Research Interests

• Bioinformatics, Proteomics and Functional Genomics
• Computational Biology, Algorithm Analysis, Pattern Recognition, and Applied Mathematics

Education

• Ph.D. (1997), Computer Science Department, SUNY at Stony Brook.
• M.S. (1995), Computer Science Department, SUNY at Stony Brook.
• B.E. (1993), Department of Computer Science and Technology, Tsinghua University, Beijing.

Academic Experience

• Assistant Professor (8/2000 -).
  Department of Math and Center for Computational and Experimental Genomics
  University of Southern California.
  
  
• Lecturer (10/1997 - 8/2000).
  George Church Lab and Lippter Center for Computational Genetics, Harvard Medical School.
  Research: Computational Biology, Proteomics and Functional Genomics.
  Teaching: Biophysics 101: Computational Biology and Genomics.
  
  
• Guest Research Associate (12/1995 - 9/1998).
  Biology Department, Brookhaven National Lab.
  Research: "Borrelia Genome Sequencing".
  
  
• Research Assistant (1996 - 1997).
  Michael Zhang Lab, Cold Spring Harbor Lab.
  Project: "Gene-Finding and Gene Structure Prediction".
  
  
• Research Assistant (1995 - 1997).
  Computer Science Department, SUNY Stony Brook.
  Research: Algorithms and Bioinformatics. Advisor: Professor Steven Skiena.

Publications

• A Case Study in Genome-Level Fragment Assembly. (Ting Chen and Steven Skiena).
  To appear at Bioinformatics, 2000.
  
  
• A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry. (Ting Chen, Ming-Yang Kao, Matthew Tepel, John Rush and George Church).
  The 11th Annual SIAM-ACM Symposium on Discrete Algorithms (SODA 2000), page 389-398, 2000.
  
  
• On the Informational Asymmetry between Upper and Lower Bounds for Ultrametric Evolutionary Trees. (Ting Chen and Ming-Yang Kao).
  The 7th Annual European Symposium on Algorithms (ESA'99), Page 248-256, 1999.
  LNCS, Lecture Notes in Computer Science, Springer-Verlag.
  
  
• Identifying gene regulartory networks from experimental data. (Ting Chen, Vladimir Filkov and Steven S. Skiena).
  ACM-SIGACT Third Annual International Conference on Computational Moledular Biology (RECOMB99), page 94-103,1999.
  
  
• Modeling Gene Expression with Differential Equations. (Ting Chen, Hongyu L. He, and George M. Church).
  Pacific Symposium on Biocomputing (PSB99), Page 29-40, 1999.
  
  
• Pombe: A Fission Yeast gene-finding and exon-intron structure prediction system, (Ting Chen and Michael Q. Zhang).
  Yeast, Vol. 14: 701-710, 1998.
  
  
• Trie-based data structures for fragment assembly, (Ting Chen and Steven S. Skiena).
  The Eighth Symposium on Combinatorial Pattern Matching (CPM97), page 206-223, 1997.
  
  
• Sorting with fixed-length reversals. (Ting Chen and Steven Skiena).
  Journal of Discrete Applied Mathematics, Special Volume on Computational Molecular Biology, page 269-296, vol.71, December 5 1996.
  
  
• Incremental Model Checking in the Modal Mu-Calculus. (with Oleg Sokolsky and Scott Smolka).
  1996. Technical Report.

Software Development

• STROLL: A Fragment Assembly Program for Large-Scale Genome Sequencing.
• Pombe: A Gene Recognition Program for Fission Yeast.
• MSfast: Peptide Identification and De novo Sequencing via Tandem Mass Spectrometry.

Professional Activities

• Conference Chair, 1997 Graduate Research Conference,
  Held at the Department of Computer Science, SUNY at Stony Brook, on April 4, 1997.
  
  
• Referee, Journal of Discrete Applied Mathematics, Algorithmatica, The International Journal on Computational Geometry and Applications, Information Processing Letters, Journal of Computational Biology, and Pacific Symposium of Biocomputing.

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