED: 18495753

  • miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

    Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, & Huang HD
    (2008) Nucleic Acids Res 36, D165-169.

    PUBMED: 18029362

  • SpliceInfo: An information repository for mRNA alternative splicing in human genome.

    Huang HD, Horng JT, Lin FM, Chang YC, & Huang CC
    (2005) Nucleic Acids Res 33, D80-85.

    PUBMED: 15608290

  • ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag data.

    Huang HD, Horng JT, Lee CC, & Liu BJ <
    (2003) Genome Biol 4, R29.

    PUBMED: 12702210