Leader » Dr. Hsien-Da Huang

Chairman, Department of Biological Science & Technology, Institute of Bioinformatics and Systems Biology National Chiao Tung University HsinChu, Taiwan

Publications

  • MicroRNA: A Master Regulator of Cellular Processes for Bioengineering Systems.

    Sun W, Li YSJ, Huang HD, Shyy JYJ, & Chien S
    Annual Review of Biomedical Engineering, Vol. 12, Aug 2010.

    PUBMED: 20415587

  • N-Ace: using solvent accessibility and physicochemical properties to identify protein N-Acetylation sites.

    Lee TY, Hsu JBK, Lin FM, Chang WC, Hsu PC, & Huang HD
    Journal of Computational Chemistry 31, 2759-2771.

    PUBMED: 20839302

  • A novel role of CPEB3 in regulating EGFR gene transcription via association with Stat5b in neurons.

    Peng SC, Lai YT, Huang HY, Huang HD, & Huang YS
    Nucleic Acids Res.

    PUBMED: 20639532

  • FMM: a web server for metabolic pathway reconstruction and comparative analysis.

    Chou CH, Chang WC, Chiu CM, Huang CC, & Huang HD
    (2009) Nucleic Acids Res 37, W129-134.

    PUBMED: 19401437

  • Incorporating Structural Characteristics for Identification of Protein Methylation Sites.

    Shien DM, Lee TY, Chang WC, Hsu JB, Horng JT, Hsu PC, Wang TY, & Huang HD
    (2009) J Comput Chem 30, 1532-1543.

    PUBMED: 19263424

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

    Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, & Lin NS
    (2009) BMC Bioinformatics 10, 328.

    PUBMED: 19821977

  • A Comprehensive Resource for Integrating and Displaying Protein Post-Translational Modifications.

    Lee TY, Hsu JB, Chang WC, Wang TY, Hsu PC, & Huang HD
    (2009) BMC Res Notes 2, 111.

    PUBMED: 195492917

  • 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

  • KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns

    Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, Yang YH, Chu CH, Huang HD, Ko MT, & Hwang JK
    (2007) Nucleic Acids Res 35, W588-594.

    PUBMED: 17517770

  • Primer Design for Multiplex PCR Using a Genetic Algorithm", Soft Computing

    L.C. Wu, J.Z. Horng, H.Y. Huang, F.M. Lin, H.D. Huang, and M.F. Tsai
    Soft Computing, Vol. 11, No. 9, 855-863, 2007

  • RINGdb: An integrated database for G protein-coupled receptors and regulators of G protein signaling

    Y.C. Fang, W.H. Sun, L.C. Wu, H.D. Huang, H.F. Juan, J.T. Horng
    BMC Genomics, 7:317, 2006

  • RNAMST: An efficient and flexible search tool for RNA structural homologs

    T.H. Chang�, H.D. Huang�,* (� joint first authorship), Zi-Neng Chung, and J.T. Horng
    Nucleic Acids Research, Vol 34, W423-W428, 2006

  • ProKware: an integrated software for presenting protein structural properties in protein tertiary structures

    J.H. Hung�, H.D. Huang�,* (� joint first authorship), and T.Y. Lee
    Nucleic Acids Research, Vol 34, W89-W94, 2006

  • RegRNA: A regulatory RNA motifs and elements finder

    H.Y. Huang, C.H. Chien, and K.H. Jen, H.D. Huang*
    Nucleic Acids Research, Vol 34, W429-W434, 2006

  • miRNAMap: genomic maps for miRNA genes and their target genes in vertebrate genomes

    W.C. Hsu�, H.D. Huang�, * (� joint first authorship), S.D. Hsu, L.Z. Lin, A.P. Tsou, C.P. Tseng, P.F. Stadler, S. Washietl, and I.L. Hofacker
    Nucleic Acids Research, Vol 34, D135-D139, 2006

  • dbPTM: An information repository of protein post-translational modification

    T.Y. Lee�, H.D. Huang�, * (� joint first authorship), J.H. Hung, Y.S. Yang, and T.H. Wang*
    Nucleic Acids Research, Vol. 34, D622-D627, 2006

  • Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data

    A.P. Tsou, Y.M. Sun, C.L. Liu, H.D. Huang*, and J.T. Horng*
    IEEE Transactions on Information Technology in Biomedicine, 10(3):550-8, 2006

  • Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures

    Li-Cheng Wu, J.T. Horng, S.L. Huang and H.D. Huang
    Journal of Computational Chemistry , Vol. 27, No. 6, 798-808, 2006

  • An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints

    T.Y. Lee, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin
    Journal of Computational Chemistry, Vol. 27, No. 9, 1020-32, 2006

  • Database to dynamically aid probe design for virus identification

    F.M. Lin, H.D. Huang, P.L. Chan, Y.C. Chang, and J.T. Horng
    IEEE Transactions on Information Technology in Biomedicine, 10 (4), 705-13, 2006

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

    H.D. Huang, J.T. Horng, F.M. Lin, Y.C. Chang, and C.C. Huang
    Nucleic Acids Research, Vol. 33, D80-D85, 2005

  • KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites

    H.D. Huang*, T.Y. Lee, S.W. Tseng, and J.T. Horng
    Nucleic Acids Research, Vol. 33, W226-229, 2005

  • MultiProtIdent: identifying proteins using database search and protein-protein interactions

    H.D. Huang, T.Y. Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou
    Journal of Proteome Research, 4(3), 690-697, 2005

  • Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites

    H.D. Huang*, T.Y. Lee, S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou
    Journal of Computational Chemistry, Vol. 26, pp. 1032-1041, 2005

  • Discovering common of structural motifs from SSU 16 S ribosomal RNA secondary structures

    H.D. Huang*, J.T. Horng, and S.F. Fang
    International Journal on Artificial Intelligence Tools, Vol. 14, No. 4, pp. 621-639, 2005

  • Identifying transcriptional regulatory sites in the human genome using an integrated system

    H.D Huang, J.T. Horng, Y.M. Sun, and A.P. Tsou
    Nucleic Acids Research, Vol. 32, No. 6, pp. 1948-56, 2004

  • i-Genome: A database to summarize oligonucleotide data in genomes

    F.M. Lin, H.D. Huang, YC, Chang, J.T. Horng
    BMC Genomics, Vol. 5, No. 1, pp.78, 2005

  • Identification of the combination of susceptibility genetic factors for cervical cancer

    J.T. Horng, K. C. Hu, L. C. Wu, H. D. Huang, F. M. Lin, H. C. Lai, and T. Y Chu
    IEEE Transactions on Information Technology in Biomedicine, Vol 8, No.1, pp. 59-66, 2004

  • A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome

    J.T. Horng, H.D. Huang, T.S. Tsou, J.Y. Hong, and B.J. Liu
    Journal of Information Science and Engineering, Vol. 20, No. 6, pp. 1141- 1159, 2004

  • A probabilistic method to correlate ion-pairs with protein thermostability
    S.L. Huang, LC. Wu, H.D. Huang, H.K. Liang, M.T. Ko, and J.T. Horng, 2004

  • A biological data warehousing, analyzing and mining system for identifying transcriptional regulatory sites in human genome

    Y.M. Sun, H.D. Huang, J.T. Horng, A.P. Tsou, and S.L. Huang
    Lecture Notes in Computer Sciences 3180: 751-760, 2004

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

    H.D. Huang, J.T. Horng, C.C. Lee, and B.J. Liu
    Genome Biology, Vol. 4, No. 4: R29, 2003

  • Database of repetitive elements in complete genomes and data mining using transcription factor binding sites

    J.T. Horng, F.M. Lin, J.H. Lin, H.D. Huang, and B.J. Liu
    IEEE Transactions on Information Technology in Biomedicine (TITB), Vol. 7, No. 2, pp. 93-100, 2003

  • Computing motif correlations in proteins

    J.T. Horng, H.D. Huang, S.H. Wang, M.Y. Chen, J.K. Hwang, and S.L. Huang
    Journal of Computational Chemistry, Vol. 24, No. 16, pp. 2032-43, 2003

  • A data mining method to predict transcriptional regulatory sites based on differentially expressed genes in human genome

    Journal of Information Science and Engineering, Vol. 19, No. 6, pp. 923-942
    H.D. Huang, H.L. Chang, T.S. Tsou, B.J. Liu, and J.T. Horng, 2003

  • Mining correlations of tissue gene expression from digital expression profiles of human tissues

    J.T. Horng, H.D. Huang, K.Y. Tseng, T.S. Tsou, and B.J. Liu
    Journal of Information Science and Engineering, Vol. 19, No. 6, pp. 909-921, 2003

  • The repetitive sequence database and mining putative regulatory elements in gene promoter regions

    J.T. Horng, H.D. Huang, F.M. Lin, L.C. Wu, and S.L. Huang
    Journal of Computational Biology, Vol. 9, No. 4, pp. 621-640, 2002

  • Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae

    J.T. Horng, H.D. Huang, S.L. Huang, U.C. Yang, and Y.C. Chang
    In Silico Biology, Vol. 2, No. 3, pp. 263-273, 2002