Hsien-Da Huang, associate professor

　

Department of Biological Science & Technology,
Institute of Bioinformatics and Systems Biology
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), ISBlab BBS

[Resources/ Publication]

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[MicroRNA Regulation: Databases and Tools]

 

Recent works have demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. 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 = 6.954). 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 71 times during last two years.

 

 

figure-2[Protein Post-translational Modification: Database and Tools]

Protein Post-Translational Modification (PTM) plays an essential role in cellular control mechanisms that adjust protein physical and chemical properties, folding, conformation, stability and activity, thus also altering protein function. Four articles in this field were published in Nucleic Acids Research (2007 SCI Impact = 6.954). dbPTM is a comprehensive information repository of protein post-translational modification (PTM) (Nucl Acids Res, 2006). Furthermore, we developed KinasePhos [1.0, 2.0], which is a web tool for identifying protein kinase-specific phosphorylation site (Nucl Acids Res, 2005, 2007, J. Comp Chem 2005). Besides, ProKware was designed as an integrated software for presenting protein structural properties in protein tertiary structures (Nucl Acids Res, 2006). These database and tools were totally cited more than 50 times during last three years.

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Resources

 

 

 

Publications

2009

1.      C.H. Chou†,, W.C. Chang†, († joint first authorship), C.M. Chiu, C.C. Huang, and H.D. Huang* (2009) “FMM: a web server for metabolic pathway reconstruction and comparative analysis”, Nucleic Acids Research, Vol. 37. (in press) (SCI, impact factor: 6.954) [PubMed]

2.      T.H. Chang, H.D. Huang*, L.C. Wu, C.T. Yeh, B.J. Liu, J.T. Horng* (2009) “Computational Identification of Riboswitches Based on RNA Conserved Functional Sequences and Conformations”, RNA (SCI, impact factor: 5.83) (in press)

3.      W.C. Tsai†,, Paul W.C. Hsu†,, T.C. Lai†,  († joint first authorship), G.Y. Chau, C.W. Lin, C.M. Chen, C.D. Lin, Y.L. Liao, J.L. Wang, Y.P. Chau, M.T. Hsu, M. Hsiao*, H.D. Huang*, A.P. Tsou*. (2009) “MicoRNA-122, a tumor suppressor microRNA that regulates intra-hepatic metastasis of hepatocellular carcinoma” Hepatology Vol. 49, No. 5, pp. 1571-1582. (SCI, impact factor: 10.734) (in press) *(Share equal contribution with Correspondence Author) [PubMed]

4.      D.M. Shien†, T.Y. Lee† († joint first authorship), W.C. Chang, J.B.K. Hsu, J.T. Horng, P.C. Hsu, T.Y. Wang and H.D. Huang*. (2009) “Incorporating Structural Characteristics for Identification of Protein Methylation Sites” Journal of Computational Chemistry Vol. 30, No. 9, pp. 1532-1543. (SCI, impact factor: 4.297)  [PubMed]

5.      W.C. Chang, T.Y. Lee, D.M. Shien, J. B.K. Hsu, P.C. Hsu, T.Y. Wang, J.T. Horng, H.D. Huang* and R.L. Pan* (2009) “Incorporating support vector machine for identifying protein tyrosine sulfation sites” Journal of Computational Chemistry (SCI, impact factor: 4.297) (in press) [PubMed]

6.      H.Y. Huang, H.Y. Chang, C.H. Chou, C.P. Tseng, S.Y. Ho, and H.D. Huang*. (2009) “sRNAMap: Genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes” Nucleic Acids Research, vol 37, D150-D154. (SCI, impact factor: 6.954). [PubMed]

7.      L.C. Wu,  H.D. Huang, Y.C. Chang, Y.C. Lee, J.T. Horng*. (2009) “Detecting LTR structures in human genomic sequences using profile hidden Markov models” Expert Systems with Applications, Vol. 36, No. 1, pp. 668-674. (SCI, impact factor: 1.177, (11/60=18%) in OPERATIONS RESEARCH & MANAGEMENT SCIENCE)

8.      L.C. Wu, J.X. Lee, H.D. Huang, B.J. Liu, J.T. Horng*. (2009) “An expert system to predict protein thermostability using decision tree” Expert Systems with Applications, Vol. 36, No. 5, pp. 9007-9014. (SCI, impact factor: 1.177)

9.      T.Y. Lee, J.B.K. Hsu, W.C. Chang, T.Y. Wang, P.C. Hsu, and H.D. Huang*. (2009) “A Comprehensive Resource for Integrating and Displaying Protein Post-Translational Modifications”, BMC Research Notes (in press)

 

2008

10.   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, 9:561. (SCI, impact factor: 4.18) [PubMed]

11.   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: 6.954)  [PubMed]

12.   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.  (SCI, impact factor: 6.954). [PubMed] (citations: 5)

13.   L.C. Wu, J.T. Horng*, H.D. Huang, W.L. Chen, (2008) “Identifying discriminative amino acids within the hemagglutinin of human influenza A H5N1 virus using a decision tree”, IEEE Transactions on Information Technology in Biomedicine, 12(6), 689-95. (SCI, impact factor: 1.436) [PubMed]

 

2007

14.   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. (citations: 7)

15.   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.    (SCI, impact factor: 6.954). [PubMed] (citations: 8)

16.   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.

 

2006

17.   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) [PubMed]

18.   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.  [PubMed] (citations: 4)

19.   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. [PubMed]

20.   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. [PubMed] (citations: 15)

21.   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] (citations: 40)

22.   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] (citations: 15)

23.   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: 1.436) [PubMed]  

24.   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: 4.297)

25.   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: 4.297). [PubMed]

26.   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: 1.436) [PubMed]

 

2005

27.   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: 6.954) [PubMed]  (citations: 16)

28.   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: 6.954) [PubMed] (citations: 32)

29.   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]

30.   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: 4.297) [PubMed] (citations: 10)

31.   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]

 

2004~2002

32.   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: 6.954) [PubMed] (citations: 8)

33.   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]

34.   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: 1.436) [PubMed]

35.   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]

36.   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.

37.   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)

38.   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] (citations: 17)

39.   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: 1.436) [PubMed]

40.   J.T. Horng, H.D. Huang, S.H. Wang, M.Y. Chen, J.K. Hwang, and S.L. Huang. (2003) “Computing motif correlations in proteins,” Journal of Computational Chemistry, Vol. 24, No. 16, pp. 2032-43. (SCI, impact factor: 4.297) [PubMed]

41.   H.D. Huang, H.L. Chang, T.S. Tsou, B.J. Liu, and J.T. Horng. (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 (SCI, EI)  [FullText]

42.   J.T. Horng, H.D. Huang, K.Y. Tseng, T.S. Tsou, and B.J. Liu. (2003) “Mining correlations of tissue gene expression from digital expression profiles of human tissues,” Journal of Information Science and Engineering, Vol. 19, No. 6, pp. 909-921. (SCI, EI)  [FullText]

43.   J.T. Horng, H.D. Huang, F.M. Lin, L.C. Wu, and S.L. Huang. (2002) “The repetitive sequence database and mining putative regulatory elements in gene promoter regions.” Journal of Computational Biology, Vol. 9, No. 4, pp. 621-640. (SCI, impact factor: 3.241) [PubMed] (citations: 12)

44.   J.T. Horng, H.D. Huang, S.L. Huang, U.C. Yang, and Y.C. Chang. (2002) “Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae,” In Silico Biology, Vol. 2, No. 3, pp. 263-273. [PubMed] [FullText]