Working Experience

9/2017-present: Vice president of the department and Professor
Department of Computer Science, Sichuan University, Chengdu, China: Computational biology

I am working for bioinformatics, numerical analysis, high performance computing and data mining.

12/2014-9/2017: Professor
College of Computer and Information Science & College of Software, Southwest University, Chongqing, China: Computational biology

I have three research direction. First, employing parallel algorithm to speedup the bioinformatics application. Second, integrating constrained numerical optimization method into classical survival analysis algorithm to process p>>n type of gene expression data. Third, using semantic web technology to develop sematic database for the big biological data.

12/2012 – 14/2014: Research Associate Professor
Biostatistics and Computational Biology Department of University of Rochester: System Biology

As a computational biologist, I am developing computational methods and innovations for cancer and immunology research. Currently, I am collaborating with experimentalist to investigate how the drug impacts cell’s molecular pathway. First, with the help of biologist, we chose important proteins which have significant changes under the drug delivery and used Ingenuity Pathway Analysis database to generate the generic signaling pathway. Second, we analyzed the high-throughput proteomics data generated from proteomic data (Reverse Phase Protein Array) and employed the data to infer the signaling transduction pathway described by systems of ordinary differential equations. Third, we employed numerical optimization methods to optimize the key parameters of the pathway by fitting the experimental data.
The inferred biological network is incorporated into my well developed multi-scale and multi-resolution agent based model (ABM) to simulate and predict tumor’s progression by C++/Java languages. Multi-scale ABM consists of intracellular, intercellular and cellular levels. The inferred biological network determines cell’s phenotype switch in the intercellular scale. The intercellular module of ABM is used to describe cell’s behavior and angiogenesis in the extracellular matrix (ECM) with respect to various phenotypes. The chemoattractants and drug, which diffuse in the tissue module of ABM, stimulate and inhibit the intracellular pathway of the cell by binding cell’s receptor. Multi-resolution design allows us to classify the millions of simulated tumor cells into active or inactive clusters regarding to biological rules. And then, we can concentrate limited compute resources onto the region of interest of the tumor. In addition, GPU (CUDA) based parallel computing algorithm is employed to increase our compute capacity. Currently, I am employing ABM to simulate the cancer progression under drug delivery, such as pharmacokinetic and pharmacodynamic (PK/PD) modeling. In addition, I am collaborating with Neurology Department of University of Rochester to employ Lasso and survival model to investigate the key genes for Glioma cancer research.

8/2008 – 2012/9: Assistant Professor
Computational Science and Engineering Institute and the Department of Mathematical Sciences of Michigan Tech University: Computational Biology

I did mathematical teaching and computational biology of cancer research. Especially, I employed Graphic programming Unit to speed up the classical agent based modeling. As a faculty member, I not only have good communication and collaboration skills, but also rich experience to write NIH, NSF and DoD proposals for my research. One of my proposals was funded by NIH in 2012.

05/2005 – 8/2008: Research Fellow
Harvard-MIT (HST) Athinoula A. Martinos Center for Biomedical Imaging: Complex Biosystems Modeling

Under the supervision of Dr. Thomas S. Deisboeck and in collaboration with other members of the Complex Biosystems Modeling Laboratory, I used Java/C++ to build up the multi-scale and multi-resolution agent based models to simulate highly malignant brain tumors as adaptive self-organizing biosystems. In addition, I was an associated administrator for the Center for the Development of a Virtual Tumor (CViT), which is part of the NIH/NCI’s Integrative Cancer Biology Program (ICBP). My duty was assisting IBM internet group to manage the database and update the webpage of CViT. For web development, I have experience in Perl and Javascript.

09/2001 – 05/2005: Research Assistant
Computational Analysis and Modeling program of Louisiana Tech University

My dissertation is focused on the treatment of skin cancer. By collaborating with Louisiana State University medical school, I built up a 3D blood flow model by the coupled PDE and ODE equations to characterize the temperature transients over the whole skin cancer area by C++ programming language. This research can help the physician to forecast a proper laser power to kill the skin tumor.

07/1999 – 09/2001: Software Engineering
Bell Lab (Chicago) & Lucent (China) Ltd., Research and Design Department

Develop and test the communication software. Develop and deliver the project of Long distance call fee calculation feature for Saudi Arab, Personal Handy Phone fee calculation feature for Yi Chang, China and Intelligence Network fee calculation feature for Wu Han China by C language.