Chao Tang, Ph.D.
Professor of Biopharmaceutical Scienes

Contact Information:
chao.tang@ucsf.edu
Tel: (415) 514-4414
Fax: (415) 826-3381
California Institute for Quantitative Biomedical Research (QB3)
1700 4th Street, N-408D
San Francisco, CA 94143-2540


Links:
Lab Website
California Institute for Quantitative Biomedical Research

Publications

 

Design and organization principles of biological systems; quantitative study and systems analysis of biological networks

The research interest of our group is at the interface between the physical and the biological sciences. We are interested in quantitative studies and the systems level analysis of biological networks. These include specific regulatory, signaling, genetic, and metabolic networks, as well as large scale genome-wide networks. We use and develop quantitative methods and ideas to address key biological questions and try to understand the design and organization principles of biological systems at various levels. The group is mainly theoretical and computational, but a small experimental effort will soon be setup.

Selected Publications:
Y. Zhang, M. Qian, Q. Ouyang, M. Deng, F. Li, and C. Tang, "A stochastic model of the yeast cell cycle network," submitted.

J. Li, R. Car, C. Tang, and N. Wingreen , "Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water," submitted.

E. Kruus, P. Thumfort, C. Tang, and N. Wingreen , "Gibbs sampling and helix-cap motifs," Nucleic Acids Research, in press.

W. Ma, C. Tang, and L. Lai, "Specificity of trypsin and chymotrypsin: Loop motion controlled dynamic correlation as a determinant," Biophys. J. 89 , 1183 (2005).

M. Kloster, C. Tang, and N. Wingreen, "Finding regulatory modules through large scale gene expression data analysis," Bioinformatics 21 (7), 1172, (2005).

S. Moelbert, E. Emberly, and C. Tang, "Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins," Protein Science 13 (3), 752 (2004).

F. Li, Y. Lu, T. Long, Q. Ouyang, and C. Tang, "The yeast cell-cycle network is robustly designed," PNAS 101 (14), 4781 (2004).

E. Emberly, R. Mukhopadhyay, C. Tang, and N. Wingreen , "Flexibility of ß-sheets: Results of a statistical analysis of database protein structures," Proteins 55, 91 (2004).

M. Kloster and C. Tang, "Simulation and analysis of in vitro DNA evolution," Phys. Rev. Lett. 92, 038101 (2004).

N. Wingreen, H. Li, and C. Tang, "Designability and Thermal Stability of Protein Structures," Polymer 45, 699 (2004).

R. Mukhopadhyay, E. Emberly, C. Tang, and N. Wingreen , "Statistical mechanics of RNA folding: Importance of alphabet size," Phys. Rev. E 68, 041904 (2003).

E. Emberly, R. Mukhopadhyay, N. Wingreen , and C. Tang, "Flexibility of a-helices: Results of a statistical analysis of database protein structures," J. Mol. Biol. 327, 229 (2003).

M. Yahyanejad, M. Kardar, and C. Tang, "Structure space of model proteins: a principle component analysis," J. Chem. Phys. 118, 4277 (2003).

H. Li, C. Tang, N. Wingreen , "The Designability of Protein Structures: A Lattice-Model Study using the Miyazawa-Jernigan Matrix," Proteins 49, 403 (2002).

E. Emberly, N. Wingreen , and C. Tang, "Designability of a-helical Proteins," Proc. Natl. Acad. Sci. USA 99, 11163 (2002).

J. Miller, C. Zeng, N. Wingreen , and C. Tang, "Emergence of highly-designable protein-backbone conformations in an off-lattice model," Proteins 47, 506 (2002).

H. Cejtin, J. Edler, A. Gottlieb, R. Helling, H. Li, J. Philbin, N. Wingreen, and C. Tang, "Fast Tree Search for Enumeration of a Lattice Model of Protein Folding," J. Chem. Phys. 116, 352 (2002).

M. Kloster, S. Maslov , and C. Tang, "Exact Solution of Stochastic Directed Sandpile Model," Phys. Rev. E, 63, 026111 (2001).

T. Wang, J. Miller, N. Wingreen , C. Tang, and K. Dill, "Symmetry and Designability for Lattice Protein Models," J. Chem. Phys. 113, 8329 (2000).

C. Tang, "Simple Models of the Protein Folding Problem," Physica A 288, 31 (2000).

S. Maslov, C. Tang, and Y.C. Zhang, "1/f Noise in Bak-Tang-Wiesenfeld Models on Narrow Stripes," Phys. Rev. Lett. 83, 2449 (1999).

C. Denniston and C. Tang, "Incommensurability in the Frustrated Two-Dimensional XY Model," Phys. Rev. B. 60, 3163 (1999).

R. Mélin, H. Li, N. Wingreen , and C. Tang, "Designability, Thermodynamic Stability, and Dynamics in Protein Folding: a Lattice Model Study", J. Chem. Phys. 110, 1252 (1999).