Hsien-Da Huang, associate professor

　

Department of Biological Science & Technology
Institute of Bioinformatics
National Chiao Tung University
HsinChu, Taiwan

　

Phone: 886-3-5712121 Ext. 56952

Fax No: 886-3-5739320

E-mail: bryan@mail.nctu.edu.tw

　

　

　

Get access to Integrative Systems Biology Laboratory (ISBLAB)
　Bidlab BBS

[Resources/Selected Publications/Full Publication Lists]

　Resources

  • Small Regulatory RNAs and microRNAs
    • miRNAMap: Genomics maps for microRNA genes and their targets in mammalian genomes (Nucl Acids Res, 2006)
    • NEW!!miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes  (Nucl Acids Res, 2008)
    • 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)
    • NEW!!RNALogo: a new approach to display structural RNA alignment (Nucl Acids Res, 2008)
    • ViTa: a database of host microRNA targets on viruses  (Nucl Acids Res, 2007)
    • miRTar: A fast and efficient microRNA target prediction web server
    • sRNAMap:  A database of small noncoding regulatory RNA in microbial genomes
    • miRStart:  A database of microRNA transcriptional start sites
  • Gene Regulation
    • RgS-Miner: A predictive system for transcriptional regulatory sites in eukaryotic genomes (Nucl Acids Res, 2004)
    • i-Genome: A database index for the genome summarized information (BMC Genomics)
    • GPMiner: Gene promoter miner
    • NEW!!PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group
  • Post-Transcriptional Regulation
    • SpliceInfo: An information repository for the modes of mRNA alternative splicing in human genome (Nucl Acids Res, 2005)
    • ProSplicer: An alternative splicing database based on protein, mRNA, and EST sequences (Genome Biololgy, 2003)
    • EdRNA: RNA editing site database
  • Proteomics
    • NEW!!dbPTM: An information repository of protein post-translational modification (PTM) (Nucl Acids Res, 2006)
    • KinasePhos: A web tool for identifying protein kinase-specific phosphorylation site (Nucl Acids Res, 2005)
    • KinasePhos2: A web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns (Nucl Acids Res, 2007)
    • ProKware: An integrated software for presenting protein structural properties in protein tertiary structures (Nucl Acids Res, 2006)
    • Sulfosite
    • N-Ace
    • MASA

 

Selected Publications

1. W.C. Chang, T.Y. Lee, H.D. Huang*, H.Y. Huang, R.L. Pan*. (2008) “PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group”, BMC Genomics. (minor revision) PlantPAN

2. T. Z. Chang, J.T. Horng, and H.D. Huang*  (2008) “RNALogo: a new approach to display structural RNA alignment”, Nucleic Acids Research, vol. 36, W91-W96. (SCI, impact factor: 6.317) RNALogo

3. S.D. Hsu, C.H. Chu, A.P. Tsou, S.J. Chen, H.C. Chen, Paul W.C. Hsu, Y.H. Wong, Y.H. Chen, G.H. Chen, and H.D. Huang*  (2008) "miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes"  Nucleic Acids Research, Vol 36, D165-D169.   miRNAMap

4. Paul W.C. Hsu, L.Z. Lin, S.D. Hsu, H.D. Huang*  (2007) "ViTa: a database of host microRNA targets on viruses"  Nucleic Acids Research, Vol 35, D381-D385.    ViTa

5. Y.H. Wong, T.Y. Lee, H.K. Liang, C.M. Huang, Y.H. Yang, C.H. Chu, H.D. Huang* , M.T. Ko, and J.K. Hwang (2007) "KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns"  Nucleic Acids Research, Vol 35, W588-594.   KinasePhos2

6. Z.H. Chang†, H.D. Huang†,* († joint first authorship), Zi-Neng Chung, and J.T. Horng, (2006) "RNAMST: An efficient and flexible search tool for RNA structural homologs"  Nucleic Acids Research, Vol 34, W423-W428. (SCI, impact factor: 6.317)  RNAMST

7. J.H. Hung†, H.D. Huang†,* († joint first authorship), and T.Y. Lee, (2006) "ProKware: an integrated software for presenting protein structural properties in protein tertiary structures" Nucleic Acids Research, Vol 34, W89-W94. (SCI, impact factor: 6.317)  ProKWare

8. H.Y. Huang, C.H. Chien, and K.H. Jen, H.D. Huang*  (2006) "RegRNA: A regulatory RNA motifs and elements finder" Nucleic Acids Research, Vol 34, W429-W434. (SCI, impact factor: 6.317) RegRNA

9. 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. (2006) "miRNAMap: genomic maps for miRNA genes and their target genes in vertebrate genomes"  Nucleic Acids Research, Vol 34, D135-D139. [PubMed] (SCI, impact factor: 6.317)  miRNAMap

10.         Tzong-Yi Lee†, H.D. Huang†, * († joint first authorship), J.H. Hung, Y.S. Yang, and T.H. Wang*. (2006) "dbPTM: an information repository of protein post-translational modification" Nucleic Acids Research, Vol. 34, D622-D627. [PubMed] (SCI, impact factor: 6.317)  dbPTM

11.         H.D. Huang, J.T. Horng, F.M. Lin, Y.C. Chang, and C.C. Huang. (2005) "SpliceInfo: An information repository for mRNA alternative splicing in human genome ", Nucleic Acids Research, Vol. 33, D80-D85. (SCI, impact factor: 6.317) [PubMed]  SpliceInfo

12.         H.D. Huang*, T.Y. Lee, S.W. Tseng,  and J.T. Horng. (2005) "KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites" Nucleic Acids Research, Vol. 33, W226-229.  (SCI, impact factor: 6.317) [PubMed] KinasePhos

13.         H.D Huang, J.T. Horng, Y.M. Sun, and A.P. Tsou. (2004) "Identifying transcriptional regulatory sites in the human genome using an integrated system," Nucleic Acids Research, Vol. 32, No. 6, pp. 1948-56.  (SCI, impact factor: 6.317) [PubMed] RgS-Miner

14.         H.D. Huang, J.T. Horng, C.C. Lee, and B.J. Liu. (2003) “ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag data,” Genome Biology, Vol. 4, No. 4: R29. (SCI, impact factor: 9.71) [PubMed] ProSplicer

15.         H.D. Huang, T.Y. Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou. (2005) "MultiProtIdent: identifying proteins using database search and protein-protein interactions", Journal of Proteome Research, 4(3), 690-697 (SCI, impact factor: 6.917) [PubMed] MultiProtIdent

16.         H.D. Huang*, T.Y. Lee,  S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou. (2005) "Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites." Journal of Computational Chemistry, Vol. 26, pp. 1032-1041. (SCI, impact factor: 3.168) [PubMed]

　

Full Publication Lists

 

1. W.C. Chang, T.Y. Lee, H.D. Huang*, H.Y. Huang, R.L. Pan*. (2008) “PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group”, BMC Genomics. (minor revision) PlantPAN

2. T. Z. Chang, J.T. Horng, and H.D. Huang*  (2008) “RNALogo: a new approach to display structural RNA alignment”, Nucleic Acids Research, vol. 36, W91-W96. (SCI, impact factor: 6.317) RNALogo

3. S.D. Hsu, C.H. Chu, A.P. Tsou, S.J. Chen, H.C. Chen, Paul W.C. Hsu, Y.H. Wong, Y.H. Chen, G.H. Chen, and H.D. Huang*  (2008) "miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes"  Nucleic Acids Research, Vol 36, D165-D169.   miRNAMap

4. Paul W.C. Hsu, L.Z. Lin, S.D. Hsu, H.D. Huang*  (2007) "ViTa: a database of host microRNA targets on viruses"  Nucleic Acids Research, Vol 35, D381-D385.    ViTa

5. Y.H. Wong, T.Y. Lee, H.K. Liang, C.M. Huang, Y.H. Yang, C.H. Chu, H.D. Huang* , M.T. Ko, and J.K. Hwang (2007) "KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns"  Nucleic Acids Research, Vol 35, W588-594.   KinasePhos2

6. L.C. Wu, J.Z. Horng, H.Y. Huang, F.M. Lin, H.D. Huang, and M.F. Tsai  (2007) "Primer Design for Multiplex PCR Using a Genetic Algorithm", Soft Computing, Vol. 11, No. 9, 855-863. [link]

7. Y.C. Fang, W.H. Sun, L.C. Wu, H.D. Huang, H.F. Juan, J.T. Horng. (2006) “RINGdb: An integrated database for G protein-coupled receptors and regulators of G protein signaling” BMC Genomics,  7:317. (SCI, impact factor: 4.092)

8. Z.H. Chang†, H.D. Huang†,* († joint first authorship), Zi-Neng Chung, and J.T. Horng, (2006) "RNAMST: An efficient and flexible search tool for RNA structural homologs"  Nucleic Acids Research, Vol 34, W423-W428.  RNAMST

9. J.H. Hung†, H.D. Huang†,* († joint first authorship), and T.Y. Lee, (2006) "ProKware: an integrated software for presenting protein structural properties in protein tertiary structures" Nucleic Acids Research, Vol 34, W89-W94. ProKWare

10.         H.Y. Huang, C.H. Chien, and K.H. Jen, H.D. Huang*  (2006) "RegRNA: A regulatory RNA motifs and elements finder" Nucleic Acids Research, Vol 34, W429-W434. RegRNA

11.         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. (2006) "miRNAMap: genomic maps for miRNA genes and their target genes in vertebrate genomes"  Nucleic Acids Research, Vol 34, D135-D139. [PubMed] miRNAMap

12.         T.Y. Lee†, H.D. Huang†, * († joint first authorship), J.H. Hung, Y.S. Yang, and T.H. Wang*. (2006) "dbPTM: An information repository of protein post-translational modification" Nucleic Acids Research, Vol. 34, D622-D627. [PubMed] dbPTM

13.         A.P. Tsou, Y.M. Sun, C.L. Liu, H.D. Huang*, and J.T. Horng*.  (2006) "Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data", IEEE Transactions on Information Technology in Biomedicine, 10(3):550-8. (SCI, impact factor: 1.575) [PubMed] RgS-Miner   

14.         Li-Cheng Wu, J.T. Horng, S.L. Huang and H.D. Huang, (2006) "Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures" , Journal of Computational Chemistry , Vol. 27, No. 6, 798-808.[PubMed] (SCI, impact Factor: 3.786)

15.         T.Y. Lee, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin. (2006) "An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints"  Journal of Computational Chemistry, Vol. 27, No. 9, 1020-32. (SCI, impact factor: 3.786). [PubMed]

16.         F.M. Lin, H.D. Huang, P.L. Chan, Y.C. Chang, and J.T. Horng, (2006) "Database to dynamically aid probe design for virus identification", IEEE Transactions on Information Technology in Biomedicine, 10 (4), 705-13. (SCI, impact factor: 1.575) [PubMed]

17.         H.D. Huang, J.T. Horng, F.M. Lin, Y.C. Chang, and C.C. Huang. (2005) "SpliceInfo: An information repository for mRNA alternative splicing in human genome ", Nucleic Acids Research, Vol. 33, D80-D85. (SCI, impact factor: 6.317) [PubMed]  SpliceInfo

18.         H.D. Huang*, T.Y. Lee, S.W. Tseng,  and J.T. Horng. (2005) "KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites" Nucleic Acids Research, Vol. 33, W226-229.  (SCI, impact factor: 6.317) [PubMed] KinasePhos

19.         H.D. Huang, T.Y. Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou. (2005) "MultiProtIdent: identifying proteins using database search and protein-protein interactions", Journal of Proteome Research, 4(3), 690-697 (SCI, impact factor: 6.917) [PubMed] MultiProtIdent

20.         H.D. Huang*, T.Y. Lee,  S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou. (2005) "Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites." Journal of Computational Chemistry, Vol. 26, pp. 1032-1041. (SCI, impact factor: 3.786) [PubMed]

21.         H.D. Huang*, J.T. Horng, and S.F. Fang. (2005) "Discovering common of structural motifs from SSU 16 S ribosomal RNA secondary structures," International Journal on Artificial Intelligence Tools, Vol. 14, No. 4, pp. 621-639. [Abstract]

22.         H.D Huang, J.T. Horng, Y.M. Sun, and A.P. Tsou. (2004) "Identifying transcriptional regulatory sites in the human genome using an integrated system," Nucleic Acids Research, Vol. 32, No. 6, pp. 1948-56.  (SCI, impact factor: 6.317) [PubMed] RgS-Miner

23.         F.M. Lin, H.D. Huang, YC, Chang, J.T. Horng. (2004) "i-Genome: A database to summarize oligonucleotide data in genomes", BMC Genomics, Vol. 5, No. 1, pp.78. (SCI, impact factor: 4.092) [PubMed] i-Genome

24.         J.T. Horng, K. C. Hu, L. C. Wu, H. D. Huang, F. M. Lin, H. C. Lai, and T. Y Chu. (2004) “Identification of the combination of susceptibility genetic factors for cervical cancer” IEEE Transactions on Information Technology in Biomedicine, Vol 8, No.1, pp. 59-66. (SCI, impact factor: 1.575) [PubMed]

25.         J.T. Horng, H.D. Huang, T.S. Tsou, J.Y. Hong, and B.J. Liu. (2004) “A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome,” Journal of Information Science and Engineering, Vol. 20, No. 6, pp. 1141- 1159. (SCI, EI) [FullText]

26.         S.L. Huang, LC. Wu, H.D. Huang, H.K. Liang, M.T. Ko, and J.T. Horng. (2004) “A probabilistic method to correlate ion-pairs with protein thermostability.” Applied Bioinformatics, Vol. 3, No. 1, pp. 21-29.

27.         Y.M. Sun, H.D. Huang, J.T. Horng, A.P. Tsou, and S.L. Huang. (2004) "A biological data warehousing, analyzing and mining system for identifying transcriptional regulatory sites in human genome," Lecture Notes in Computer Sciences 3180: 751-760. (SCI)

28.         H.D. Huang, J.T. Horng, C.C. Lee, and B.J. Liu. (2003) “ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag data,” Genome Biology, Vol. 4, No. 4: R29. (SCI, impact factor: 9.71) [PubMed] ProSplicer

29.         J.T. Horng, F.M. Lin, J.H. Lin, H.D. Huang, and B.J. Liu. (2003) “Database of repetitive elements in complete genomes and data mining using transcription factor binding sites,” IEEE Transactions on Information Technology in Biomedicine (TITB), Vol. 7, No. 2, pp. 93-100. (SCI, impact factor: 1.575) [PubMed]