个人简介

2001-2003 Postdoctoral Fellow, Stanford University 2000 American Chemical Society CCG Excellence Award

研究领域

Biochemistry

We are interested in understanding the regulatory mechanisms underlying cell fate decision. Especially, we take a multi-scale approach that integrates computational and experimental investigation of epigenetic regulation in cell fate decision from molecular level to genomic level then to systems level. We aim to build computational and theoretical models to uncover fundamental principles that govern cell fate decision in development and cellular reprogramming and design strategies to intelligently manipulate cell state. Our research is highly interdisciplinary. The methods we use range from molecular modeling of protein structures, to bioinformatics analysis of epigenomic data generated by sequencing technology, to statistical learning of genetic network, to biophysical modeling of epigenetic landscape. The theoretical work is tightly coupled with experimental investigation that exploits molecular biology, biochemistry, cell biology and genomic techniques.

近期论文

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A systematic approach to reconstructing transcirption networks in Saccharomyces cerevisiae. With J. M. Cherry, D. Botstein and H. Li., Proceeding of the National Academy of Sciences of the United States of America, 99, 16893 (2002). An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations and sequence analysis. With W. A. Lim, A. Jakalian, J. Wang, J. Wang, R. Luo, C. Bayly, and P. A. Kollman. Journal of the American Chemical Society. 123, 3986 (2001). Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis and protein-ligand, protein-protein and protein-nucleic acid non-covalent interactions. With O. Donnii, C. M. Reyes and P. A. Kollman. Annual Review of Biophysics and Biomolecular Structure. 30, 211 (2001). Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. With P. A. Kollman. Proceeding of the National Academy of Sciences of the United States of America. 98, 14937 (2001). Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA. With J. Wang, P. Morin and P. A. Kollman. Journal of the American Chemical Society. 123, 5221 (2001). Free energy calculations on the HIV-1 protease dimmer stability using molecular dynamics and a continuum model. With P. A. Kollman. Journal of Molecular Biology. 303, 567 (2000). What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? With J. Wang and P. A. Kollman. Proteins. 34, 395 (1999).