GUOLI WANG, Ph.D.
1505 Seneca Run, Ambler, PA 19002
Home: (215) 628-2798; Lab: (215) 214-4261; Fax: (215) 728-3574
E-mail: GL_Wang@fccc.edu
summary of Qualifications:
Education:
| Ph. D. | Theoretical Chemistry | Jilin University, China | June 1994 |
| M. S | Theoreticl Chemistry | Jilin University, China | June 1991 |
| B. Sc. | Physics | Inner Mongolia University, China | June 1988 |
Working Experience:
2006-present: Sr. Program Analyst II at Fox Chase Cancer Center
Abstract: New statistical energy functions development, and their application in Rosetta protein modeling package. Evaluate and optimize Rosetta protocols based on new energy functions for homology modeling, ab initio prediction, and sequence and structure design. Integrate SDPro into MolIDE2 to provide more powerful homology modeling platform. SDPro is a in-house software package which integrates all my individual algorithms and applications involving sequence space searching, sequence alignment/analysis, structure analysis, homology modeling, algorithm benchmarking, and data mining.
Technologies and tools: Rosetta, homology modeling, .NET/C#, Mono, C++, Fortran, MPICH2, Perl.
Abstract: Provide HPC support for researches at Fox Chase Cancer Center, which include molecular simulation, docking, drug screening and design, microarray data analysis, and other structural biology and bioinformatics studies.
Technologies and tools: Schrodinger/Glide, Amber, Charmm, Modeller, Rosetta, NMF, C++, MPICH2, Perl, Php.
2005: Research Associate in Bioinformatics Group at Fox Chase Cancer Center
Abstract: Non-negative factorization (NMF) is a machine learning algorithm, I developed a novel variant of NMF by utilizing the uncertainty estimate information. LSNMF significantly improved the power of NMF in term of linking functionally related genes, and it is also much more stable than NMF during the simulation. I have implemented a C++ package for NMF and LSNMF with HPC version available.
Technologies and tools: C++, LAM/MPI, Perl, Matlab, biostatistics.
Download: http://bioinformatics.fccc.edu/software/OpenSource/LS-NMF/lsnmf.shtml.
Technologies and tools: C/C++, Perl, R, Matlab, NCBI toolkit and databases.
2004: Research Associate in Dr. Roland Dunbrack's lab at Fox Chase Cancer Center
Abstract: Dirichlet process mixture models and the corresponding simulation techniques are well-developed methodology in statistics to address classification and pattern recognition problems. I have adapted Neal’s various implementations to derive Dirichlet mixtures for amino acid counts in multiple alignment columns and genome sequence domains, and have used the derived Dirichlet mixture models to develop new sequence alignment and sequence segmentation algorithms.
Technologies and tools: C/C++, Perl, Bayesian statistics, HMM, MCMC.
Abstract: Integrated all related sequence alignment software pieces into a package for an in house platform which can be used for algorithm development on sequence alignment and homology modeling.
Technologies and tools: C/C++, Perl, Php, Java, HTML/Javascript, CGI, LAM/MPI, MySQL
Abstract: I was the key member in the assessor group to evaluate algorithms of fold recognition in CASP6. CASP is the most prestigious international contest for algorithm developers in protein structure prediction. I introduced a new scoring system to judge the algorithm performance, I also developed a pipeline for large scale data visualization.
Technologies and tools: sequence and structure alignment, Perl, csh, Grace, InsightII, Rasmol, Modeller.
2000-2003: Post-doctoral fellow in Dr. Roland Dunbrack's lab at Fox Chase Cancer Center
Abstract: Developed a new structure dependent profile-profile alignment algorithm, which integrated multiple scoring systems together to yield more accurate and more specific result. The new algorithm combines position specific profile-profile alignment score with location dependent secondary structure alignment score, makes use of as much as possible available sequence and structure information. It had been showed more powerful than other profile-profile alignment algorithms which were available at that time.
Technologies and tools: C++, Perl, PsiPred, 3D-profile, HMM, MySQL.
Abstract: Set up a comprehensive benchmark system based on SCOP database which contains total 1627 representative SCOP entries, 3442 true alignment pairs for alignment accuracy training and test, 2207890 decoys for homology detection test. I have tested 7 different scoring functions, 3 approaches of converting MSA to PSSM, 3 gap penalty schemes, 3 different ways of building MSA from sequence space searching.
Technologies and tools: C++, Perl, NCBI toolkit, HMM, secondary structure prediction.
Technologies and tools: NCBI toolkit, InsightII, Modeller, Loopy.
Abstract: I was the key player in this contest, my major role was building sequence alignments for all targets against known PDB structures.
Technologies and tools: NCBI toolkit, Perl, C++, shell script, LAM/MPI.
1999-2000: Post-doctoral fellow in Dr. Huan-Xiang Zhou's lab of Drexel University
1996-1999: Associate professor in Beijing Institute of Biotechnology, China.
1997-1999: Support scientist of Biosym/MSI simulation system (Accelrys) for NeoTrident Technology Limited,China.
1994-1996: Post-doctoral fellow in Beijing Institute of Biotechnology, China.
ACADEMIC ACTIVITIES
Reviewer of BMC bioinformatics and Journal of Biomedical Informatics.