1. 新穎化合物於癌細胞之系統生物學研究。

2. 探討靈芝多醣體於人類單核球細胞之分子調控:從基因表現到網路建構。

3. 微型RNA (microRNA)在癌症上所扮演的角色及其調控的蛋白質交互作用網路。

4. 光合菌Rhodopseudomonas palustris功能性基因體應用於生質能源技術平台之研發。

系統生物學是在生物學上一個新興的領域，它著重於以系統的觀點來了解生物系統的運作。由於高通量藥物合成、蛋白質體、微陣列及生物資訊技術的發展，使得系統生物學的研究愈發可行了。生物轉變的整體研究將能加快闡明生化路徑及疾病治療的速度。除此之外，系統生物學也著重於描述和了解複雜的生物系統如何運作以及發展預測人類疾病的模式。雖然疾病生物學很複雜，而藥物開發則必需倚靠生物反應，但是"基因到藥物"的希望之路已經是一觸即發，即將成功。對於改善現行的癌症治療，如何使藥物能專一地作用在癌細胞上仍然是一個主要的挑戰。因為RGD motif與很多重要的生化反應機制息息相關，在我們先前的研究中，發現環狀RGD胜肽抑制乳癌細胞生長的能力比直鏈RGD胜肽好，這樣的問題激起我們去研究環狀RGD胜肽是如何抑制癌細胞的生長以及它的分子機制 (Figure 1)，並藉此找出最有效含RGD胜肽的抗癌藥物。本研究主要的目標是要整合化學、生物學和計算學，並使用系統生物學研究法來研究在RGD胜肽誘導下乳癌細胞進行細胞凋亡的作用機制；進一步地利用系統生物學研究法來開發新的藥物以治療癌症。

靈芝是一種中草藥，在中國又稱"仙草"，在日本則稱之為"吉祥茸"。中研院翁啟惠院長的研究室純化靈芝多醣體(F3) ，在我們的研究中發現它具有抗癌的效果，這樣的結果激起了我們去探討F3是如何作用在癌細胞上而使癌細胞走向細胞凋亡的命運? 我們利用微陣列基因表現及生物資訊方法建構一個完整的基因網路，並結合生物學實驗技術證實這個基因網路，結果我們得知靈芝多醣體會誘發血癌細胞透過死亡接受器(death receptor) ，而引發一連串Caspase 蛋白質的訊息傳遞，最後細胞走向凋亡。

        微型RNA (microRNA)是在植物、動物及某些病毒中發現的，它非常小(~22鹼基對)而且是non-coding調控性的RNA分子，愈來愈多研究顯示它與癌症的發生息息相關。自2002年以來發現它在癌症發生上所扮演的角色，已經有非常多的學者投入這個行列，使得它與癌症的研究變成是一個愈發重要的課題。它可以調控非常多的蛋白質(幾十個甚或幾百個)，這些被它調控的蛋白質間是否有一個重要的交互作用網路出現呢? 它們的改變又是如何使正常細胞轉變成癌細胞的呢?這是本實驗室目前的研究主題之一。

本研究室除了利用系統生物學研究癌症的相關課題外，目前與美國加州大學洛杉磯分校James Liao教授合作，將系統生物學應用於能源開發上。主要使用的微生物為Rhodopseudomonas palustris（R. palustris），它是一種紫色非硫光合細菌，為水中底泥及土壤中常見的光合細菌，不僅能轉換二氧化碳成為體內所需能量，還能將氮氣(N2)轉化成氨(NH4)及氫氣(H2)。我們以系統生物學來研究R. palustris的代謝路徑，著重於描述和了解複雜的R. palustris生物系統如何運作，並將之應用於生質能源技術平台之研發。

→ 系統生物學研究室

A)期刊論文

W.-M. Hsu, 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* "Identification of GRP75 as an Independent Favorable Prognostic Marker of Neuroblastoma by a Proteomics Analysis" Clinical Cancer Research (in press)

Hsu, C.-W., Juan, H.-F.^*, Huang, H.-C.^* (2008) "Characterization of microRNA-Regulated Protein-Protein Interaction Network" Proteomics 8:1975-1979

Lin, L.-L., C.-N. Chen*, Lin, W.-C., Lee, P.-H., Chang, K.-J., Lai, Y.-P., Wang, J.-T., 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

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 Proteome Research 7:1379–1387

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 Proteome Research 7:1433-1444 ( Science Daily news & American Chemical Society weekly news)

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.

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

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.

Fang, Y.-C., Huang, H.-C.^*, Juan, H.-F.^* "MeInfoText: Associated Gene Methylation and Cancer Information from Text Mining" BMC Bioinformatics 9:22

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 26:7859-7871

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

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

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

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.

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

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.

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

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

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

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(3): 690-697

Juan, H.-F.*, Chang, S.-C., Huang, H.-C., Chen, S.-T. (2005) “A New Application of Microwave Technology to Proteomics” Proteomics 5(4): 840-842

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: 3691-3

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

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.

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

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)

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.

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.

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

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.

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.

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” Biochemical Biophysical Research Communication 257: 500-510.

B)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 7^th 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 InternationalSymposium 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

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, Göteborg, Sweden, August 22-28.

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.

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.

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

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

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

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.

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

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

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

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

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

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

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

Chang, H.-Y., Huang, H.-C., Mori, H., Juan, H.-F.^* (2007) "Screening and proteomics study of butanol-tolerant E. coli" (Abstract#P80) The Taiwan Society Biochemistry and Molecular Biology Fall Camp (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)

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) The Taiwan Society Biochemistry and Molecular Biology Fall Camp (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)

Huang, T.-C., Chang, H.-Y., Juan, H.-F.^* (2007) "Targeting therapy on breast carcinoma by ATP synthase inhibitor Aurovertin B" (Abstract#P19) The Taiwan Society Biochemistry and Molecular Biology Fall Camp (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.

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) The Taiwan Society Biochemistry and Molecular Biology Fall Camp (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)

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.

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.

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.

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.

Hwang, Y.-C, Juan, H.-F., Huang, H.-C.^* (2007) "Predicting Essential Genes Based on Network and Sequence Analysis" (Abstract# P22) 2007 Symposium of Bioinformatics and Systems Biology in Taiwan, Chiayi, Taiwan, September 4-5.

Chen, H.-W., Ni, K.-C., Huang, H.-C., Juan, H.-F.^* (2007) "MiLink – a Web Tool to Analyze the Association between Gene Expression Profiles with microRNAs" (Abstract# P23) 2007 Symposium of Bioinformatics and Systems Biology in Taiwan, Chiayi, Taiwan, September 4-5.

Lin, C.-C., Juan, H.-F., Hsiang, J.-T., Mori, H., Huang, H.-C.^* (2007) "An Essential Core of Protein Interaction Network in Escherichia coli" (Abstract# P25) 2007 Symposium of Bioinformatics and Systems Biology in Taiwan, Chiayi, Taiwan, September 4-5.

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.

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.

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.

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.

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.

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.

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.

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.

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)

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.

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, 2006. (Oral presentation)

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, 2006.

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, 2006.

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.

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)

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)

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)

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)

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)

 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.

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.

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.

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.

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.

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.

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, 優良看板論文) 20th Joint Annual Conference of Biomedical Sciences, Taipei, Taiwan, March 26-27.

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.

Peng, C.-L., Lin, Y.-C., Huang, H.-C., ao, C. -Y., Chen, S.-T., andJuan, 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.

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)

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.

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.

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.

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.

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.

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.

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.

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" 2003第六屆工程科技與中西醫學應用研討會, Taichun, Taiwan, Sep 13, 2003.

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.

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.

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.

C)專書及專書論文

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

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)]