USC College Department of Biology

Faculty

Biological Sciences has more than 60 full-time faculty members, as well as more than 20 faculty with joint appointments and 15 visiting or adjunct professors. Among its many distinctions and honors, the Ph.D. program faculty includes two members of the National Academy of Sciences, four members of the American Academy of Arts and Sciences, and 18 holders of endowed chairs and professorships.

Ting Chen

Associate Professor of Biological Sciences and Computer Science

Contact Information
E-mail: tingchen@usc.edu
Phone: (213) 740-2415
Office: MCB 408H

LINKS
Faculty Profile on Departmental Website

Education

BE Computer Science and Engineering, Tsinghua University, Beijing, China, 6/1993
Ph.D. Computer Science, State University of New York at Stony Brook, 12/1997

Academic Appointment, Affiliation, and Employment History

Tenure Track Appointments

Associate Professor of Biological Sciences, Computer Science and Mathematics, University of Southern California, 03/01/2006-
Assistant Professor of Biological Sciences, Computer Science and Mathematics, University of Southern California, 09/01/2000-03/01/2006

Non-Tenure Track Appointments

Lecturer of Genetics, Harvard Medical School, 10/01/1997-07/30/2000

Visiting and Temporary Appointments

Guest Research Associate, Brookhaven National Laboratory, 1995-1998

Description of Research

Summary Statement of Research Interests

Within the fields of computational biology and bioinformatics, Professor Chen seeks to apply computer algorithms and mathematical methods to answer questions in biology and medicine, specifically in studies of human genetics, proteomics, and genomics. Dr. Chen's research includes (1) analysis of next-generation sequencing data, (2) analysis of variations of the human genome and their relationships to human diseases, (3) analysis of protein functions and protein interaction networks, and (4) identification of proteins through analyzing mass spectrometry data.

Affiliations with Research Centers, Labs, and Other Institutions

NIH Center of Excellence in Genome Sciences
Center for Computational and Experimental Genomics,http://www-hto.usc.edu

Publications

Book Chapter

Chen, T., Waterman, M. Dynamic Programming. Nature Publishing: Nature Encyclopedia of Human Genome; 2003.

Journal Article

Chen, Y., Souaiaia, T., Chen, T. (2009). PerM: Efficient Mapping of Short Sequencing Reads with Periodic Full Sensitive Spaced Seeds. Bioinformatics. Vol. 25 (19), pp. 2514-21.
Wang, L., Sun, F., Chen, T. Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy., Genome Biology 2008; Vol. 9 (R174).
Jiang, R., Yang, H., Kuo, C. J., Sun, F., Chen, T. (2007). Sequence-based prioritization of nonsynonymous single nucleotide polymorphisms for the study of disease mutations. American Journal of Human Genetics.. Vol. 81 (2), pp. 346-60.
Mo, L., Dutta, D., Wan, Y., Chen, T. MSNovo: A new dynamic programming algorithm for de novo peptide sequencing., Analytical Chemistry 2007; Vol. 79(13) (4870-8).
Dutta, D., Chen, T. Speeding up Tandem Mass Spectrometry Database Search: Metric Embeddings and Fast Near Neighbor Search., Bioinformatics 2007; Vol. 23(5) (612-8).
Chen, T., Wan, Y., Yang, A. (2006). PepHMM: A hidden Markov model based scoring function for tandem mass spectrometry. Analytical Chemistry. Vol. 78 (2), pp. 432-7.
Zhidong, T., Wang, L., Arbeitman, M. N., Chen, T., Sun, F. (2006). An integrative approach for causal gene identification and expression regulatory pathway inference. Bioinformatics. Vol. n/a
Jiang, R., Tu, Z., Chen, T., Sun, F. (2006). Network Motif Identification in Stochastic Networks. The Proceeding of National Academy of Sciences. Vol. 103 (2), pp. 9404-9.
Jiang, R., Yang, H., Sun, F., Chen, T. Searching for interpretable rules for disease mutations: A simulated annealing bump hunting strategy., BMC Bioinformatics 2006; Vol. 7(1) (417).
Lee, H., Deng, M., Sun, F., Chen, T. Inferring domain-domain interactions from multiple biological data sources., BMC Bioinformatics 2006; Vol. 7(1) (269).
Huang, Y., Chao, K., Chen, T. An approximation algorithm for haplotype inference by maximum parsimony., Journal of Computational Biology 2005; Vol. 12(10) (1261-74).
Huang, Y., Zhang, K., Chen, T., Chao, K. Approximation algorithms for the selection of robust tag SNPs., BMC Bioinformatics 2005; Vol. 6 (263).
Su, S., Kuo, C., Chen, T. Inference of Missing SNPs and Haplotype Block Partitioning., Bioinformatics 2005; Vol. 21(9) (2001-7).
Deng, M., Chen, T., Sun, F. An Integrative Analysis of Protein Function Prediction., Journal of Computational Biology 2004; Vol. 11(2-3) (463-75).
Deng, M., Tu, Z., Sun, F., Chen, T. Mapping Gene Ontology to Proteins Based on Protein-protein Interaction Data., Bioinformatics 2004; Vol. 20(6) (895-902).
Zhang, K., Sun, F., Waterman, M., Chen, T. (2003). Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. American Journal of Human Genetics. Vol. 73, pp. 63-73.
Deng, M., Zhang, K., Mehta, S., Chen, T., Sun, F. Prediction of protein function using protein-protein interaction data., Journal of Computational Biology 2003; Vol. 10(6) (947-960).
Deng, M., Sun, F., Chen, T. Assessment of the reliability of protein-protein interactions and protein function prediction., Pacific Symposium on Biocomputing 2003; Vol. Page (140-51).
Lu, B., Chen, T. A Suffix Tree Approach to the Interpretation of Tandem Mass Spectra: Applications to Peptides of Nonspecific Digestion and Post-translational Modifications., Bioinformatics (Suppl 2) 2003; Vol. 113-121.
Lu, B., Chen, T. A Suboptimal Algorithm for De novo Peptide Sequencing via Tandem Mass Spectrometry., Journal of Computational Biology 2003; Vol. 10(1): 1-12.
Zhang, K., Deng, M., Chen, T., Waterman, M., Sun, F. (2002). A dynamic programming approach for haplotype partitioning. The Proceeding of National Academy of Sciences. Vol. 99 (11), pp. 7335-9.
Deng, M., Metah, S., Sun, F., Chen, T. (2002). inferring Domain-Domain Interactions from Protein-Protein Interactions. Genome Research. Vol. 12, pp. 1540-8.
Chen, T., Kao, M. Y., Tepel, M., Rush, J., Church, G. M. A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry., Journal of Computational Biology 2001; Vol. Vol 8 (Num 3): Page 325-337.
Chen, T., He, H., Church, G. M. Modeling Gene Expression with Differential Equations., Pacific Symposium on Biocomputing (PSB99) 1999; 29-40.
Chen, T., Skiena, S. Sorting with fixed-length reversals., Journal of Discrete Applied Mathematics 1996; Vol. 71: 269-296.

Advisement

Other Advisement or Time Devoted to Students

Computational Biology Graduate Student Advisor, 08/2006-08/2010

Honors and Awards

Sloan Research Fellowship Recipient, Alfred P. Sloan Fellowship in Evolutionary and Computational Biology, 2004

Service to the University

Committees

Member, USC High Performance Computing Committee, 2008-
Member, USC Clinical Translational Science Institute (CTSI): Computational Biology Advisory Committee, 2008-
Member, USC College Biology Undergraduate Curriculum Committee, 2007-2008
Member, USC College Faculty Council, 2005-2006

Review Panels

NIH, BST-Q, 2008-2009
NIH, ZRG1 GGG-A, 2008-2009

Service to the Profession

Editorships and Editorial Boards

Editorial Board, BMC Bioinformatics, 2003-

Review Panels

NIH, BST-Q, 2008-2009
NIH, ZRG1 GGG-A, 2008-2009