====== Publication ======


**CV in PDF**: {{:pi:cv_2015.pdf|}} (Jan. 2015)

See also
  * [[https://www.researchgate.net/profile/Hsuan-Cheng_Huang/|HCH]] @ ResearchGate
  * [[https://www.researchgate.net/profile/Hsuan-Cheng_Huang2/|HCH]] @ ResearchGate
  * [[http://scholar.google.com/citations?user=K-h6CjIAAAAJ&hl=en|HCH]] @ Google Scholar

===== Selected Journal Papers / 期刊論文 =====

1.Tseng CW, Yang JC, Chen CN*, Huang HC, Chuang KN, Lin CC, Lai HS, Lee PH, Chang KJ, Juan HF*. “Identification of 14-3-3β in human gastric cancer cells and its potency as a diagnostic and prognostic biomarker.” Proteomics, in press.

2.Chen CY, Chen ST, Fuh CS, Juan HF*, Huang HC*, “Coregulation of transcription factors and microRNAs in human transcriptional regulatory network.” BMC Bioinformatics, 12 (Suppl 1), S41 (2011).

3.Lin CC, Hsiang JT, Wu CY, Oyang YJ, Juan HF*, Huang HC*, “Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy.” BMC Syst Biol, 4, 138 (2010).

4.Wu TH, Chang IYF, Huang HC*, Ng WV*, “Modularity of Escherichia coli sRNA regulation revealed by sRNA-targets and protein network analysis.” BMC Bioinformatics, 11 (Suppl 7), S11 (2010).

5.Hsu JW, Huang HC, Lee TY, Chen ST, Wong CH, Juan HF, “Ganoderma lucidum polysaccharides induce macrophage-like differentiation in human leukemia THP-1 cells via caspase and p53 activation.” Evid.-based Complement Altern. Med., doi: 10.1093/ecam/nep107(2009).

6.Hwang YC, Lin CC, Chang JY, Mori H, Juan HF*, Huang HC*, “Predicting essential genes based on network and sequence analysis.” Mol BioSyst, 5, 1672–1678 (2009).

7.Lin CC, Juan HF, Hsiang JT, Hwang YC, Mori H*, Huang HC*, “Essential core of protein-protein interaction network in Escherichia coli.” J Proteome Res, 8, 1925–1931 (2009).

8.Hsu CW, Juan HF*, Huang HC*, “Characterization of microRNA-regulated protein-protein interaction network.” Proteomics, 8, 1975-9 (2008).

9.Chen HW†, Huang HC†, Lin YS, Chang KJ, Kuo WH, Hwa HL, Hsieh FJ*, Juan HF*, “Comparison and identification of estrogen-receptor related gene expression profiles in breast cancer of different ethnic origins.” Breast Cancer: Basic and Clinical Research, 1, 35-49 (2008).

10.Fang YC, Huang HC*, Juan HF*, “MeInfoText: associated gene methylation and cancer information from text mining” BMC Bioinformatics 9, 22 (2008). [Highly accessed]

11.Cheng KC†, Huang HC†, Chen JH, Hsu JW, Cheng HC, Ou CH, Yang WB, Chen ST, Wong CH, Juan HF*. “Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction.” BMC Genomics 8, 411 (2007). [Highly accessed]

12.Huang TC, Huang HC, Chang CC, Chang HY, Ou CH, Hsu CH, Chen ST, Juan HF*. “An apoptosis-related gene network induced by novel compound-cRGD in human breast cancer cells.” FEBS Lett 581, 3517-22 (2007).

13.Leu JH, Chang CC, Wu JL, Hsu CW, Hirono I, Aoki T, Juan HF, Lo CF, Kou GH*, Huang HC*. “Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon.” BMC Genomics 8, 120 (2007). [Highly accessed]

14.Tseng HW, Juan HF, Huang HC, Lin JY, Sinchaikul S, Lai TC, Chen CF, Chen ST, Wang GJ. “Lipopolysaccharide-stimulated responses in rat aortic endothelial cells by a systems biology approach.” Proteomics 6, 5915-28 (2006).

15.Chen YR, Juan HF, Huang HC, Huang HH, Lee YJ, Liao MY, Tseng CW, Lin LL, Chen JY, Wang MJ, Chen JH, Chen YJ. “Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells.” J Proteome Res 5, 2727-42 (2006).

16.Lee TY, Horng JT, Juan HF, Huang HD, Wu LC, Tsai MF, Huang HC. “An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.” J Comput Chem 27, 1020-32 (2006).

17.Juan HF, Wang IH, Huang TC, Li JJ, Chen ST, Huang HC*. “Proteomics analysis of a novel compound: cyclic RGD in breast carcinoma cell line MCF-7.” Proteomics 6, 2991-3000 (2006).

18.Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H. “Large-scale identification of protein-protein interaction of Escherichia coli K-12.” Genome Res 16, 686-91 (2006).

19.Juan HF, Chang SC, Huang HC, Chen ST. “A new application of microwave technology to proteomics.” Proteomics 5, 840-2 (2005).

20.Wu CC, Huang HC*, Juan HF, Chen ST*. “GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data.” Bioinformatics 20, 3691-3 (2004).

21.Wu CY, Jan JT, Ma SH, Kuo CJ, Juan HF, Cheng YS, Hsu HH, Huang HC, Wu D, Brik A, Liang FS, Liu RS, Fang JM, Chen ST, Liang PH, Wong CH. “Small molecules targeting severe acute respiratory syndrome human coronavirus.” Proc Natl Acad Sci U S A 101, 10012-7 (2004).

22.Chang DT, Chen CY, Chung WC, Oyang YJ, Juan HF, Huang HC. “ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.” Nucleic Acids Res 32, W76-82 (2004).

23.P. Chang, et al. (Belle Collaboration), “Measurements of branching fractions and CP asymmetries in B → eta h decays”, Phys. Rev. D 71, 091106 (2005).

24.M.-Z. Wang, et al. (Belle Collaboration), “Observation of B+ → pppi+, B0 → ppK0, and B+ → ppK*+”, Phys. Rev. Lett. 92, 131801 (2004).

25.H.-C. Huang*, et al. (Belle Collaboration), “Evidence for B→phi phi K”, Phys. Rev. Lett. 91, 241802 (2003).

26.M.-Z. Wang, et al. (Belle Collaboration), “Observation of B0 → p Lambda(pi)(-)”, Phys. Rev. Lett. 90, 201802 (2003).

27.KEK-E246 Collaboration, V.V. Anisimovsky, et al., “First measurement of the T -violating muon polarization in the decay K+ →μ+ nu gamma ”, Phys. Lett. B562, 166 (2003).

28.R.-S. Lu, …, H.-C. Huang*, et al. (Belle Collaboration), “Observation of B→omega K Decay”, Phys. Rev. Lett. 89, 191801 (2002).

29.K. Abe, et al. (Belle Collaboration), “Observation of B→p pbar K”, Phys. Rev. Lett. 88, 181803 (2002). [Equal contribution to the corresponding author]

30.K. Abe, et al. (Belle Collaboration), “Observation of the Color-Suppressed Decay B→D0 pi0”, Phys. Rev. Lett. 88, 052002 (2002). [Equal contribution to the corresponding author]

31.Belle Collaboration, A. Abashian et al., “The Belle detector”, Nucl. Instr. and Meth. A479, 117 (2002).

32.K. Abe, et al., (Belle Collaboration), “Measurement of the branching fraction for B→η'K and search for B→η'π+”, Phys. Lett. B517, 309 (2001).

33.M.Z. Wang, H.C. Huang, et al. “Beam test of the BELLE extreme forward calorimeter at KEK”, Nucl. Instr. and Meth. A455, 319 (2000).

34.M. Abe, et al. (KEK-E246 Collaboration), “Search for T-Violating Transverse Muon Polarization in K+ → π0 μ+ ν Decay Using Stopped Kaons”, Phys. Rev. Lett. 83, 4253 (1999).

35.K. C. Peng, et al., “Performance of undoped BGO crystals under extremely high dose conditions”, Nucl. Instr. and Meth. A427, 524 (1999).

36.H.C. Huang, K.C. Peng, S.K. Sahu, K. Ueno, Y.H. Chang, C.H. Wang, W.S. Hou, “Measurement of radiation damage on an epoxy based optical glue”, Nucl. Instr. and Meth., A385, 559 (1997).

37.S. K. Sahu, et al., “Radiation hardness of undoped BGO crystals”, Nucl. Instr. and Meth. A388, 144 (1997).

38.K. C. Peng, et al., “Measurement of radiation damage on an optical reflector”, Nucl. Instr. and Meth. A384, 544 (1997).

39.W.S. Hou and H.C. Huang, “Singlet charge 2/3 quark hiding the top: Tevatron and LEP implications”, Phys. Rev. D 51, 5285 (1995).

40.S.-H. Chiou, M.-H. Chuang, C.-C. Hung, H.-C. Huang, S.-T. Chen, K.-T. Wang, C.-L. Ho, “Inhibition of Protein Kinase C by Snake Venom Toxins: Comparison of Enzyme Inhibition, Lethality and Hemolysis among Different Cardiotoxin Isoforms”, Biochem. Mol. Biol. Int. 35, 1103 (1995).

41.S.-H. Chiou, Hung CC, Huang HC, Chen ST, Wang KT, Yang CC., “Sequence Comparison and Computer Modeling of Cardiotoxins and Cobratoxin Isolated from Taiwan Cobra”, Biochemical and Biophysical Research Communications 206, 22 (1995).

42.S.-T. Chen, et al., “Probing the S-1’ Subsite Selectivity of an Industrial Alkaline Protease in Anhydrous t-Butanol”, Bioorg. Med. Chem. Lett., 3, 727-733 (1993).

43.S.T. Chen, C.C. Tu, S.Y. Chen, H.C. Huang, K.T. Wang, “Investigating the S-2 Subsite Selectivity of Alkaline Proteases in Hydrolysis of Diastereo-Peptide Esters and Molecular-Modeling Interpretation”, Bioorg. Med. Chem., 1, 361-367 (1993).

===== Selected Conference Proceedings / 研討會論文 =====

==== Peer-reviewed ====

1.Chang, D. T.-H, Chen, C.-Y., Chung, W.-C., Oyang, Y.-J., Juan, H.-F., Huang, H.-C, “An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures”, Proceedings of the IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE2004), Taichung, Taiwan, ROC, May 19-21, 2004.

2.H.-C. Huang*, “Baryonic B Decays at Belle”, Proceedings of the International Europhysics Conference on High Energy Physics, Aachen, Germany, July 17-23, 2003; Eur. Phys. J. C33, S216-S218; DOI: 10.1140/epjcd/s2003-03-110-9. [SCI, 3.486]

3.H.C. Huang*, “Performance of a Small Angle BGO Calorimeter at Belle”, Proceedings of the 10th International Conference on Calorimetry in High Energy Physics, Pasadena, USA, March 25-29, 2002.

Invited 

4.H.-C. Huang*, “Elucidating the essentiality of essential genes”, NCTS Symposium on Network Biology, Hsinchu, Taiwan, Nov. 11, 2005.

5.H.-C. Huang*, “Identification of RNA-Binding Protein Residues Using Machine Learning Approaches”, Proceedings of the Bioinformatics in Taiwan 2005 Symposium and Workshop (BIT2005), Tainan, Taiwan, Sep. 9-10, 2005.

6.H.-C. Huang*, “Identification of RNA-Binding Protein Residues Using Machine Learning Approaches”, Proceedings of the 5th Emerging Information Technology Conference (EITC 2005), Taipei, Taiwan, Aug. 15-16, 2005.

7.H.-C. Huang*, “Systems Biology Study of a Novel Drug on Cancer Cells”, Proceedings of the First K.I.T. Bioinformatics Workshop and Symposium, Iizuka, Fukuoka, Japan, December 9-11, 2004.

8.H.-C. Huang*, “Proteomics Study of Cyclic RGD in Breast Cancer Cell Using Bioinformatics Techniques”, Proceedings of Proteomics Symposium and 2004 Annual Meetings of Taiwan Bioinformatics Society, Chung-Li, Taiwan, Mar. 5, 2004.

9.H.C. Huang* (for the Belle Collaboration), “Rare B Decays at Belle”, Proceedings of the XXXVII Rencontres de Moriond on Electroweak Interactions and Unified Theories, Les Arcs, France, March 9-16, 2002; hep-ex/0205062.

==== Contributed ====

10.Lin, N., Chiou, S.-H., Juan, H.-F., Huang, H.-C., “Bioinformatics Approach to Study the Correlation between Gene Expression Profiles and Protein-Protein Interactions Using Matrices”, Fourth Asia Pacific Bioinformatics Conference, , Taipei, Taiwan, Feb. 13-16, 2006.

11.Ou, C.-H., Chang, C.-C., Hsia, H.-C., Wang, F.-S., Juan, H.-F.*, Huang, H.-C.*, “BSIP – a Web Server for Systems-Biology Structure Identification Program Development”, Fourth Asia Pacific Bioinformatics Conference, , Taipei, Taiwan, Feb. 13-16, 2006.

12.Bow, Y.-Y., Chang, J.-Y., Juan, H.-F., Mori, H., Huang, H.-C.*, “Elucidating the essentiality of essential genes in E. coli K-12”, Fourth Asia Pacific Bioinformatics Conference, , Taipei, Taiwan, Feb. 13-16, 2006.

13.Hwang, Y.-C., Lin, C.-C., Juan, H.-F., Mori, H., Huang, H.-C.*, “Topologial Characteristics of Protein Interaction Network and Roles of Essential Genes in E. coli K-12 Fourth Asia Pacific Bioinformatics Conference, , Taipei, Taiwan, Feb. 13-16, 2006.

14.Li, J.-J., Juan H.-F.*, Chung, I.-F., Huang, H.-C.*, “Identification of RNA-binding Protein Residues Using Machine Learning Approaches”, Fourth Asia Pacific Bioinformatics Conference, , Taipei, Taiwan, Feb. 13-16, 2006.

15.Bow, Y.-Y., Chang, J.-Y., Juan, H.-F., Mori, H., Huang, H.-C.*, “Elucidating the essentiality of essential genes in E. coli K-12”, Sixth International Conference on Systems Biology, Boston, MA, USA, Oct. 19-24, 2005.

16.Huang, T.-C., Chang, C.-C., Huang, H.-C., Juan, H.-F.*, “Cyclic RGD-induced cell death in human breast carcinoma cell line MCF-7: the influence of caspase pathway”, Sixth International Conference on Systems Biology, Boston, MA, USA, Oct. 19-24, 2005.

17.Tseng, H.-W., Chen, S.-T., Juan, H.-F., Huang, H.-C., Chen, C.-F., and Wang, G.-J., “High-throughput Proteomic Analysis of the Anti-inflammatory Effect of Berberine in Rat Cultured Vascular Endothelial Cells” (Abstract#O100, Oral Presentation) 20th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, Mar. 26-27, 2005.

18.Chang, S.-C., Huang, H.-C., Chen, S.-T., and Juan, H.-F., “A Subcellular Proteomics Analysis of Human Myeloid Leukemia Cells Differentiation to Macrophages Using Microwave Technology Combined with Mass Spectrometry” (Abstract#O87, Oral Presentation), 20th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, Mar. 26-27, 2005.

19.Huang, T.-C., Huang, H.-C., Chen, S.-T., and Juan, H.-F.*, “Cyclic RDG-induced Cell Death in Human Breast Carcinoma (MCF-7) Cells: the Influence of Caspase Pathway” (Abstract#O80, Oral Presentation) 20th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, Mar. 26-27, 2005.

20.Li, J.-J. Juan, H.-F., Ko, R.-S., Chung, I-F., Huang, H.-C.* (2005) “Identification of RNA-binding Protein Residues Using Machine Learning Approaches” (Abstract#O39, Oral Presentation), 20th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, Mar. 26-27.

21.Li, J.-J., Huang, H.-C.*, Ko, R.-S., Chen, S.-T., Juan, H.-F.*, “BGSSJ: an Interactive Tool for Biological Interpretation of Gene Expression and Proteomics Data” (Abstract#258), Bioinformatics in Taiwan, Taipei, Taiwan, September 9-11, 2004. [2nd Prize]

22.Peng, C.-L., Lin, Y.-C., Huang, H.-C., Kao, C. -Y., Chen, S.-T., and Juan, H.-F., “ProtExt, a Web-based Protein-protein Interaction Extraction System for PubMed Abstracts”, 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB 2004), Glasgow, UK, Jul. 31 - Aug. 4, 2004.

23.Juan, H.-F.*, Chang, S.-C., Huang, H.-C., Chen, S.-T., “A New Application of Microwave Technology to Proteomics”, International Symposium on Microwave Science and Its Application to Related Fields 2004, Takamatsu, Japan, Jul. 26-30, 2004. [Financial Support]

24.Wang, I-H., Huang, H.-C., Chen, S.-T., Juan, H.-F.*, “Proteomic Analysis of a Novel Compound – Cyclic RGD in Breast Carcinoma Cell Line MCF-7 Using Biomic Approach” (Abstract#PB18) 3rd International Proteomics Conference 2004 (IPC’03), Taipei, Taiwan, May 15-17, 2004.

25.Tseng, H. W., Wang, G. J., Juan, H.-F., Chen, C. F., Huang, H. C., and Chen, S. T., “Systems Biology Study of LPS-induced Inflammatory Responses Endothelial Cells”  (Abstract#PB14) 3rd International Proteomics Conference 2004 (IPC’03), Taipei, Taiwan, May 15-17, 2004.

26.Li, J.-J., Huang, H.-C., Ko, R.-S. Chen, S.-T., Juan, H.-F.*, "BGSSJ: an Interactive Tool for Biological Interpretation of Gene Expression and Proteomics Data" (Abstract#PA12) 3rd International Proteomics Conference 2004 (IPC’03), Taipei, Taiwan, May 15-17, 2004. [Top 10 Prize]

27.Peng, C.-L., Lin, Y.-C., Huang, H.-C., Kao, C. -Y., Chen, S.-T., and Juan, H.-F.*, “ProtExt: a Web-based Protein-protein Interaction Extraction System for PubMed Abstract” (Abstract#PA05), 3rd International Proteomics Conference 2004 (IPC’03), Taipei, Taiwan, May 15-17, 2004.

28.Juan, H.-F., Huang, H.-C., and Chen, S.-T., "The Molecular Effect of cyclic-RGD peptide on MCF-7 Cells"(Poster #149) The 4th International Conference on Systems Biology, Saint Louis, MO, USA, November 5-9, 2003.

29.H.C. Huang* (for the Belle Collaboration), “K+K− and K0SK0S production in two-photon collisions at Belle”, Proceedings of the 4th International Conference on B Physics and CP Violation (BCP4), Ise-Shima, Japan, Feb. 19-23, 2001, pp.351-354; hep-ex/0104024. [Best Poster Award]

30.Belle Collaboration, A. Abashian et al., “Measurement of K0SK0S production in two-photon collisions with Belle”, BELLE-CONF-0018, contributed to the XXXth International Conference on High Energy Physics, Osaka, July 2000.

31.H.-C. Huang*, “Proteomics Study of Cyclic RGD in Breast Cancer Cell Using Bioinformatics Techniques”, Proceedings of Proteomics Symposium and 2004 Annual Meetings of Taiwan Bioinformatics Society, Chung-Li, Taiwan, Mar. 5, 2004.

32.H.C. Huang* (for the Belle Collaboration), “Rare B Decays at Belle”, Proceedings of the XXXVII Rencontres de Moriond on Electroweak Interactions and Unified Theories, Les Arcs, France, March 9-16, 2002; hep-ex/0205062.

===== Books (Chapters) / 專書（章節） =====

1.Juan, H.-F. and Huang, H.-C. (2007) "Bioinformatics: Microarray Data Clustering and Functional Classification" (Chap. 25) in Microarrays (2nd ed): Applications and Data Analysis, ed. Jang B. Rampal, Humana Press, pp. 405-416 (2007).

2.Baba, T., Huang, H.-C., Datsenko, K, Wanner, B.L., and Mori H., “The Applications of Systematic In-frame, Single-gene Knockout Mutant Collection in Escherichia coli K-12” (Chap. 12) in Microbial Gene Essen-tiality — Protocols and Bioinformatics, ed. Osterman, Andrei L. & Gerdes, Svetlana, HumanaMethods in Molecular Biology, Humana Press, pp. 183-194 (2007).