epigenomics, cellular reprogramming, protein recognition, computational biology, systems biology
University of California, San Francisco
University of Miami
Awards and Academic Honors
Postdoctoral Fellow, Stanford University
American Chemical Society CCG Excellence Award
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.
Primary Research Area
Computational and Theoretical
Participant of the outreach program of Center for Theoretical Biological Physics (CTBP) at UCSD. This program is sponsored by NSF to promote research interests in basic sciences among undergraduate and high school students particularly those in underrepresented groups. For example, I gave seminars in California State University, San Marcus (CSUSM), in which a significant number of students are from underrepresented groups.
Mentor of high school students, undergraduate and graduate students and postdoctoral students from underrepresented groups in my laboratory.
- 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).