Chien-Sheng Chen

• 2005 – 2007　Postdoc.　Department of Pharmacology and Molecular Sciences Johns Hopkins University
• 2001 – 2005　Ph.D.　Department of Food Science and Technology Cornell University
• 1996 – 1998　M.S.　Graduate Institute of Food Science and Technology National Taiwan University
• 1992 – 1996　B.S.　Department of Marine Food Science National Taiwan Ocean University

Work Experience:

• 2019　Department of Population Medicine and Diagnostic Science College of Veterinary Medicine Cornell University / Visiting Scholar
• 2018 -　Department of Food Safety Hygiene and Risk Management National Cheng Kung University / Professor
• 2016 – 2018　Department of Biomedical Science and Engineering Graduate Institute of Systems Biology and Bioinformatics National Central University / Professor
• 2017　Department of Chemistry and Chemical Biology Cornell University / Visiting Scholar
• 2015 – 2017　Graduate Institute of Systems Biology and Bioinformatics Director Department of Biomedical Science and Engineering, National Central University / Vice chair
• 2012 – 2016　Graduate Institute of Systems Biology and Bioinformatics, National Central University / Associate Professor
• 2008 – 2012　Graduate Institute of Systems Biology and Bioinformatics, National Central University / Assistant Professor
• 2008 – 2011　Department of Health, Executive Yuan, Taiwan / Food Safety Consultant
• 2007 – 2008　Department of Food Science, National Taiwan Ocean University / Assistant Professor
• 2005 – 2007　High Throughput Biology Center, Johns Hopkins University / Postdoctoral fellow

Teaching Experience

Cornell University

1. Graduate Teaching Assistant of FOOD 396 Food Safety Assurance

NTOU

1. Food Chemistry
2. Molecular Biology
3. Biochemistry
4. Biosensing Technology

NCU (All in English)

1. High Throughput Biomedical Science and Technology
2. Proteome Microarray Technology
3. Biosensing Technology
4. Biochemistry and Molecular Biology
5. High Throughput Biosensing Technology
6. Special topic: Protein Microarray
7. Amino Acid and Protein
8. Systems Biology

NCKU (All in English)

1.  Food Chemistry
2. Biosensing Technology
3. Rapid Detection
4. High Throughput Biomedical Detection Technology
5. Advanced Molecular Biology

 Professional Services

1. Council member of Taiwan Proteomics Society
2. Council member of Taiwan Society Developmental Origins of Health and Disease
3. Academic editor for PLoS One
4. Associate editor for Journal of Integrated OMICS
5. Editorial board member for Journal of Translational Proteomics Research
6. Editorial board member of SM Journal of Bioinformatics and Proteomics
7. Session chair for World Gene Convention-2013 and PepCon 2014
8. Scientific and local organizing committee member for Human Proteome Organization World Congress 2016
9. The Secretary-general for the 8th Asian Oceania Human Proteome Organization Congress
10. Grant proposal reviewers for Austrian Science Fund, Hong Kong Innovation and Technology Support Programme and Taiwan National Science Council
11. Manuscript reviewers for Analytical and Bioanalytical Chemistry, PLoS One, Journal of Proteomics Research, Bioanalysis, Molecular & Cellular Proteomics and Biosensors & Bioelectronics

• 2024 President, Taiwan Proteomics Society 台灣蛋白體學會理事長
• 2023 National Innovation Excelsior Award, Taiwan國家新創精進獎
• 2022 National Innovation Award, Taiwan 國家新創獎
• 2021 National Innovation Award, Taiwan 國家新創獎
• 2018 National Innovation Award, Taiwan 國家新創獎
• 2017-2019 Distinguished Professor, National Central University 特聘教授
• 2014-2016 Distinguished professor, National Central University
• 2013 Academia Sinica Research Award for Junior Research Investigators 中央研究院年輕學者研究著作獎

• 2013 Award for Excellent Contributions in Technology Transfer, National Central University
• 2013 Outstanding research award, National Central University
• 2013 Career Development Grant award, National Health Research Institutes
• 2008 Outstanding new faculty award, National Central University

Patent

• ASSAY KIT AND ANALYSIS METHOD, Taiwan I472369 (20150211-20320723)

Technology Transfer

• Collagen peptide production, 2012, F.C. BIOTECHNOLOGY CO., LTD

1. Yang J.-Y., Chen Y.-Z., Tsai R.-Y., Chen R.-P., Hsieh L.-F., Chang T.-H., Chen C.-S*. (2024, Dec). Development of multiple genome-wide proteome microarrays comprised wafer substrate-based chip and its scanner: An advanced high-throughput and sensitivity for molecular interactions studies. Biosensors and Bioelectronics. Pages 117110.
2. Lin, C. C., Chen, C. S*. (2024, Dec). Bacterial Proteome Microarray Technology in Biomedical Research. Trends in Biotechnology. (Accepted).
3. Yang, T. H., Syu, G. D., Chen, C. S., Chen, G. R., Jhong, S. E., Lin, P. H., Lin, P. C., Wang, Y. C., Shah, P., Tseng, Y. Y. & Wu, W. S. BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies. (2024, Sep) Computer Methods and Programs in Biomedicine. 254, 108260. Co-first author. 
4. Herianto S., Subramani B., Chen B.-R., Chen C.-S*. Recent advances in liposome development for studying protein-lipid interactions. (2024) Critical Reviews in Biotechnology, 44(1):1-14.
5. Keskin, B. B., Chen, C. S., Tsai, P. S., Du, P. X., Santos, J. H. M. & Syu, G. D. Reverse-Phase Protein Microarrays for Overexpressed Escherichia coli Lysates Reveal a Novel Tyrosine Kinase. (2024 May) Analytical Chemistry. 96, 21, p. 8721-8729 9 p.
6. Ahmadi AR, Song G, Gao T, Ma J, Han X, Hu M-W, Cameron AM, Wesson RN, Philosophe B, Ottmann S, King E, Gurakar A, Qi L, Peiffer B, Burdick J, Anders R, Zhou Z, Lu H, Feng D, Chen C-S, Qian J, Gao B, Zhu H, Sun Z* .(2023, Dec) Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis. elife12:RP86678.
7. Chen, YC., Hsu, JY., Chen, C-S., Chen, YT. & Liao, PC*.(2023, Jun) Development of a lateral flow immunoassays-based method for the screening of ractopamine in foods and evaluation of the optimal strategy in combination of screening and confirmatory tests. Journal of Food and Drug Analysis. 31, 2, p. 289-301.
8. Syu GD*, Reymond Sutandy FX, Chen K, Cheng Y, Chen C-S*, Shih JC*. (2023, Jan) Autoantibody Profiling of Monoamine Oxidase A Knockout Mice, an Autism Spectrum Disorder Model. Brain, Behavior, and Immunity. 107:193‐200.
9. Chen, B.-Y., Hsu, C.-C., Chen, Y.-Z., Lin, J.-J., Tseng, H.-H., Jang, F.-L., Chen, P.-S., Chen, W.-N., Chen, C.-S*., Lin, S.-H*. (2022, Nov) Profiling antibody signature of schizophrenia by Escherichia coli proteome microarrays. Brain, Behavior, and Immunity. 106:11-20. 
10. Rathod J, Yen C-H, Liang B-Q, Tseng Y-Y, Chen C-S* and Wu W-S*(2021, Jun). YPIBP: A repository for phosphoinositide-binding proteins in yeast. Computational and Structural Biotechnology Journal.19: 3692-3707.
11. Shah P and Chen C-S* (2021, Jan.). Systematic identification of protein targets of Sub-5 using Saccharomyces cerevisiae proteome microarrays. International Journal of Molecular Sciences. 22(2):760.
12. Herianto S, Rathod J  Shah P, Chen Y-Z, Wu W-S, Liang B, Chen C-S* (2021, Jan.). Systematic analysis of phosphatidylinositol-5-phosphate-interacting proteins using yeast proteome microarrays. Analytical Chemistry. 93(2) 868–877.
13. Shah P and Chen C-S* (2020, Dec). Systematic identification of protein targets of Sub-5 using Saccharomyces cerevisiae proteome microarrays. International Journal of Molecular Sciences. 22(2):760.
14. Hsu P-C, Chen C-S*, Wang S, Hashimoto1 M, Huang W-C and Teng C-H* (2020, Aug). Identification of MltG as a Prc Protease Substrate Whose Dysregulation Contributes to the Conditional Growth Defect of Prc-Deficient Escherichia coli. Front. Microbiol., doi: 10.3389/fmicb.2020.02000. co-first author
15. Hsiao FS-H, Yang S-K, Lin J-M, Chen Y-W, Chen C-S* (2019, Sep). Protein interactome analysis of iduronic acid-containing glycosaminoglycans reveals a novel flagellar invasion factor MbhA. Journal of Proteomics. 208:103485. 
16. Shah P, Wu W-S, Chen C-S* (2019, Sep). Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays. International Journal of Molecular Sciences. 20(17):4218. 
17. Chien F-C, Lo J-L, Zhang X, Cubukcu E, Luo Y-T, Huang K-L, Tang X, Chen C-S*, Chen C-C, Lai K-Y (2018, Oct). Nitride-Based Microarray Biochips: A New Route of Plasmonic Imaging. ACS Appl. Mater. Interfaces, 10 (46), 39898–39903. 
18. Feng Y, Chen C-S, Ho J, Pearce D, Hu S, Wang B, Desai P, Kim KS, Zhu H (2018, Sep). High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood–Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology). Analytical Chemistry 90(18):10958-10966. 
19. Hsu T-Y, Lin J-M, Nguyen MT, Chung F-H, Tsai C-C, Cheng H-H, Lai Y-J, Hung H-N, Chen C-S*. (2018) Antigen Analysis of Pre-Eclamptic Plasma Antibodies Using Escherichia coli Proteome. Molecular & Cellular Proteomics. 17 (8) 1457-1469.
20. Kuo HC, Huang YH, Chung FH, Chen PC, Sung TC, Chen YW, Hsieh KS, Chen C-S*, Syu GD* (2018, Mar). Antibody Profiling of Kawasaki Disease Using Escherichia coli Proteome Microarrays. Molecular & Cellular Proteomics. 17(3):472-481. 
21. Yang A-M, Inamine T, Hochratch K, Chen P, Wang L, Izquierdo CL, Bluemel S, Hartman P, Xu j, Koyama Y, Kisseleva T, Torralba M, Moncera K, Beeri K, Chen C-S, Freese K, Hellerbrand C, Lee S, Hoffman HM, Mehal W, Garcia-Tsao G, Mutlu E, Keshavarizian A, Brown G, Ho SB, Bataller R, Starkel P, Fouts D, Schnabl B. (2017, Jun). Intestinal fungi contribute to development of alcoholic liver disease. Journal of Clinical Investigation, 127(7):2829-2841. (SCI, 3/140 MEDICINE, RESEARCH & EXPERIMENTAL ). MOST 104-2320-B-006-053-MY3. 
22. Huang B-Y, Chen P-C, Chen B-H, Wang C-C, Liu H-F, Chen Y-Z, Chen C-S*, Yang Y-S* (2017, Mar). High-throughput screening of sulfated proteins by using a genome-wide proteome microarray and protein tyrosine sulfation system. Analytical Chemistry, 89(6):3278-3284. (SCI, 6/98, Chemistry, Analytical). MOST 104-2320-B-006-053-MY3.
23. Tsai C-H, Ho Y-H, Sung T-C, Wu W-F, Chen C-S* (2016, Nov). E. coli proteome microarrays identified the substrates of ClpYQ protease. Molecular & Cellular Proteomics, 16(1):113-120. (SCI, 8/78, Biomedical Research Methods).
24. Lin J-M, Tsai Y-T, Liu Y-H, Lin Y, Tai H-C*, Chen C-S* (2016, Sep). Identification of 2-oxohistidine interacting proteins using E. coli proteome chips. Molecular & Cellular Proteomics. Molecular and Cellular Proteomics, 15 (12), 3581-3593. (SCI, 8/78, Biomedical Research Methods). MOST 104-2320-B-008-002-MY3.
25. Ho Y-H, Shah P, Chen Y-W, Chen C-S* (2016, Jun). Systematic analysis of intracellular targeting antimicrobial peptides Bac 7, PR-39, P-Der and Lfcin B, using E. coli proteome microarrays. Molecular & Cellular Proteomics, 15(6):1837-47. (SCI, 8/78, BIOCHEMICAL RESEARCH METHODS). MOST 103-2627-M-008-001.
26. Hsiao F S-H, Sutandy F.X.R, Syu G-D, Chen Y-W, Lin J-M, Chen C-S* (2016, Jun). Systematic protein interactome analysis of glycosaminoglycans revealed YcbS as a novel bacterial virulence factor. Scientific Reports, 6:28425. (SCI, 17/72, MULTIDISCIPLINARY SCIENCES). MOST 104-2320-B-008-002-MY3.
27. Shah P, Hsiao F S-H, Ho Y-H, Chen C-S* (2016, Feb). The proteome targets of intracellular targeting antimicrobial peptides. Proteomics, 16(6), 1225-37. (SCI, 23/78, BIOCHEMISTRY & MOLECULAR BIOLOGY ). MOST 103-2627-M-008-001.
28. Sung T-C, Chen Y-W, Shah P, Chen C-S* (2016, Feb). A replaceable liposomal aptamer for the ultrasensitive and rapid detection of biotin. Scientific reports, 6, 21369. (SCI, 17/72, MULTIDISCIPLINARY SCIENCES). MOST 103-2627-M-008-001.
29. Chen PC, Syu GD, Chung KH, Ho YH, Chung FH, Chen PH, Lin JM, Chen YW, Tsai SY*, and Chen C-S* (2015, Mar). Antibody Profiling of Bipolar Disorder using Escherichia coli Proteome Microarrays. Molecular & Cellular Proteomics,14(3):510-8. 
30. Chen YW, Teng CH, Ho YH, Ho TYJ, Huang WC, Hashimoto M, Chiang IY, and Chen C-S* (2014, Jun). Identification of bacterial factors involved in type 1 fimbria expression using an Escherichia coli K12 proteome chip. Molecular & Cellular Proteomics, 13(6):1485-94. 
31. Chen C-S, Korobkova E, Chen H, Zhu J, Jian X, Tao S-C, He C*, Zhu H* (2008) A proteome chip approach reveals new DNA base damage recognition activities in Escherichia coli. Nature Methods 5: 69-74.

My research has been focused on human-microbe interaction, especially systematical analysis of E. coli proteome interaction. My lab has a novel high-throughput protein purification technique to purify ~4800 E. coli proteins. These proteins were then spotted onto various glass surfaces to form high-density proteome array chips, which allow us to develop all kinds of assays for proteome interactions, including nucleic acid-, peptide-, human cell-, lipid-, small molecule drug-, carbohydrate-, and plasma-E. coli proteome interactions. For example, my research team used the Escherichia coli proteome microarray to systematically identify the protein targets of four intracellular targeting AMPs: lactoferricin B, bactenecin 7, a hybrid of pleurocidin and dermaseptin, and proline-arginine-rich peptide. By analyzing their specific target proteins, we revealed their target similarity and differences. We further predicted the synergistic effects between peptides and got successful validation. We also discovered that lactoferricin B inhibits the phosphorylation of the two-component system response regulators. This is the first study to show that an antimicrobial peptide inhibits the growth of bacteria by influencing the phosphorylation of TCS directly.

In addition to the host peptide-microbial proteome interaction study, we also systematically analyzed the protein interactome of four human glycosaminoglycans, which are responsible for the bacterial invasion. We further identified a novel bacterial virulence factor YcbS, which bound to the laminin-binding site of heparin with a high affinity, causing displacement of heparin from laminin to affect the host extracellular matrix structure. E. coli proteome microarrays also helped us to identify that YbaB is a novel substrate of ClpYQ protease and Spr is involved in the regulation of type 1 fimbria expression through direct interaction with the invertible element fimS.

We also analyzed the antibody profile of certain disease patients’ plasma using E. coli proteome array chips to identify the distinguished E. coli proteins able to recognize the antibody difference between health controls and patients with certain diseases, including bipolar diseases, Kawasaki disease, Pre-eclampsia disease, and schizophrenia. All the studies mentioned above were published in the prestigious journals: Nature Methods, Brain, Behavior & Immunity and Molecular & Cellular Proteomics.

For the study of E. coli proteome interactions with human cells, we developed a high throughput chip-based cell probing assay to probe with fluorescent live human brain microvascular endothelial cells (HBMEC, which constitute the brain blood barrier). We identified several transmembrane proteins, which are effectively bound to live HBMEC. This study enables rapid, unbiased discovery of pathogen proteins that are involved in pathogen-host interactions for human infectious diseases in a high throughput manner. This technique was published in Analytical Chemistry and we will develop a chip assay based on this method for this proposal.

In summary, we are experienced in using E. coli proteome microarrays for host-microbe interaction studies. We are confident that our proteome microarray techniques will decipher the molecular interactions between UPEC proteins and bladder epithelial cells.

1. (2024) Fabrication and application of  coliproteome microarray chips. Invited Speaker at 1 st International Symposium on Living Systems Design Research, Matsue, Japan.
2. (2023) Systems Biology on a Chip: From Biobank, Through Proteome Microarray, to Big Data at Lithuanian University of Health Sciences, Invited Speaker at Lithuanian University of Health Sciences, Kaunas, Lithuania
3. (2022) Translating extraordinary scientific and technology advances from biomedical research into actual patient care practices, Invited Speaker at The 3rd International Conference on Health, Technology, and Life Sciences, Universitas Sebelas Maret Surakarta, Surakarta, Central Java, Indonesia.
4. (2019) Antibodyome analysis using proteome microarrays. Invited Speaker at 2019 KHUPO, Seoul, Korea.
5. (2018) Proteomics on a chip. Invited speaker at 1st International Conference on Health, Technology and Life Sciences, Universitas Sebelas Maret Surakarta, Surakarta, Central Java, Indonesia.

1. Chen C-S (2019) Antibodyome analysis using proteome microarrays. Invited Speaker at 2019 KHUPO, Seoul, Korea.
2. Chen C-S (2018) Proteomics on a chip. Invited speaker at 1^st International Conference on Health, Technology and Life Sciences, Surakarta, Central Java, Indonesia.
3. Chen C-S (2016) Functional and interaction proteomics on a chip. Invited speaker at 8^th Annual Meeting of Proteomics Society, India. New Delhi.
4. Chen C-S (2016) Heterogeneous ribonucleoprotein K (hnRNP K) binds the 5′ terminal sequence of the hepatitis C virus RNA and mature miR-122. Speaker at 15^th Human Proteome Organization World Congress, Taipei.
5. Chen C-S (2015) High throughput protein interactome studies using genome-wide proteome microarrays. Invited speaker at International Symposium on Targeted Proteomics at Indian Institute of Technology, Bombay, India.
6. Chen C-S (2015) Human proteome array revealed that hnRNPK binds and affects the accumulation of mature miR-122. Poster presented at the 14^th Human Proteome Organization World Congress, Vancouver, Canada
7. Chen C-S (2015) From biobank, through proteome microarray, to big data. Invited speaker at Health Information Technology with Telemedicine 2015, Ho Chi Minh City, Vietnam.
8. Chen C-S (2015) Fabrication and applications of proteome microarrays. Invited speaker at The 3^rd EITA-Bio Conference, Taipei, Taiwan.
9. Chen C-S (2015) Autoantibody profiling of MAO-A KO mice using human proteome microarrays-in search of biomarkers for ASD. Oral presentation at The 15^th Society of Chinese Bioscientists in America International Symposium, Taipei, Taiwan.
10. Chen C-S (2014) A human proteome microarray identifies that the heterogeneous nuclear ribonucleoprotein K (hnRNP K) recognizes the 5’ terminal sequence of the hepatitis C virus. Poster presented at 2014 FEBS EMBO Annual Meeting, Paris, France
11. Chen C-S (2014) Development of a novel bead-based 96-well filtration plate competitive immunoassay for the detection of gentamycin. Poster presented at the 24th World Anniversary Congress on Biosensors, Melbourne, Australia.
12. Chen C-S (2014) Genome-wide proteome microarray technology: an example of coli proteome chips. Invited speaker at BIT’s 7^th Annual Protein & Peptide Conference, Dalian, China.
13. Chen C-S (2013) Deciphering genome-wide protein interactions using coli proteome chips. Invited speaker at World Gene Convention-2013, Haikou, China.
14. Chen C-S (2013) Deciphering human-microbe proteome interactions using coli proteome chips. Poster presented at 2013 HUPO, Yokohama, Japan.
15. Chen C-S (2013) Identification of human-microbe protein interactions using coli proteome microarrays. Invited speaker at 2013 KHUPO, Seoul, Korea.
16. Chen C-S (2012) Fabrication of an  coli proteome microarray and its application on human-microbe interactions. Poster presented at 2012 HUPO, Boston, USA.
17. Chen C-S (2011) Fabrication and application of an coli proteome microarray. Invited speaker at 2011 Taiwan-US S&T Workshop for International Collaborative Research, Joungli, Taiwan.
18. Chen C-S (2010) Fabrication of an coli proteome microarray and its applications in basic and clinical researches. Invited speaker at 1st Chinese Molecular Diagnosis Technology Conference, Beijing, China.
19. Chen C-S (2010) Fabrication and application of an coli proteome microarray. Invited speaker at 2010 SBBS Systems Biology and Bioinformatics Symposium, Hsinchu, Taiwan.
20. Chen C-S, Sullivan S, Anderson T, Tan AC, Alex PJ, Brant SR, Cuffari C, Bayless TM, Talor MV, Burek L, Wang H, Li R, Datta LW, Wu Y, Winslow RL, Zhu H, Li X (2009) Identification of novel serological biomarkers for inflammatory bowel disease using coli proteome chip. Poster presented at 2009 Systems Biology of Human Disease Conference, Boston, USA.
21. Chen C-S, Sullivan S, Anderson T, Tan AC, Alex PJ, Brant SR, Cuffari C, Bayless TM, Talor MV, Burek L, Wang H, Li R, Datta LW, Wu Y, Winslow RL, Zhu H, Li X (2009) Identification of novel serological biomarkers for inflammatory bowel disease using coli proteome chip. Poster presented at The 10th International Conference on Systems Biology, Stanford, California, USA.
22. Chen C-S, Sullivan S, Anderson T, Tan AC, Alex PJ., Brant SR, Cuffari C, Bayless TM, Talor MV, Burek L, Wang H, Li R, Datta LW, Wu Y, Winslow RL, Zhu H, Li X (2009) Identification of novel serological biomarkers for inflammatory bowel disease using coli proteome chip. Invited speaker at Conference of Biochip Application in China, Chongqing, China.
23. Chen C-S (2009) Fabrication and application of an coli proteome microarray. Invited speaker at 10^th Frontier Science Symposium, Chungli, Taiwan
24. Chen CS , Korobkova E, Chen H, Zhu J, Jian X, Tao SC, He C, Zhu H (2009) 蛋白質體晶片方法揭示大腸桿菌中新的 DNA 鹼基損傷識別活動。 韓國首爾 PepCon2009特別演講嘉賓。
25. Chen CS ,Durst RA ( 2007) 同時檢測大腸桿菌O157 :H7、沙門氏菌。
26. Chen CS、Tao SC、Zhu J、Sullivan S、Anderson T、Tan AC、Li X、Kim KS 和 Zhu H (2007)大腸桿菌蛋白質組微陣列的研究及其在人類血清分析中的應用。
27. 陳春生，陶紹昌，朱菁，李建軍，朱華 (2006)大腸桿菌蛋白質晶片的建構及應用。
28. Chen CS、Yao J、Durst RA（2005）脂質體覆熒光納米粒子：量子點和二氧化矽納米粒子。
29. Chen CS , Durst RA（2004）蛋白 G 標記物為免疫測定的通用試驗劑。