Faculty Profile, National Health Research Institutes, Taiwan

Faculty Profiles

Chiou-Hwa Yuh, Ph.D.

Associate Investigator
Institute of Molecular and Genomic Medicine


Ph.D., Microbiology and Immunology, National Yang-Ming Medical College, Taipei, Taiwan (1992)
B.S., Biology, Fu-Jen Catholic University, Taipei, Taiwan (1987)


- Adjunct Associate Professor, Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taiwan (2006-present)
- Associate Investigator, Division of Molecular and Genetic Medicine, National Health Research Institutes, Taiwan (2005-present)
- Adjunct Assistant Professor, Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taiwan (2005-2006)
- Member of the Professional Staff, Biology Division, California Institute of Technology, CA, USA (2002-2004)l Director, Transcription Factor Center, Beckman Institute, California Institute of Technology, CA, USA (2001-2002)
- Research Associate, Stowers Institute of Medical Research, MO, USA (1996-2001)
- Senior Research Fellow, California Institute of Technology, CA, USA (1995-2001)
- Research Fellow, California Institute of Technology, CA, USA (1992-1995)


Dr. Yuh's research interests include transcription regulation, developmental biology, cancer biology, and systems biology. In Yuh's lab, researchers are using high throughput methods to establish the genomic regulatory networks underlying the early development and cancer formation.

1. Zebrafish endoderm and mesoderm genomic regulatory networks. Dr. Yuh uses zebrafish as model organism to uncover the mystery of how the endoderm and mesoderm form from a single cell using systematic approaches. Yuh establishes the dynamic genomic regulatory networks to integrate the literatures data as well as experimental knockdown data. The most sophisticated integrated biological networks defined to date is the sea urchin endomesoderm specification GRN (Davidson et al, 2002) from Dr. Eric Davidson’s lab at Caltech where Yuh had been working for more than 12 years. In Yuh’s lab at NHRI, researchers used the similar approaches to decode the gene regulatory networks in zebrafish. The genomic regulatory code consists of the sequence specific templates for networks of cis-regulatory elements and trans-transcription regulatory factors. Understanding the function of genes and the interrelationship of genes in regulating endomesoderm formation in zebrafish will benefit us to understand the basic of how the human genome works. The endomesoderm gene network is not only a blueprint of how genes work together to make the endoderm and mesoderm in zebrafish embryo, it also provides a tool to let us understand how those evolutionarily conserved transcription factors work together.

2. Oncogenomic study of human colorectal, liver, lung cancer Cancer is a complicated disease that results from abnormal overexpression of oncogenes and down-regulation of tumor suppressor genes. From the point of view of Systems Biology, cancer is formed from disturbed networks. To find out the genomic regulatory networks underlying the cancer formation, Dr. Yuh uses drug to re-248 engineer the circus and correct the networks to make people back to normal. Dr. Yuh has been collaborating with medical doctors, pathologist, computational scientists as well as statisticians to analyze the cancer genome-wide. Researchers in Yuh’s lab are using high throughput technologies, for example, NimbleGen Microarray, Illuminar in bead expression analysis and 454 sequencing technologies to get enormous amount of data. The data ranges from genomic changes (array CGH study), transcriptome analysis (RNA expression array), mutational analysis (SNP, microdeletion, microamplification), epigenomic changes (methylation on CpG island) and proteomic analysis. Yuh will establish the gene regulatory networks of different kind of cancer based on those high-throughput data.

3. Linked the embyonic networks and oncogenomic networks together. Cancer is formed from cancer stem cells, if cancer stem cells exist, the cancer will grow back. By compare the embryonic networks and oncogeomic networks, Yuh’s group hopes to find the common nodes or circuis between them, and that is probablythe most important kernel of the cancer stem cell GRN. Dr. Yuh design drug to target those nodes, and hopefully to destroy the cancer from the very beginning.


Dr. Yuh has been studying transcription regulation since 1987. She started on studying the transcription regulation of Hepatitis B Virus in hepatoma cell line, and had published five international papers regarding this issue. Then, Dr. Yuh switched her studying subject into development biology at Caltech. Within the 12 years at Caltech, Dr. Yuh involved the decoding of the Endo16 gene’s transcription regulation and published the first bioinformatics methods on using the computational algorisms to explain the transcription regulation. Then she became the director of the transcription factor center with incredible amount of experience on biochemical purification of the transcription factors and sequencing the amino acid. Later, Dr. Yuh participated on establishment of the Gene Regulatory Networks for the endomesoderm specification in sea urchin embryo. In this collaboration, Yuh obtained the skill of managing large scale of Q-PCR data, and integrating them using computation program, this lab successfully established the first and the only one fantastic logical networks model. In Caltech, Dr. Yuh had published 14 scientific high impact papers including two published on science, and two book chapters. Dr. Yuh started zebrafish study in NHRI and have the first and only one zebrafish culture system in the entire NHRI, and Yuh´s lab had done ennormous micorinjection into zebrafish embryos and have established the gene regulatory networks for zebrafish embryogenesis.


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. 15;281(2):286-98, 2005.

2. 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. 15;269(2):536-51, 2004.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

(*=Corresponding Author)