CHIOU-HWA (CATHY) YUH

喻秋華

OFFICE ADDRESS: HOME ADDRESS:

No. 35, Keyan Road, Zhunan Town, No. 158, Goung-Don Road

Miaoli County 350, Taiwan, R.O.C. HsinChu City 300, Taiwan, R.O.C.

Office: 886-037-246-166 ext. 35338 Home: 886-03-563-7757

Lab: 886-037-246-166 ext. 35337 Cell: 886-0912-281-578

Fax: 886-037-586-459

E-mail: chyuh@nhri.org.tw


EDUCATION:

National Yang-Ming Medical College, Taipei, Taiwan (Fall 1992)

Ph.D. Microbiology and Immunology

Thesis: The action mechanisms of second enhancer and core promoter of the Hepatitis B virus.


Fu-Jen Catholic University, Taipei, Taiwan. (Fall 1987)

B.S., Biology


PROFESSIONAL EXPERIENCE:

Associate Investigator (2005-date)

Division of Molecular and Genomic Medicine, National Health Research Institutes

Develop the Endomesoderm Gene Network in regulation the development of zebrafish, and establish the cancer model for studying variable cancer.


Joint Associate Professor (2007/3/22-date)

Department of the Biological Science & Technology, National Chiao Tung University

Promote the “systems biology” and “gene regulatory networks” idea. Teaching and directing PhD and M.S. students.


Adjunct Associate Professor (2006/8/1-date)

Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Promote the “systems biology” and “gene regulatory networks” idea. Teaching and directing PhD and M.S. students.


Adjunct Assistant Professor (2005/8/1-2006/7/31)

Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Promote the “systems biology” and “gene regulatory networks” idea. Teaching and directing PhD and M.S. students.


Member of the Professional Staff (2002-2004)

Biology Division, California Institute of Technology,

Discovered the important linkage of endomesoderm gene regulatory network on Otx1/2 promoter. Characterizing the negative module of Endo16 gene, design a new tool to test the function of repression modules and proposed the “transposable negative regulatory module” theory.


Director (2001-2002)

Transcription Factor Center, Beckman Institute, California Institute of Technology

The Center acquired combined computational and experimental technologies to develop novel facilities for transcription factor research and gene regulatory network genomic. Successfully applying “FamilyRelations” algorithms to identify the active cis-regulatory elements in sea urchin Otx gene.


Research Associate (1996-2001)

Stowers Institute of Medical Research

Thoroughly studied the modular organization of Endo16 gene, a gut specific marker, in sea urchin, focusing on the importance of B module of Endo16. Collaborated with Dr. Klein’s lab to study the Spec2a gene expression and the relationship with Otx.


Senior Research Fellow (1995-2001)

California Institute of Technology

Genomic cis-regulatory logic for Endo16: the first case of combined computational simulation for analyzing gene regulation. The study laid the fountain of Gene Network study.


Research Fellow (1992-1995)

California Institute of Technology

Characterizing and mapping the DNA-protein interaction on the Endo16 promoter. Discovering the modular organization of the Endo16 promoter.


Teaching Assistant (1989-1991)

National Yang-Ming Medical College

Teaching medical students at microbiology and immunology laboratory.


FELLOWSHIPS AND AWARDS:


Biology Divisional Fellowship, California Institute of Technology August 1995


Gordon Ross Fellowship, California Institute of Technology August 1994


Procter and Gamble Fellowship, California Institute of Technology August 1993


1st among competitors of Wang Ming-Ning Scholarship December 1991

Wang Ming-Ning Memorial Foundation, Taiwan


Research Fellowship, Taiwan National Science Council, Taiwan 1987-1992


Ranked-First Scholarship Award, Fu-Jen Catholic University, Taiwan 1984-1987


PUBLICATIONS:

Books:

1. Yuh, C. H. and Ting, L. P.

Cooperation of Two Elements within the Second Enhancer of the Human Hepatitis B viral Genome in "Viral Hepatitis and Liver Disease" p.176-182, Harper Graphics, Inc. Waldorf, MD. 1990.


2. Yuh, C. H., Bolouri, H., Bower, J. M. and Davidson, E. H.

A Logical Model of Cis-Regulatory Control in a Eukaryotic System, Computational Modeling of Genetic and Biochemical Networks (Bower and Bolouri, editors) The MIT press, 73-100, 2000.


3. Coffman, J. A. and Yuh, C. H.

Identification of Sequence-specific DNA Binding Proteins, Academic Press/Elsevier Science, "Methods in Cell Biology" Series, 74:653-675, 2004.


Journals:


  1. Chang, H. K., Wang, B. Y., Yuh, C. H., Wei, C. L. and Ting, L. P.

A Liver-Specific Nuclear Factor Interacts with the Promoter Region of the Large Surface Protein Gene of the Human Hepatitis B virus. Mol. Cell Biol. 9: 5189-5197, 1989.


  1. Yuh, C. H. and Ting, L. P.

The genome of the Hepatitis B virus Contains a Second Enhancer: Cooperation of Two Elements within This Enhancer Is Required for Its Function. J. of Virol. 64: 4281-4287, 1990.


  1. Yuh, C. H. and Ting, L. P.

C/EBP-like Proteins Binding to the Functional Box-a and Box-b of the Second Enhancer of Hepatitis B Virus. Mol. Cell Biol. 11: 5044-5052, 1991.


  1. Yuh, C. H. Chang, Y. L.and Ting, L. P.

Transcriptional Regulation of the Precore and Pregenomic RNAs of Hepatitis B Virus. J. of Virol. 66: 4073-4084, 1992.


  1. Yuh, C. H. and Ting, L. P.

Differentiated Liver Cell Specificity of the Second Enhancer of Hepatitis B Virus. J. of Virol. 67: 142-149, 1993.


  1. Yuh, C. H., Ransick, A., Martinez, P., Britten, R. J. and Davidson, E. H.

Complexity and Organization of DNA-Protein Interactions in the 5’-Regulatory Region of an Endoderm-Specific Marker Gene in the Sea Urchin, Embryo. Mech. Development. 47: 165-186, 1994.


  1. Wang, H. D., Yuh, C. H., Dang, C.V., and Johnson D.L.

The Hepatitis B Virus X Protein Increases the Cellular Level of TATA-binding Protein which Mediates Transactivation of RNA Polymerase IIIGenes. Mol. Cell. Biol., 15: 6720-6728, 1995.


  1. Yuh, C. H. and Davidson, E. H.

Modular Cis-Regulatory Organization of Endo16, a Gut-Specific Gene of the Sea Urchin Embryo. Development. 122, 1069-1082, 1996.


  1. Kirchhamer, C. V., Yuh, C. H. and Davidson, E. H.

Modular Cis-Regulation of Developmentally Expressed Genes: Two Genes Transcribed Territorially in the Sea Urchin Embryo and Additional Examples. Proc. Natl. Acad. Sci. USA. 93, 9322-9328, 1996.


  1. Yuh, C. H., Moore, J. G. and Davidson, E. H.

Quantitative Functional Interrelations within the Cis-Regulatory System of the S. purpuratus Endo16 Gene. Development. 122, 4045-4056, 1996.


  1. Yuh, C. H., Bolouri, H. and Davidson, E. H.

Genomic Cis-regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene. Science, 279, 1896-1902, 1998.


  1. Yuh, C. H., Li, X., Davidson, E. H. and Klein, W. H.

Correct Expression of spec2a in the Sea Urchin Embryo Requires Both Otx and Other Cis-Regulatory Elements. Developmental Biology, 232(2):424-38, 2001.


  1. Yuh, C. H., Bolouri, H. and Davidson, E. H.

Cis-Regulatory Logic in the Endo16 Gene: Switching from a Specification to a Differentiation Mode of Control. Development, 128(5):617-29, 2001.


  1. Yuh, C. H., Brown T.B., Livi C., Clarke, P.J.C. and Davidson E. H.

Patchy Interspecific Sequence Similarities Efficiently Identify Active Cis-Regulatory Elements in the Sea Urchin, Developmental Biology, 246(1):148-161, 2002.


  1. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh C. H., Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Schilstra MJ, Clarke PJ, Rust AG, Pan Z, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H.

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo, Developmental Biology, 246(1):162-190, 2002.


  1. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh C. H., Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Z, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H.

A genomic regulatory network for development, Science, 295, 1669-1678, 2002.


  1. Yuh, C. H., Dorman E. R., Howard M. L. and Davidson, E. H.

An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network. Dev Biol. 2004 May 15;269(2):536-51.


  1. Yuh, C. H., Dorman E. R. and Davidson, E. H.

Brn1/2/4, the predicted midgut regulator of the Endo16 gene of the sea urchin embryo. Dev Biol. 2005 May 15;281(2):286-98.


  1. Pang-Kai Liu , Yuh, C. H., and Feng-Sheng Wang (2008).

Inference of Genetic Regulatory Networks Using S-system and Hybrid Differential Evolution. Proceedings of 2008 IEEE Congress on Evolutionary Computation, 1736-1743 (EI)


  1. Pin-Chao Liao, Hung-Yu Lin, Yuh, C. H., Lin-Kwei Yu, and Horng-Dar Wang (2008).

The effect of neuronal expression of heat shock proteins 26 and 27 on lifespan, neurodegeneration and apoptosis in Drosophila. Biochem Biophys Res Commun. 2008 Nov 28;376(4):637-41. Epub 2008 Sep 15.


  1. Tzu-Min Chan, William Longabaug, Hamid Bolouri, Hua-Ling Chen, Wen-Fang Tseng, Chung-Hao Chao, Te-Hsuan Jang, Yu-I Lin, Shao-Chin Hung, Horng-Dar Wang and Yuh, C. H. (2008).

Developmental Gene Regulatory Networks in the Zebrafish Embryo. Biochim Biophys Acta. - Gene Regulatory Mechanisms 2008 Oct 8. [Epub ahead of print]


  1. Tzu-Min Chan, Chung-Hao Chao, Yen-Ju Yu, Horng-Dar Wang and Yuh, C. H. (2008).

Functional Analysis of the Evolutionarily Conserved Cis-Regulatory Elements on the Sox17 Gene in Zebrafish. Developmental Biology (In Press) Accepted Manuscript, Available online 24 November 2008


23. Ting-Fen Tsai, Shwu-Rong Grace Shieh, Pei-Ting Lin, Yu-I Lin, Chao-Chin Li, Ko-Wei Chang, Shih-Feng Tsai, and Yuh, C. H. (2008). Pathway analysis of the gene expression profile in the HBx induced HCC mouse model. Cancer Research (submitted)


Oral presentation, poster and workshop:


1. Yuh, C. H. and Ting, L. P. "Human Hepatitis B Virus Contains Second Enhancer" (Oral) The Twenty Third Annual Meeting of the Chinese Society of Microbiology. December 10, 1989.


2. Yuh, C. H. and Ting, L. P. "Identification of the Second Enhancer in the Human Hepatitis B Virus and Its Action Mechanism" (Oral), The Fifth Joint Annual Conference of Biomedical Sciences. April 7-8, 1990.


3. Yuh, C. H., Chang, Y. L. and Ting, L. P. "Action Mechanism of the Second Enhancer of Human Hepatitis B Virus" (Oral). The Sixth Molecular Biology Retreat, September 6-8, 1990.


4. Yuh, C. H., Lee, S. C. and Ting, L. P. "Cooperation Between II-and II-Regions of the Human Hepatitis B Viral Second Enhancer" (Poster). The First Asian Conference on Transcription (ACT-I). December 6-8, 1990.


5. Yuh, C. H. and Ting, L. P. "Dual Regulatory Roles of 106-bp Sequence on Gene Expression of Hepatitis B Virus" (Oral). The Sixth Joint Annual Conference of Biomedical Sciences. March 23-24, 1991.


6. Yuh, C. H. and Ting, L. P. "Functional Organization of the HBV Second Enhancer: C/EBP-Like Proteins Binding to the Box-and Box-Elements and Cooperation of the two Elements Is Required for Its Function" (Oral). The Seventh Joint Annual Conference of Biomedical Sciences. March 21-22, 1992.


7. Yuh, C. H. and Davidson, E. H. "Transcriptional Regulation of Endo16 in the Sea Urchin Embryo" (Oral). The Forth Southwest Transcription Factor Meeting May 5-6, 1995.


8. Yuh, C. H. and Davidson, E. H. "Complex Spatial and Temporal Transcriptional Regulation of an Endoderm-Specific Marker Gene in the Sea Urchin Embryo" (Oral). The Fifth Biology Annual Retreat of Caltech. October 20-22, 1995.


9. Yuh, C. H. and Davidson, E. H. "Modular Cis-Regulatory Organization of Endo16, a Gut-Specific Gene of the Sea Urchin Embryo” (Poster). The Research Directors Conference of Caltech. February 1, 1996.


10. Yuh, C. H. and Davidson, E. H. "Mutagenesis analysis of Endo16 Promoter" (Oral) The Sixth Biology Annual Retreat of Caltech. October 20-22, 1996.


11. Yuh, C. H. and Davidson, E. H. "Quantitative investigation and Mutagenesis analysis of Endo16 Promoter" (Oral) The Fifth Southwest Transcription Factor Meeting, Nov. 15-16, 1996.


12. Yuh, C. H. and Davidson, E. H. " The interaction and output of the functional elements in the module A of Endo16 Promoter" (Oral) The Sixth Southwest Transcription Factor Meeting, Apr. 11-12, 1997.


13. Yuh, C. H. “Functional intermodular interrelation and dedicated Cis-regulatory elements within module A of Endo16 promoter” (Oral) Developmental Biology of the sea urchin XI, Marine Biology Laboratories, Woods Hole, MA, September 10-14, 1997.


14. Yuh C. H. and Davidson, E. H. “Gene regulatory networks in sea urchin” (speaker). Genetic Regulatory Networks in Embryogenesis and Evolution, A workshop sponsored by the Center for Advanced Studies in the Space Life Sciences at the MBL. June 11-14, 1998.


15. Yuh, C. H. and Davidson, E. H. " 1. Developmental transfer of control within the Endo16 Cis-regulatory system: experimental extension of the computational model; 2. Multiple roles of Otx transcription factor and Otx-interacting factors in the endoderm and ectoderm of sea urchin embryos " (Oral) Developmental Biology of the sea urchin XIII, September 28 to October 2, 2000.


16. Yuh, C. H., Hamid Bolouri and Davidson, E. H. “Cis-regulatory logic in the Endo16 gene: switching from a specification to a differentiation mode of control.” (Poster) 40th Annual Meeting of the American Society for Cell Biology, December 9 to December 13, 2000.


17. Yuh C. H. (Customer Training) Procise-cLC Customer training class, Applied Biosystem, Foster city, June 26-29, 2001.


18. Yuh, C. H. and Davidson, E. H. “Systemamatic study of transcriptional regulation in the endo-mesoderm gene network” (Oral) Developmental Biology of the sea urchin XIV, Woods Hole MA, May 1 to May 5, 2002.


19. Yuh, C. H. and Davidson, E. H. “A genomic regulatory network for development 1. Mapping the functional elements in the Otx endodermal specific modules and the interrelationship of the inputs of Krox, GATA (e) and Otx 2. Identify the negative elements regulate the Endo16 promoter and developing a useful tool for identified the unknown negative modules.” (invited speaker) Institute for Systems Biology and Fred Hutchinson Cancer Research Center, Seattle WA, June 13, 2003.


20. Yuh, C. H. and Davidson, E. H. “Understanding Otx gene regulation by comparative methods” (Oral) Developmental Biology of the sea urchin XV, Woods Hole MA, September 24 to September 29, 2003.


21. Yuh, C. H. and Davidson, E. H. “Identify the negative elements, regulate the Endo16 promoter and develop a useful tool for identifying the unknown negative module in the sea urchin genome”. (Poster presentation) Systems Biology: Genomic Approaches to Transcriptional Regulation, Cold Spring Harbor, USA Sponsored by Caltech, March 4- March 7, 2004


22. Yuh, C. H. and Davidson, E. H. “The inter-relationship of the inputs of krox, GATA(e) and Otx on the regulation of Otxb1/2 transcripts” (Poster presentation) Systems Biology: Genomic Approaches to Transcriptional Regulation, Cold Spring Harbor, USA, Sponsored by Caltech., March 4- March 7, 2004


23. Yuh, C. H. Develop a High-throughput way to identify the inter-relationship between regulatory modules, and the completeness of the endomesoderm Gene Regulatory Network in the sea urchin embryo. Kenting winter workshop for the molecular biology (invited speaker), January 26-28, 2005.


24. Yuh, C. H. “Brn1/2/4, the Predict Midgut Regulator of the Endo16 Gene of the Sea Urchin Embryo”. 4th NHRI Conference on Developmental Biology (invited speaker), April 29-30, 2005.


25. Yuh, C. H. “Systematic approach toward the transcription regulation: Networks building to understand the development and disease formation”, 21st Biology Summer Camp (invited speaker), Chia-i, Taiwan, August 24-26, 2005


26. Jang, T. H., Lin, Y. I., Chen, H. L., Tseng, W. F., Chan, T. M., Davidson, E. H. and Yuh, C. H. “Systematic Approach to Transcriptional Regulation: Establish the Gene Regulatory Network for Endoderm Differentiation in Sea Urchin, Zebrafish and Colorectal Cancer”, Taiwan-India joint symposium on functional genomics, (invited speaker) India, New Delhi., October 20-21,2005


27. Chan, T. M., Jang, T. H., Wang, H. D. and Yuh, C. H. “Mapping Mesendoderm Gene Regulatory Network in Zebrafish”, Keystone Symposia on Systems Biology: Integrating Biology, Technology and Computation (poster), Taos, New Mexico, USA, March 5-10, 2006


28. Chan, T.-M*., Jang, T.-H., Wang, H.-D., and Yuh, C.-H. “Mapping
Embryonic Gene Regulatory Network in Zebrafish”. The 21st Joint Annual Conference of Biomedical Science. (Selected oral presentation) Taipei, March 19, 2006


29. Yuh, C. H. , “Developmental gene regulatory networks (GRNs) of zebrafish embryo” 2006 Bioinformatics in Taiwan (invited speaker), September 12~15, 2006


30. Chan, T. M., Chen, H. L., Tseng, W. F., Chao, C. H., Jang, T. H., Lin, Y. I., Hsu, H. I., Huang, C. B. and Yuh, C. H., “Systematically decipher the genomic regulatory networks for early embryogenesis in Zebrafish”, The Sixth across the Taiwan Strait Symposium on Cell Biology (invited speaker), May 19~21, 2007


31. Chan, T. M., Chen, H. L., Tseng, W. F., Chao, C. H., Jang, T. H., Lin, Y. I., Hsu, H. I., Huang, C. B. and Yuh, C. H., “The Transcriptional Regulatory Networks of the Zebrafish Endoderm”, Symposium of Bioinformatics and Systems Biology in Taiwan (invited speaker), September 4~5, 2007


32. Chan, T. M., Longabaugh W., Bolouri H., and Yuh, C. H. “Developmental gene regulatory networks (GRNs) of the zebrafish embryo”, Gene Networks in Animal Development and Evolution Colloquia (poster), February 14~16, 2008



33. Chan, T. M., Wang H. D. and Yuh, C. H. “The Endoderm Gene Regulatory Networks: Subcircuits of Sox32 and Sox17 in Zebrafish Development”, 9th International Conference on Systems Biology (poster), Gothenburg, Sweden, August 23- 27, 2008.


34. Tsai, T, F., Lin, P. T., Tsai, S. F., Shieh S. R. G. and Yuh, C. H. “Pathway analysis for gene expression profile in the Hepatitis B Virus X protein induced Hepatocellular Carcinoma mouse model” 9th International Conference on Systems Biology workshop 3: Inferring network for disease (invited speaker), Gothenburg, Sweden, August 27-28, 2008.


35. Chan, T. M., Longabaugh, W., Bolouri, H., Chen, H. L., Tseng, W. F., Chao, C. H., Jang, T. H., Lin, Y. I., Hung, S. C., Wang H. D. and Yuh, C. H. , “Developmental Gene Regulatory Networks in the Zebrafish Embryo”, 2008 Women in Marine Science & Biotechnology Academic Conference and Career Development, Taipei, Taiwan, October 27 - 28, 2008.


36. Chen, W. C., Lai, J. G., Jang, T. H., Huang, C. L. and Yuh, C. H., “WNK1, the downstream effector of VEGF-PI3K/Akt pathway on angiogenesis/vasculogenesis in Zebrafish”, JOINT MEETING OF The 6th Korea-Japan Joint Symposium on Vascular Biology and The 16th Annual Meeting of the Japanese Vascular Biology and Medicine Organization- New Dimensions in Vascular Biology and Medicin", December 3 -5, 2008, ISHIKAWA ONGAKUDO KANAZAWA JAPAN


Teaching experience:

Caltech

Taiwan