1.Lin, L.-L., Wang, Y.-H., Lai, C.-Y., Chau, C.-L., Su, G.-C., Yang, C.-Y., Lou, S.-Y., Chen, S.-K., Hsu, K.-H., Lai, Y.-L., Wu, W.-M., Huang, J.-L., Liao, C.-H. and Juan, H.-F.* “Systems biology of meridians, acupoints, and Chinese herbs in disease” Evidence-Based Complementary and Alternative Medicine (in press)

2.Chen, C.-Y., Chen, S.-T., Juan, H.-F.* and Huang, H.-C.* “Lengthening of 3’UTR Increases Morphological Complexity in Animal Evolution” Bioinformatics (in revision)

3.Hu, C.-W., Lin, M.-H., Huang, H.-C., Ku, W.-C., Yi, T.-H., Tsai, C.-F., Chen, Y.-J., Sugiyama, N., Ishihama, Y.*, Juan, H.-F.*, and Wu, S.-H.* “Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production” Journal of Proteome Research (in press)

4.Fu, S.-C., Huang, H.-C., Horton, P.* and Juan, H.-F.* “ValidNESs: a database of validated leucine-rich nuclear export signals” Nucleic Acids Research (accepted)

5.Lu, K.-Y., Tao, S.-C., Yang, T.-C., Ho, Y.-H., Lee, C.-H., Lin, C.-C., Juan, H.-F., Huang, H.-C. , Yang, C.-Y., M,-S, Chen, H. Zhu*, and C.-S. Chen* “Profiling lipid-protein interactions using non-quenched fluorescent liposomal nanovesicles and proteome microarrays” Molecular and Cellular Proteomics (in press)

6.Lin, L.-L., Huang, H.-C., Ogihara, S., Wang, J.-T., Wu, M.-C., McNeil, P. L.*, Chen, C.-N.* and Juan, H.-F.* (2012) “Helicobacter pylori disrupts host cell membranes, initiating a repair response and cell proliferation” International Journal of Molecular Sciences 13:10176-10192.

7.Lin, L.-L., Huang, H.-C.*, and Juan, H.-F.* (2012) “Revealing the molecular mechanism of gastric cancer marker Annexin A4 in cancer cell proliferation using exon arrays” PLoS ONE 7(9):e44615.

8.Chang, H.-Y., Huang, H.-C., Huang, T.-C., Yang, P.-C.*, Wang, Y.-C.*, and Juan, H.-F.* (2012) “Ectopic ATP synthase blockade suppresses lung adenocarcinoma growth by activating the unfolded protein response” Cancer Research 72(18):4696-4706.

9.Lin, L.-L., Huang, H.-C.* and Juan, H.-F.* (2012) “Discovery of biomarkers for gastric cancer: a proteomics approach” Journal of Proteomics 75(11):3081-3097.

10.Chang, M.-W., Lo, J.-M., Juan, H.-F., H.-Y. Chang, Chuang, C.-Y. (2012) “Combination of RGD compound and low-dose Paclitaxel induces apoptosis in human glioblastoma cells” PLoS ONE 7(5):e37935

11.Tseng, C.-W., Huang, H.-C., Shih, A. C.-C., Chang, Y.-Y., Hsu, C. C., Chang, J.-Y., Li, W.-H.* and Juan, H.-F.* (2012) “Revealing the anti-tumor effect of artificial miRNA p-27-5p on human breast carcinoma cell line T-47D” International Journal of Molecular Sciences 13:6352-6369.

12.Lin, C.-C., Chen, Y.-J., Chen, C.-Y., Oyang, Y.-J., Juan, H.-F.* and Huang, H.-C.* (2012) “Crosstalk between transcription factors and microRNAs in human protein interaction network” BMC Systems Biology 6(1):18.

13.Shih, Y.-Y., Nakagawara, A., Lee, H., Juan, H.-F., Jeng, Y.-M., Lin, D.-T., Yang, Y.-L., Tsay, Y.-G., Huang, M.-C., Pan, C.-Y. *, Hsu, W.-M.*, and Liao, Y.-F.* (2012) “Calreticulin mediates nerve growth factor-induced neuronal differentiation” Journal of Molecular Neuroscience 47(3):571-81.

14.Hu, C.-W., Chang, Y.-L., Chen, S. J., Kuo-Huang, L.-L., Liao, J. C., Huang, H.-C.*, Juan, H.-F.* (2011) “Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach” PLoS ONE 6:e28329.

15.Huang, T.-C., Chang, H.-Y., Chen, C.-Y., Wu, P.-Y., Lee, H., Liao, Y.-F., Hsu, W.-M.*, Huang, H.-C.*, Juan, H.-F.* (2011) “Silencing of miR-124 induces neuroblastoma SK-N-SH cell differentiation, cell cycle arrest and apoptosis through promoting AHR” FEBS Letters 585:3582-3586.

16.Tsai, S.-R.#, Huang, T.-C.#, Liang, C.-M., Chang, H.-Y., Chang, Y.-T., Huang, H.-C., Juan, H.-F.*, Lee, S.-C.* (2011) “The effect of narrow bandwidth infrared radiation on the growth of Escherichia coli” Applied Physics Letters 99, 163704. (# equal contribution)

17.Shih, Y.-Y., Pan, C,-Y, Lee, H., Juan, H.-F., A. Nakagawara, Clagett-Dame, M., Tsay, Y.-G., Hsieh, F.-J., Hsu, W.-M.*, Liao, Y.-F. * (2011) “Nuclear GRP75 binds retinoic acid receptors to promote neuronal differentiation of neuroblastoma” PLoS ONE 6(10):e26236

18.Chen, S.-T., Jeng, Y.-M., Chang, C.-C., Chang, H.-H., Huang, M.-C., Juan, H.-F., Hsu, C.-H., Lee, H.-Y., Liao, Y.-F, Lee, Y.-L., Hsu, W.-M.*, Lai, H.-S.* (2011) “Insulin-like growth factor II mRNA-binding protein 3 expression predicts unfavorable prognosis in patients with neuroblastoma” Cancer Science 102:2191-2198.

19.Lee, C.-H., Huang, H.-C.*, Juan, H.-F.* (2011) “Reviewing ligand-based rational drug design: the search for an ATP synthase inhibitor” International Journal of Molecular Sciences 12:5304-5318.

20.Chen, C.-M., Lin, C.-H., Juan, H.-F., Hu, F.-J., Hsiao, Y.-C., Chang, H.-Y., Chao, C.-Y., Chen, I.-C., Lee, L.-C., Wang, T.-W., Chen, Y.-T., Chen, Y.-T., Lee-Chen, G.-J.*, Wu, Y.-R. (2011) ATP13A2 variability in Taiwanese Parkinson's disease. Am J Med Genet B Neuropsychiatr Genet. 156:720-729.

21.Tseng, C.-W., Lin, C.-C., Chen, C.-N.*, Huang, H.-C.*, Juan, H.-F.* (2011) “Integrative network analysis reveals active microRNAs and their functions in gastric cancer” BMC Systems Biology 5:99. (Highly accessed)

22.Tseng, C.-W., Yang, J.-C., Chen, C.-N.*, Huang, H.-C., Chuang, K.-N., Lin, C.-C., Lai, H.-S., Lee, P.-H., Chang, K.-J., Juan, H.-F.* (2011) “Identification of 14-3-3β in human gastric cancer cells and its potency as a diagnostic and prognostic biomarker” Proteomics 11:2423-2439.

23.Chen, J.-Y., Huang, S.-M., Tang, Y.-A., Juan, H.-F., Wu, L.-W., Sun, Y.-C., Wang, S.-C., Wu, K. W., Balraj, G., Chang, T.-T., Li, W.-S.*, Cheng, H.-C.*, Wang, Y.-C.* (2011) “A novel sialyltransferase inhibitor suppresses FAK/paxillin and angiogenesis signaling and cancer metastasis.” Cancer Research, 71:473-483.

24.Chen, C.-Y., Chen, S.-T., Fuh, C.-S., Juan, H.-F.*, Huang, H.-C.*, “Coregulation of transcription factors and microRNAs in human transcriptional regulatory network”, BMC Bioinformatics, 12(Suppl 1):S41 (2011).

25.Lin, C.-C., Hsiang, J.-T., Wu, C.-Y., Oyang, Y.-J., Juan, H.-F*, Huang, H.-C.* “Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy.” BMC Systems Biology, 4:138 (2010).

26.Chang, H.-H., Lee, H.-Y., Hu, M.-K., Tsao, P.-N., Juan H.-F., Huang, M.-C., Shih, Y.-Y., Wang, B.-J., Jeng, Y.-M., Chang, C., Huang, S.-F., Y.-G. Tsay, Hsieh, F.-J., Lin, K.-H.*, Hsu, W.-M.*, and Liao, Y.-F.* (2010) “Notch1 expression predicts an unfavorable prognosis and serves as a therapeutic target of patients with neuroblastoma.” Clinical Cancer Research, 16:4411-20.

27.Hsu J.-W., Huang H.-C., Lee T.-Y., Chen S.-T., Wong C.-H., Juan H.-F.* (2009) “Ganoderma lucidum polysaccharides induce macrophage-like differentiation in human leukemia THP-1 cells via caspase and p53 activation.” Evidence-based Complementary and Alternative Medicine, doi: 10.1093/ecam/nep107.

28.Hwang Y.-C., Lin C.-C., Chang J.-Y., Mori H., Juan H.-F.*, Huang H.-C.* (2009) “Predicting essential genes based on network and sequence analysis.” Molecular BioSystems, 5:1672–1678.

29.Lin, C.-C., Juan, H.-F., Hsiang, J.-T., Hwang, Y.-C., Mori, H.*, Huang, H.-C.* (2009) “Essential core of protein-protein interaction network in Escherichia coli.” Journal of Proteome Research 8:1925–1931.

30.Chang, Y.-M., Juan, H.-F., Lee, T.-Y., Chang, Y.-Y., Yeh, Y.-M., Li, W.-H.*, Shih, A. C.-C.* (2008) “Prediction of human miRNAs using tissue-selective motifs in 3' UTRs.” Proc. Natl. Acad. Sci. U S A 105:17061-17066. (highlighted in Nature Biotechnology and featured in Science-Business eXchange SciBX).

31.Fang, Y.-C., Huang, H.-C., Chen, H.-H. and Juan, H.-F.* (2008) “TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining.” BMC Complementary and Alternative Medicine 8:58.

32.Hsu, W.-M., H.-Y. Lee, Juan, H.-F., Y.-Y. Shih, B-J. Wang, C.-Y. Pan, Y.-M. Jeng, H.-H. Chang, M.-Y. Lu, K.-H. Lin, H.-S. Lai, W.-J. Chen, Y.-G. Tsay*, Y.-F. Liao*, F.-J. Hsieh* (2008) “Identification of GRP75 as an Independent Favorable Prognostic Marker of Neuroblastoma by a Proteomics Analysis.” Clinical Cancer Research 14:6237-6245.

33.Hsu, C.-W., Juan, H.-F.*, Huang, H.-C.* (2008) “Characterization of microRNA-regulated protein-protein interaction network” Proteomics, 8:1575-1579.

34.Lin, L.-L., C.-N. Chen*, Lin, W.-C., Lee, P.-H., Chang, K.-J., Lai, Y.-P., Wang, J.-T. and Juan, H.-F.* (2008) “Annexin A4: A novel molecular marker for gastric cancer with Helicobacter pylori infection using proteomics approach.” Proteomics: Clinical Applications 2:619–634.

35.Chen, H.-W., Huang, H.-C., Lin, Y.-S., Chang, K.-J., Kuo, W.-H., Hwa, H.-L., Hsieh, F.-J.*, Juan, H.-F.* (2008) “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.

36.Tan, Y-H., Lee, K.-H., Sun, Y.-C., Juan, H.-F.* and Y.-C. Wang* (2008) “Cytotoxicity and proteomics analyses of OSU03013 in lung cancer.” Clinical Cancer Research, 14:1823-1830.

37.Huang, T.-C., Chang, H.-Y., Hsu, C.-H., Kuo, W.-H., Chang, K.-J., Juan, H.-F.* (2008) “Targeting Therapy on Breast Carcinoma by ATP Synthase Inhibitor Aurovertin B” Journal of Proteome Research 7:1433-1444. (featured in ACS Weekly News)

38.Chen, S.-T., Pan, T.-L., Juan, H.-F., Chen, T.-Y., Lin, Y.-S., Huang, C.-M.* (2008) “Breast Tumor Microenvironment: Proteomics Highlights the Treatments Targeting Secretome and Extracellular Matrix” Journal of Proteome Research, 7:1379–1387. (review)

39.Fang, Y.-C., Huang, H.-C.*, Juan, H.-F.* (2008) “MeInfoText: Associated Gene Methylation and Cancer Information from Text Mining” BMC Bioinformatics 9:22.

40.Huang, B., Ni, K.-C., Chen, S.-L., Juan, H.-F.*, Chen, Y.-M.* (2008) “Elucidating the Growth Regulation of Brassinosteroids in Mung Bean Epicotyls using a Proteomics Approach.” Proteomics Research Journal 1:1-18.

41.Lien, H.-C., Hsiao, Y.-H., Lin, Y.-S., Yao, Y.-T., Juan, H.-F., Kuo, W.-H., Hung, M.-C., Chang, K.-J., Hsieh, F.-J.* (2007) “Molecular Signatures of Metaplastic Carcinoma of the Breast by Large-Scale Transcriptional Profiling: Identification of Genes Potentially Related to Epithelial-Mesenchymal Transition.” Oncogene 26:7859-71.

42.Cheng, K.-C., Huang, H.-C., Chen, J.-H., Hsu, J.-W., Cheng, H.-C., Ou, C.-H., Yang, W.-B., Chen, S.-T., Wong, C.-H. and Juan, H.-F.* (2007) “Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction” BMC Genomics 8:411.

43.Huang, T.-C., Huang, H.-C., Chang, C.-C., Chang, H.-Y., Ou, C.-H., Hsu, C.-H., Chen, S.-T. and Juan, H.-F.* (2007) “An Apoptosis-related Gene Network Induced by Novel Compound-cRGD in Human Breast Cancer Cells.” FEBS Letters 581:3517-3522.

44.Leu, J.-H., Chang, C.-C., Wu, J.-L., Hsu, C.-W., Hirono, I., Aoki, T., Juan, H.-F., Lo, C.-F., Kou, G.-H.*, Huang H.-C.* (2007) “Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon.” BMC Genomics 8:120.

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

46.Tseng, H.-W., Juan, H.-F., Huang, H.-C., Lin, J. Y.-C., Sinchaikul, S., Chen, C.-F., Chen, S.-T.*, Wang*, G.-J. (2006) “A systems biology study of lipopolysaccharide-stimulated responses in rat aortic endothelial cell.” Proteomics 6:5915-5928.

47.Chen, Y.-R., Juan, H.-F., Huang, H.-C., Huang, H.-H., Lee, Y.-J., Liao, M.-Y., Tseng, C.-W., Lin, L.-L., M.-Y. Chen, J.-Y., Wang, M.-J., J.-H. Chen*, Y.-J. Chen* (2006) “Quantitative Proteomic and Genomic Profiling Reveals Metastasis-Related Protein Expression Patterns in Gastric Cancer Cells.” Journal Proteome Research 5:2727-2742.

48.Huang, B., Chu, C.-H., Chen, S.-L., Juan, H.-F.* and Chen, Y.-M.* (2006) “Proteomics Study of Mung Bean Epicotyl Regulated by Brassinosteroid under Chilling Condition.” Cellular & Molecular Biology Letters 11:264-278.

49.Juan, H.-F.*, Wang, I-H., Huang, T.-C., Li, J.-J., Chen, S.-T., Huang, H.-C. (2006) “Proteomics analysis of a novel compound – cyclic RGD in breast carcinoma cell line MCF-7.” Proteomics 6:2991-3000. (Cover Picture)

50.Lee, T.-Y., Horng, J.-T., Juan, H.-F., Huang, H.-D., Wu, L.-C., Lin, F.-M., Huang, H.-C (2006) “An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.” Journal of Computational Chemistry 27:1020-1032.

51.Horng, J.-T., Lee, T.-Y., Wu, L.-C., Huang, H.-D., Juan, H.-F., Lin, F.-M. (2005) “MultiProtIdent: Identifying Proteins Using Database Search and Protein-Protein Interactions.” Journal Proteome Research 4:690-697.

52.Juan, H.-F.*, Chang, S.-C., Huang, H.-C., Chen, S.-T. (2005) “A New Application of Microwave Technology to Proteomics.” Proteomics 5:840-842.

53.Wu, C.-C., Huang, H.-C., Juan, H.-F., Chen, S.-T. (2004) “GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data.” Bioinformatics 20: 3691-3693.

54.Chen, C.-Y., Oyang, Y.-J., Juan, H.-F. (2004) “Incremental generation of summarized clustering hierarchy for protein family analysis.” Bioinformatics 20:2586-96.

55.Juan, H.-F., Chen, J.-H., Hsu, W.-T., Huang, S.-C., Chen, S.-T., Lin, J. Y. C., Chang, Y.-W. Chiang, C.-Y., Wen, L.-L., Chan, D.-C., Liu, Y.-C., Chen, Y.-J. (2004) “Identification of tumor-associated plasma biomarkers using proteomic techniques: from mouse to human.” Proteomics 4: 2766-2775. (Cover Picture).

56.Wu, C.-Y. Jan, J.-T., Ma, H.-H., Kuo, C.-J., Juan, H.-F., Cheng, Y.-S. E., Hsu, H.-H., Huang, H.-C., Wu, D., Brik, A., Liang, F.-S., Liu, R.-S., Fang, J.-M., Chen, S.-T., Liang, P.-H. and Chi-Huey Wong (2004) “Small molecules targeting Severe Acute Respiratory Syndrome (SARS) human coronavirus.” Proc. Natl. Acad. Sci. U S A 101: 10012-10017.

57.Juan, H.-F., Liu, H.-L., Hsu, J.-P. (2004) “Recent developments in structural proteomics: from protein identifications and structure determinations to protein-protein interactions” Current Proteomics 1: 183-197. (Invited review paper)

58.Chang, D. T.-H, Chen, C.-Y., Chung, W.-C., Oyang, Y.-J., Juan, H.-F., Huang, H.-C. (2004) “ProteMiner-SSM: A web server for efficient analysis of similar protein tertiary substructures” Nucleic Acids Research. 32: W76-82.

59.Wu, S.-F., Liu, T.-M., Lin, Y.-C., Sytwu, H.-K., Juan, H.-F., Chen, S.-T., Shen, K.-L., Hsi, S.-C., Hsieh, S.-L. (2004) “Immunomodulatory effect of decoy receptor 3 on the differentiation and function of bone-marrow-derived dendritic cells in non-obese diabetic mice: From regulatory mechanism to clinical implication” Journal of Leukocyte Biology 75: 1-14.

60.Juan, H.-F., Lin, J. Y. C., Chang, W. H., Wu, C. Y., Pan, T. L. Tseng, M. J., Khoo, K. H. and Chen, S. T. (2002) “Biomic study of human myloid leukemia cell (HL-60) differentiated to macrophage using DNA array , proteomic, and bioinformatic analytical methods” Electrophoresis 23: 2490 -2504.

61.Sinchaikul, S., Sookkheo, B., Topanuruk, S., Juan, H.-F., Phutrakul, S., and Chen, S.-T. (2002) “The bioinformatics, functional genomics, and proteomics study of Bacillus sp.” J. Chromatogr B 771: 261-287.

62.Xu, D.-H., Juan, H.-F., Nohda, M., Ban, T. (2001) “Optimization of AFLP method in wheat and its application to QTL mapping for spike characters” Breeding Research 3: 25.

63.Juan, H.-F., Hung, C.-C., Wang, K.-T., Chiou, S.-H.* (1999) “Comparison of three classes of snake neurotoxins by homology modeling and computer simulation graphics.” Biochem Biophys Res Commun. 257: 500-510.

Conference Proceedings / 研討會論文

Peer-reviewed

1.Yang, R.-T., Juan, H.-F., and Chen, M.-S. (2003) “Using Discretization Techniques to Discover Trends and Differential Equations to Infer Gene Networks for Diagnostics” Proceedings in 7th Join Conference on Information Sciences, North Carolina, USA, 962-966.

2.Chen, C.-Y., Juan H. -F.*, Hsiao P.-J., Chen S.-T., Tseng H.-W., and Oyang Y.-J. (2003) “Design of an Incremental Clustering Package for Protein Function and Family Analysis” The Fifth International Symposium on Multimedia Software Engineering (MSE), Taichung, Taiwan, ROC, December 10-12.

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

Contributed

1.Chang, H.-Y., Huang, H.-C., Huang, T.-C., H. Mori, Juan, H.-F.* (2008) “Application for biofuel production: development of 1-Butanol tolerant Escherichia coli” (Poster #7 & Short Talk #4) 4th International Symposium of the Kanagawa University-National Taiwan University Exchange Program 2008, Taipei, Taiwan, Dec. 27, 2008.

2.Huang, T.-C., Chang, H.-Y., Hsu, C.-H., Kuo, W.-H., Chang, K.-J., Juan, H.-F.* (2008) “Targeting Therapy on Breast Carcinoma by ATP Synthase Inhibitor Aurovertin B” (Poster #8) 4th International Symposium of the Kanagawa University-National Taiwan University Exchange Program 2008, Taipei, Taiwan, Dec. 27, 2008.

3.Tseng, C.-W., Chen, C.-N., Juan, H.-F.* (2008) “14-3-3b is a novel biomarker for early detection and prognosis in gastric cancer” (Abstract#P-44, 1st Prize) 2008 Taiwan – Japan Proteomics Symposium, Taipei, Taiwan, Dec. 03 - 05, 2008.

4.Hu, C.-W., Huang, H.-C., Juan, H.-F.* (2008) “Regulation of carbon dioxide assimilation in R. palustris through CBB gene and GroEL overexpression” (Abstract#P-58, 3rd Prize) 2008 Taiwan – Japan Proteomics Symposium, Taipei, Taiwan, Dec. 03 - 05.

5.Lin, C.-C., Juan, H.-F., Huang, H.-C. (2008) “Comparative Analysis of Co-expressed Protein Interaction Networks Reveals Heart Failure Related Modules” (Travel Award, Oral Presentation) The 2nd Taiwan-Japan Young Researchers Conference on Computational and Systems Biology, Tokyo, Japan, Nov. 4-6.

6.Tseng, C.-W., Chen, C.-N., Huang, H.-C., C.-C., Chang, Chang, K.-J., Lee, P.-H., Kuo, M.-L., Jeng, Y.-M., Juan, H.-F.* (2008) “Clinical significance of connective tissue growth factor, its mediated microRNAs and target genes in gastric cancer” (Abstract#B-03) 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) symposium, Taipei, Taiwan, Oct. 23-25.

7.Chang, H.-Y., Huang, H.-C., Huang, T.-C., H. Mori, Juan, H.-F.* (2008) “Development of 1-Butanol Tolerant Microorganism for Biofuel Production” (Travel Award, Oral Presentation) The Fourth International Meeting on Synthetic Biology (SB4.0), Hong Kong, China, October 10-12.

8.Chang, H.-Y., Huang, T.-C., , Hsu, C.-H., Kuo, W.-H., Chang, K.-J., Juan, H.-F.* (2008) “Targeting Therapy on Breast Carcinoma by ATP Synthase Inhibitor Aurovertin B” 2008前瞻生物醫學科學新知研討會暨第七屆海峽兩岸生物醫學會議, Jun 27-28 (財團法人林榮耀教授學術教育基金會壁報展示獎 Poster Award)

9.Hsu, J.-W., Huang, H.-C, Juan, H.-F.* (2008) “Systems Analysis Reveals the Differentiation Mechanism of Leukemia Cells to Macrophages Induced by Ganoderma lucidum Polysaccharides” (Abstract#DS1-3-18) The 9th International Conference on Systems Biology (ICSB2008), Göteborg, Sweden, August 22-28.

10.Cheng, K.-L., Huang, H.-C., Hsu, C.-W., Hsu*, W.-M., Juan, H.-F.* (2008) “Protein-protein Interaction Network of AHR and MYCN Involved in Neuroblastoma” (Abstract#B73) Advances in Neuroblastoma Research (ANR2008), Chiba, Japan, May 21-24.

11.Liao, Y.-F., Hsu, W.-M., Lee, H.-Y., Juan, H.-F., Tsay Y.-G., Shih, Y.-Y., Wang, B.-J., Chang, H.-H., Hsieh, F.-J. (2008) “GRP75 Promotes the Neuronal Differentiation of Neuroblastoma Cells” (Abstract#B124) Advances in Neuroblastoma Research (ANR2008), Chiba, Japan, May 21-24.

12.Hsu, W.-M., Liao Y.-F., Lee, H.-Y., Tsay Y.-G., Juan, H.-F., Hsieh, F.-J., Jeng,Y.-M., Chang, H.-H., Lin, K.-H.(2008) “Identification of GRP75 as an Independent Favorable Prognostic Marker of Neuroblastoma by a Proteomics Analysis” (Abstract#TR45) Advances in Neuroblastoma Research (ANR2008), Chiba, Japan, May 21-24.

13.Chang, H.-H., Hsu, W.-M., Lee, H.-Y., Juan, H.-F., Lai, H.-S., Chen, W.-J., Lee, Y.-L., Liao, Y.-F., Hsieh, F.-J., Lin, K.-H.(2008) “Notch Signaling Pathway and Calreticulin in Neuroblastoma: Interactions and Prognostic Significance” (Abstract#TR115) Advances in Neuroblastoma Research (ANR2008), Chiba, Japan, May 21-24.

14.Juan, H.-F.*, Huang, H.-C., Chen, T.-Y., Chang, Y.-L., Hu, C.-W., Yi, T.-H., Bernstein, J. R., Liao, J. C. (2008) “Overexpression of Calvin Cycle Genes in Rhodopseudomonas palustris Improves the Efficiency of Carbon Dioxide Fixation” (Abstract#23) An International Symposium: Biotechnology for Better Crops, Energy and Health: ABRC 10thAnniversary, Taipei, Taiwan, April 29-May 1.

15.Chang, H.-Y., Huang, H.-C., Huang, T.-C., Mori, H., Juan, H.-F.* (2008) “Application for Biofuel Production: Development of 1-Butanol Tolerant Escherichia coli” (Abstract#24) An International Symposium: Biotechnology for Better Crops, Energy and Health: ABRC 10thAnniversary, Taipei, Taiwan, April 29-May 1.

16.Lee, T.-A., Juan, H.-F.* (2008) “Identification of human novel miRNAs and their targets” (Abstract#O115, Oral Presentation) 23th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 29-30.

17.Hsu, J.-W., Huang, H.-C, Cheng, K.-C., Chen, S.-T., Wong, C.-H., Juan, H.-F.* (2008) “Ganoderma lucidum polysaccharides induce apoptosis and differentiation in human monocytic leukemia cell line THP-1” (Abstract#O107, Oral Presentation) 23th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 29-30.

18.Huang, T.-C., Chang, H.-Y., Wang, Y.-C., Juan, H.-F.* (2008) “The effect of ATP synthase inhibitor Aurovertin B in non-small cell lung cancer” (Abstract#O79, Oral Presentation) 23th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 29-30.

19.Chang, H.-Y., Huang, H.-C., Huang, T.-C., Mori, H., Juan, H.-F.* (2008) “Proteomics analysis of 1-butanol tolerant Escherichia coli for bioenergy application” (Abstract#O53, Oral Presentation) 23th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 29-30.

20.Chen, T.-Y., Huang, H.-C., Juan, H.-F.* (2008) “Profiling transcriptome and proteome of Rhodopseudomonas palustris in different metabolic states for bioenergy application” (Abstract#P275) 23th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 29-30.

21.Wu, C.-Y., Chen, H.-W., Huang, H.-C., Juan, H.-F.* (2008) “Identifying the regulatory relationships between miR-218 and NPY1R in MCF-7 and MDA-MB-231 breast cancer cell lines” (Abstract#P66) 23th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 29-30.

22.Lin, L.-L., C.-N. Chen*, Lin, W.-C., Lee, P.-H., Chang, K.-J., Lai, Y.-P., Wang, J.-T. and Juan, H.-F.* (2007) “Annexin A4: A novel molecular marker for gastric cancer with Helicobacter pylori infection using proteomics approach” (Abstract#P069) Taiwan Proteomics Society International Conference 2007 (TPSIC2007), NCKU, Tainan, Taiwan, December, 4-5.

23.Chang, H.-Y., Huang, H.-C., Mori, H., Juan, H.-F.* (2007) “Screening and proteomics study of butanol-tolerant E. coli” (Abstract#P80)台灣生物化學及分子生物學學會: 馬武督秋令營, Hsinchu, Taiwan, October 19-20. (Poster Award)

24.Hsu, J.-W., Huang, H.-C., Cheng, K.-C., Chen, S.-T., Wong, C.-H., Juan, H.-F.* (2007) “Ganoderma lucidum polysaccharides induce apoptosis in uman monocytic leukemia cell line” (Abstract#P99)台灣生物化學及分子生物學學會: 馬武督秋令營, Hsinchu, Taiwan, October 19-20. (Poster Award)

25.Huang, T.-C., Chang, H.-Y., Juan, H.-F.* (2007) “Targeting therapy on breast carcinoma by ATP synthase inhibitor Aurovertin B” (Abstract#P19) 台灣生物化學及分子生物學學會: 馬武督秋令營, Hsinchu, Taiwan, October 19-20.

26.Chang, C.-C., Leu, J.-H., , Wu, J.-L., Hsu, C.-W., Hirono, I., Aoki, T., Juan, H.-F., Lo, C.-F., Kou, G.-H.*, Huang H.-C.* (2007) “Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon” (Abstract#P92)台灣生物化學及分子生物學學會: 馬武督秋令營, Hsinchu, Taiwan, October 19-20. (Poster Award)

27.Chen, C.-P., Huang, H.-C., Juan, H.-F.* (2007) “MicroRNAs-involved regulatory network of ATRA- and Am80-induced human leukemia cell line HL-60 differentiation” (Abstract#I10) The 8th International Conference on Systems Biology, Long Beach, USA, October 1-6.

28.Chiu, Y.-W., Juan, H.-F., Huang, H.-C. (2007) “Prediction of Functional Associated Proteins Using Topological Similarity in Protein-Protein Interaction Network” (Abstract#H14) The 8th International Conference on Systems Biology, Long Beach, USA, October 1-6. (Travel Award)

29.Lin, C.-C., Juan, H.-F., Hsiang, J.-T., Mori, H., Huang, H.-C. (2007) “An Essential Core of Protein-Protein Interaction Network in Escherichia coli” (Abstract#H15) The 8th International Conference on Systems Biology, Long Beach, USA, October 1-6.

30.Hsu, C.-W., Juan, H.-F., Huang, H.-C. (2007) “Characterization of microRNA-Regulated Protein-Protein Interaction Network” (Abstract#H16) The 8th International Conference on Systems Biology, Long Beach, USA, October 1-6.

31.Chang, Y.-W., Chang, S.-C., Juan, H.-F.* (2007) “Localizomics study in TPA-induced HL-60 cells differentiation into macrophages” (Abstract#SB2) The 12th Symposium on Recent Advances in Biophysics, Miaoli, Taiwan, May 23-25.

32.Chang, Y.-W., Chang, S.-C., Juan, H.-F.* (2007) “Localizomics study in TPA-induced HL-60 cells differentiation into macrophages” (Abstract#SB2) The 12th Symposium on Recent Advances in Biophysics, Miaoli, Taiwan, May 23~25.

33.Ni, K.-C. , Huang, H.-C., Chen, H.-W., Yi, T.-H., Chen, S.-T. Juan, H.-F.* (2007) “Regulatory mechanism of tpa-induced hl-60 cell differentiation” (Abstract#O031, Oral Presentation) 22th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 17-18.

34.Shih, C.-Y., Huang, T.-C., Juan, H.-F.* (2007) “Effect of cyclic RGD on phosphoprotein signaling in human breast cancer cell MCF-7” (Abstract# O081, Oral Presentation) 22th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 17-18.

35.Chen, C.-P., Huang, H.-C., Chen, H.-W., Juan, H.-F.* (2007) “Identification of differenciation related gene networks and micrornas in ATRA- and AM80-treated human hl-60 leukemia cells” (Abstract#P591, Poster Award) 22th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 17-18.

36.Lin, L.-L., Chen, C.-Y., Juan, H.-F.* (2007) “A potential new therapeutic target of gastric cancer: annexin A4” (Abstract#P592) 22th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 17-18.

37.Leu, J.-H., Chang, C.-C., Wu, J.-L., Hirono, I., Aoki, T., Juan, H.-F., Lo, C.-F., Huang, H.-C., and Kou, G.H. (2007) “Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected penaeus monodon” (Abstract#P587) 22th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 17-18.

38.Chen, H.-W. , Huang, H.-C., Lin, Y.-S., Chang, K.-J., Kuo, W.-H., Hwa, H.-L., Hsieh, F.-J., Juan, H.-F.* (2006) “Gene expression profiles reveals association of single nucleotide polymorphisms with estrogen receptor status in breast cancer populations” (Oral Presentation) 2006 International Symposium on Biomedical Engineering, Taipei, Taiwan, December 14-16.

39.Juan, H.-F.*, Cheng, K.-C., Huang, H.-C., Ou, C.-H., Chen, J.-H., Yang, W.-B., Chen, S.-T., Wong, C.-H. (2006) “Elucidating the molecular regulation of Ganoderma lucidum polysaccharides in human monocytic cells: from gene expression to network construction” The 7th International Conference on Systems Biology, Yokohama, Japan, October 9-11.

40.Ou, C.-H., Chang, C.-C., Hsia, H.-C., Wang, F.-S., Juan, H.-F.*, Huang, H.-C.* (2006) “BSIP – a web server for systems-biology structure identification program development” The sixth annual Emerging Information Technology Conference (EITC-06), Dallas, USA, Aug 10-12. (Oral presentation)

41.Lin, C.-C., Hwang, Y.-C., Juan, H.-F., Mori, H., and Huang, H.-C. (2006) “Topological Characteristics of Essential Genes in the Protein Interaction Network of Escherichia coli” Bioinformatics in Taiwan (Abstract#P15), Taichung, Taiwan, Sep 12-15.

42.Y.-C. Fang, H.-C. Huang and Juan, H.-F.* (2006) “Text Extraction and Mining of DNA Methylation Information” The sixth annual Emerging Information Technology Conference (EITC-06), Dallas, USA, Aug 10-12. (Oral presentation)

43.Tseng, C.-W., Juan, H.-F.* (2006) “To investigate the effect of anti- cancer drug 5-FU on the molecular mechanism of gastric cancer cell line SCM1” 20th Symposium Of The Protein Society, San Diego, California, U.S, Aug 5-9.

44.Huang, T.-C. , Chang, C.-C., Huang, H.-C., Juan, H.-F.* (2006) “Induction of caspase-dependent cell death pathway by cyclic RGD in human breast carcinoma cell line MCF-7” 20th Annual symposium of the Protein Society & 20th Anniversary Celebration, San Diego, California, U.S.A., Aug 5-9.

45.Juan, H.-F.*, Cheng, K.-C., Huang, H.-C., Ou., C.-H., Chen, J.-H., Yang, W.-B., Chen, S.-T., Wong, C.-H. (2006) “Elucidating the molecular regulation of Ganoderma lucidum polysaccharides in human monocytic cells: from gene expression to network construction” The 11th Symposium on Recent Advances in Biophysics, Taipei, Taiwan, May 24-26, 2006.

46.Ou, C.-H., Chang, C.-C., Hsia, H.-C., Wang, F.-S., Juan, H.-F. *, Huang, H.-C.* (2006) “BSIP – a web server for systems-biology structure identification program development” 4th Asia-Pacific Bioinformatics Conference (APBC2006), Taiwan, Feb 13-16. (Abstract#P028, 2nd Poster Award)

47.Bow, Y.-Y., Chang, J.-Y., Juan, H.-F., Mori, H., Huang, H.-C. (2006) “Elucidating the essentiality of essential genes in E. coli K-12” 4th Asia-Pacific Bioinformatics Conference (APBC2006), Taiwan, Feb 13-16. (Abstract#P027, 1st Poster Award)

48.Hwang, Y.-C., Lin, C.-C., Juan, H.-F., Mori, H., Huang, H.-C. (2006) “Topologial characteristics of protein interaction network and roles of essential genes in E. COLI K-12” 4th Asia-Pacific Bioinformatics Conference (APBC2006), Taiwan, Feb 13-16. (Abstract#P026)

49.Li, J.-J., Juan, H.-F.*, Chung, I-F., Huang, H.-C.* (2006) “Identification of RNA-binding protein residues using machine learning approaches” 4th Asia-Pacific Bioinformatics Conference (APBC2006), Taiwan, Feb 13-16. (Abstract#P025)

50.Lin, N., Chiou, S.-H., Juan, H.-F.*, Huang, H.-C.* (2006) “Bioinformatics approach to the study of the correlation between gene expression profiles and protein-protein interactions using matrices” 4th Asia-Pacific Bioinformatics Conference (APBC2006), Taiwan, Feb 13-16. (Abstract#P029)

51.Huang, T.-C. Chang, C.-C., Huang, H.-C., Juan, H. F.* (2005) “Cyclic RGD-induced cell death in human breast carcinoma cell line MCF-7: the influence of caspase pathway” The 6th International Conference on Systems Biology, Boston, MA, U. S. A., October 19-24, 2005.

52.Bow, Y.-Y., Chang, J.-Y., Juan, H. F., Mori, H., Huang, H.-C. (2005) “Elucidating the essentiality of essential genes in E. coli K-12” The 6th International Conference on Systems Biology, Boston, MA, U. S. A., October 19-24.

53.Tseng, H.-W., Chen, S.-T., Juan, H. F., Huang, H.-C., Chen, C.-F., and Wang, G.-J. (2005) “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, March 26-27.

54.Chang, S.-C., Huang, H.-C., Chen, S.-T., and Juan, H.-F.* (2005) “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, March 26-27.

55.Huang, T.-C., Huang, H.-C. Chen, S.-T., and Juan, H.-F.* (2005) “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, March 26-27.

56.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, March 26-27.

57.Chang, H.-Y., Chien, K.-C., Wang, Y.-C., and Juan, H.-F.* (2005) “Discovery of Biomarkers in Human Lung Cancer by Proteomics Approach” (Abstract#P567, Best Poster Paper) 20th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 26-27.

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

59.Peng, C.-L., Lin, Y.-C., Huang, H.-C., ao, C. -Y., Chen, S.-T., and Juan, H.-F.* (2004) “ProtExt: a Web-based Protein-protein Interaction Extraction System for PubMed Abstract” (Abstract#A-2) 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) and Conference on Computational Biology (ECCB), Glasgow, Scotland, Jul 31-Aug 4.

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

61.Wang, I-H., Huang, H.-C., Chen, S.-T., Juan, H.-F.* (2004) “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.

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

63.Chang, S.-C., Topanurak, S., Chen, S.-T., Juan, H.-F.* (2004) “A New Application of Microwave Technology to Proteomics” (Abstract#PA24) 3rd International Proteomics Conference 2004 (IPC’03), Taipei, Taiwan, May 15-17.

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

65.Peng, C.-L., Lin, Y.-C., Huang, H.-C., ao, C. -Y., Chen, S.-T., and Juan, H.-F.* (2004) “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.

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

67.Yang, R.-T., Juan, H.-F., and Chen, M.-S. (2003) “Using Discretization Techniques to Discover Gene Patterns for Diagnostics” (Abstract#PC12). 4th East Asian Biophysics Symposium (4th EABS), Taipei, Taiwan, November 3-6.

68.Huang, S.-C., Chen, J.-H., Juan, H.-F., Chen, S.-T., Hsu, W.-T., Chen, Y.-J., Chiang, C.-Y., Chang, Y.-W. (2003) “Identification of Acute Phase Proteins in Sera from Tumor-burden Mice: a Proteomics-based Approach” (Abstract#341).18th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, Mar. 22-23.

69.Juan, H.-F., Chen, J. -H., Shyu, W. T., Huang, S.-C., Chiang, C.-Y., Chang, Y.W., Chen, S.-T., Chen, Y.J. (2002) “Tumor Marker Discovery by Proteomic Approach” (Abstract#BC05) 70th Chinese Chemical Society Annual Meeting, Taipei, Taiwan, Oct. 25-27.

70.Xu, D.-H., Juan, H.-F., Nohda, M., Ban, T. (2001) “QTLS mapping of type I and type II resistance to FHB in wheat.” National Fusarium Head Blight Forum, Erlanger, KY, U. S. A., December 8 -10, Biotechnology 40-42.

1. Juan, H.-F. and Huang, H.-C. (2012) Systems Biology: Applications in cancer-related research (World Scientific Publishing, Singapore).

2. Juan, H.-F. (2011) “Transcriptomics and proteomics study in regulation of brassinosteroids” in Brassinosteroids: A Class of Plant Hormone, ed. Shamsul Hayat and Aqil Ahmad (Springer, Netherlands), pp. 393-402.

3.Juan, H.-F. and Huang, H.-C. (2007) “Bioinformatics: Microarray Data Clustering and Functional Classification” in Microarrays (2nd ed): Applications and Data Analysis, ed. Jang B. Rampal (The humana press inc.), pp. 405-416.

4.陳水田、曾銘仁、阮雪芬等 (2003) 基因體科學入門, 藝軒. [A Primer of Genome Science, Gibson, G. and Muse, S. V., Sinauer Associates Inc. (2001)]