MCB Faculty


Ting Chen

Professor of Biological Sciences and Computer Science

Contact Information
E-mail: tingchen@usc.edu
Phone: (213) 740-2415
Office: RRI 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
    • Professor of Biological Sciences and Computer Science, University of Southern California, 2011-  
    • Associate Professor of Biological Sciences, Computer Science and Mathematics, University of Southern California, 2006-2011  
    • Assistant Professor of Biological Sciences, Computer Science and Mathematics, University of Southern California, 2000-2006  

    Non-Tenure Track Appointments
    • Lecturer of Genetics, Harvard Medical School, 10/01/1997-07/30/2000  

    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
    • Chen, T., BW, L., Soreghan, S., Thomas, S., Yang, A. (2005). Proteomics data management and visualization.

    Book Chapter
    • Chang, Q., Luan, Y., Chen, T., Fuhrman, J., Sun, F. (2011). Computational methods for the analysis of tag sequences in metagenomics studies. Frontiers in Bioscience.
    • Chen, T., Sun, F., Deng, M., Lee, H., Tu, Z. (2006). Data integration for the study of protein interactions. (Vol. NA). Meta-analysis and Combining Information in Genetics/Chapman and Hall.
    • Chen, T., Zhang, K., Huang, Y., Chao, K. (2006). Approximation Algorithms for the Selection of Robust Tag SNPs. (Vol. NA). Handbook of Approximation Algorithms and Metaheuristics/Chapman and Hall.
    • Chen, T., Waterman, M. Dynamic Programming. Nature Publishing: Nature Encyclopedia of Human Genome; 2003.

    Conference Proceeding
    • Mehta, G., Deelman, E., Knowles, J., Chen, T., et al., e. (2012). Enabling Data and Compute Intensive Workflows in Bioinformatics. pp. 23-32. Lecture Notes in Computer Science, 2012, Volume 7156, EURO-PAR 2011: PARALLEL PROCESSING WORKSHOPS.

    Journal Article
    • Hao, X., Chen, T. (2012). OTU Analysis Using Metagenomic Shotgun Sequencing Data. PLoS ONE.
    • Souaiaia, T., Zhang, Z., Chen, T. (2012). FadE: Whole Genome Methylation Analysis for Multiple Sequencing Platforms. Nucleic Acid Research.
    • Lehmann, K., Chen, T. (2012). Exploring functional variant discovery in non-coding regions with SInBaD. Nucleic Acid Research.
    • Wan, L., Yan, X., Chen, T., Sun, F. (2012). Modeling RNA degradation for RNA-Seq with applications. Biostatistics.
    • Wang, Y., Mehta, G., Mayani, R., Clark, A., Lu, J., Chen, Y., Knowles, J., Deelman, E., Chen, T. (2011). RseqFlow: Workflows for RNA-seq data analysis. Bioinformatics. Vol. 27 (18), pp. 2598-2600.
    • Souaiaia, T., Frazer, Z., Chen, T. (2011). ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms. Journal of Computational Biology. Vol. 18 (6), pp. 795-807.
    • Hao, X., Jiang, R., Chen, T. (2011). Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics. Vol. 27 (5), pp. 611-618.
    • 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.
    • Chen, Y., Chen, T. (2009). An Integer Programming Approach for the Selection of Tag SNPs using Multi-allelic LD. Communications in Information and Systems.
    • Jiang, R., Chen, T., Sun, F. (2009). Bayesian models and Gibbs sampling strategies for local graph alignment and network motif identification in stochastic biological networks. Communications in Systems and Information. Vol. 9 (4), pp. 347-370.
    • 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).
    • Peña-Castillo, L., et, a. (2008). A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol. Vol. 9(Suppl 1), pp. S2.
    • Jia, L., Berman, B., Jariwala, U., Yan, X., Cogan, J., Walters, A., Chen, T., Buchanan, A., Frenkel, B., Coetzee, G. Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity., PLoS ONE 2008; Vol. 3(11) (e3645).
    • Wan, Y., Cripps, D., Thomas, S., Campbell, P., Ambulos, N., Chen, T., Yang, A. (2008). PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. J Proteome Res. Vol. 7 (7), pp. 2803-11.
    • 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).
    • Su, S., Kuo, J. C., Chen, T. Signal Processing Techniques for SNP (Single Nucleotide Polymorphism) Data Analysis., IEEE Signal Processing Magzine: Special Issue on Signal Processing Methods in Genomics and Proteomics. 2007.
    • 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).
    • Guha, R., Dutta, D., Wild, D., Chen, T. Counting Clusters Using R-NN Curves., J Chem Inf Model 2007; Vol. 47(4): 1308-18.
    • Dutta, D., Guha, R., Wild, D., Chen, T. Ensemble Feature Selection: Consistent Descriptor Subsets for Multiple QSAR Models., ACS J Chem. Inf. Model 2007; Vol. 47 (3): 89-97.
    • 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).
    • Tu, Z., Wang, L., Xu, M., Zhou, J., Chen, T., Sun, F. Further understanding human disease genes by comparing with housekeeping genes and other genes., 2006 2006; Vol. 7 (31).
    • Lee, H., Tu, Z., Deng, M., Sun, F., Chen, T. Diffusion kernel based logistic regression models for protein function prediction., OMICS: : Integrative Biology 2006; Vol. 10(1) (40-55).
    • Guha, R., Dutta, D., Jurs, P., Chen, T. R-NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method., ACS J Chem Inf Model 2006; Vol. 46 (4): 713-22.
    • Dutta, D., Guha, R., Jurs, P., Chen, T. Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions., ACS J Chem Inf Model 2006; Vol. 46 (4): 836-47.
    • Dutta, D., Guha, R., Jurs, P., Chen, T. Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing., ACS J Chem Inf Model 2006; Vol. 46 (1): 21-33.
    • Chen, T., Smith, E., Meyerrose, T., Kohler, T., Namdar-Attar, M., Bab, N., Lahat, O., Noh, T., Li, J., Karaman, M. (2005). Leaky ribosomal scanning in mammalian genomes: Physiological consequences of histone H4 alternative translation. No Journal Defined. Vol. 1;33(4), pp. 1298-308.
    • Chen, T., Soreghan, B., Lu, B., Thomas, S., Duff, K., Rakhmatulin, E., Nikolskaya, T., Yang, A. (2005). Redox proteomic analysis of a PS1+APP mouse model of Alzheimer’s disease. No Journal Defined. pp. p.;8(3).
    • 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).
    • Zhang, K., Qin, Z., Chen, T., Liu, J., Waterman, M., Sun, F. HapBlock: Haplotype Block Partitioning and Tag SNP Selection Software Using a Set of Dynamic Programming Algorithms., Bioinformatics 2005; Vol. 21(1) (131-4).
    • Lee, H., Sun, F., Chen, T. Assessment of the Reliability of Protein-Protein Interactions Using Protein Localization and Gene Expression Data., BIOINFO 2005.
    • Zhang, K., Qin, Z., Liu, J., Chen, T., Waterman, M., Sun, F. Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies., Genome Res 2004; Vol. 14(5) (908-16).
    • 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. (2001). Wyrick, J. J., Aparicio, J. G., Chen, T., Barnett, J. D., Jennings, E. G., Young, R. A., Bell, S. P., and Aparicio, O. M. Genome-Wide Location Analysis of ORC and MCM Proteins: High Resolution Mapping of Replication Origins Reveals Novel Origin Classes in Saccharomyces cerevisiae. Science, 2357-2360, Dec 14, 2001. Science. pp. 2357-2360.
    • Chen, T., Jaffe, J., Church, G. M. (2001). Algorithms for Identifying Protein Cross-links via Tandem Mass Spectrometry. Journal of Computational Biology,. Vol. 8 (6), pp. 571-583.
    • Chen, T. (2001). Identifying gene regulartory networks from experimental data. Journal of Parallel Computing. Vol. 27 (1-2), pp. 141-162.
    • 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., Filkov, V., Skiena, S. Identifying gene regulartory networks from experimental data., Journal of Parallel Computing 2001; Vol. 27(1-2): 41-162.
    • Chen, T., Skiena, S. A Case Study in Genome-Level Fragment Assembly., Bioinformatics 2000; Vol. 16: 494-500.
    • Chen, T., He, H., Church, G. M. Modeling Gene Expression with Differential Equations., Pacific Symposium on Biocomputing (PSB99) 1999; 29-40.
    • Chen, T., Kao, M. Y. On the Informational Asymmetry between Upper and Lower Bounds for Ultrametric Evolutionary Trees., The 7th Annual European Symposium on Algorithms (ESA’99 1999; 248-256.
    • Chen, T., Zhang, M. Q. Pombe A Fission Yeast gene-finding and exon-intron structure prediction system., Yeast 1998; Vol. 14: 701-710.
    • Chen, T., Skiena, S. Trie-based data structures for fragment assembly., The Eighth Symposium on Combinatorial Pattern Matching (CPM97 1997; 206-223.
    • Chen, T., Skiena, S. Sorting with fixed-length reversals., Journal of Discrete Applied Mathematics 1996; Vol. 71: 269-296.

    Proceedings
    • Mehta, G., Deelman, E., Knowles, J., Chen, T. (2011). Enabling Data and Compute Intensive Workflows in Bioinformatics. High Performance Bioinformatics and Biomedicine (HiBB).
    • Cho, S., Kuo, J. C., Chen, T. (2011). MetaSEQ: De Novo Sequence Assembly of Short Regions in Metagenomics. IEEE International Workshop on Genomic Signal Processing.

    Advisement

    Other Advisement or Time Devoted to Students
    • Computational Biology Graduate Student Advisor, 08/2006-08/2011  

    Honors and Awards

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

    Service to the University

    Committees
    • Member, USC College Biology Undergraduate Curriculum Committee, 2007-2013  
    • Member, USC High Performance Computing Committee, 2007-2013  
    • Chair, Graduate Student Advisory for Computational Biology and Bioinformatics, 2006-2013  
    • Chair, Faculty Recruit Committee, Computational Biology and Bioinformatics, 2012-2013   
    • Member, USC Clinical Translational Science Institute (CTSI): Computational Biology Advisory Committee, 2007-2010  
    • Member, USC College Faculty Council, 2005-2006   

    Service to the Profession


    Committees
    • Member, RECOMB PROGRAM COMMITTEE, 2012-2013   
    • Member, APBC PROGRAM COMMITTEE, 2012-2013   
    • Member, ISMB PROGRAM COMMITTEE, 2005-2006   
    • Member, RECOMB PROGRAM COMMITTEE, 2002-2005  

    Conferences Organized
    • Organizing Committee Member, 30 Year Computational Biology Research at USC, USC, Spring 2012   
    • Organizing Committee Member, Computational Proteomics Workshop, MBI, OSU, Spring 2005   
    • Program Chair, Proteomics Workshops, IPAM, UCLA, Spring 2004   

    Editorships and Editorial Boards
    • Editorial Board, BMC Bioinformatics, 2003-  

    Review Panels
    • NIH, BDMA, Fall 2012   
    • NIH, BST-Q, 2009-2010   
    • NIH, BST-Q, 2008-2009   
    • NIH, ZRG1 GGG-A, 2008-2009   




  • Department of Biological Sciences
  • University of Southern California
  • Allan Hancock Foundation Building
  • Los Angeles, CA 90089-0371