PUBLICATIONS

1. 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)

2. 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

3. 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]

4. 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.

5. 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)

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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.

19. 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.

20. 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.

21. 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.

22. 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.

23. Yuh, C. H. and Ting, L. P. C/EBP-like Proteins Binding to the Functional Box- and Box- of the Second Enhancer of Hepatitis B Virus. Mol. Cell Biol. 11: 5044-5052, 1991.

24. 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.

25. 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.

26. 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.