Curriculum Vitae

Complete CV (PDF)
Last modified: July 30, 2009

Current Position

Assistant Professor of Pathology and Laboratory Medicine, University of Pennsylvania

Education and Training

07/2003-12/2006	Postdoctoral Fellow, University of Pennsylvania. Advisor: Junhyong Kim.
05/2003	Ph.D., Computer Sciences, University of Texas at Austin. Dissertation Title: Large-Scale Phylogenetic Analysis. Advisor: Tandy Warnow.
06/2000	M.S., Computer Sciences, University of Texas at Austin.
06/1996	M.S., Electrical Engineering, National Taiwan University. Thesis Title: Design and Implementation of an Adaptive Modeling Unit for Multialphabet Arithmetic Compression. Advisor: Tzi-Dar Chiueh.
06/1994	B.S., Electrical Engineering, National Taiwan University.

Research Interests

• Disease-related bioinformatic research: aging, neurodegenerative diseases, and cancer
• High-throughput genomic bioassays: Genome-wide SNP genotyping (and GWAS), Solexa sequencing.
• Computational methods for microarray analysis and systems biology: semi-parametric and nonparametric analysis, transcription factor prediction and regulatory networks
• Computational phylogenetics: genome rearrangement phylogeny, phylogenetic multiple sequence alignment, nontree evolution

Professional Services

• Program Committee/Co-chair for Bioinformatics Session I, The Fourth Annual Emerging Information Technology Conference (EITC), 2004.
• Program Committee, The Second Annual RECOMB Satellite Workshop on Comparative Genomics, 2004.
• Coordinator, The Third Annual Emerging Information Technology Conference (EITC), 2003.
• Publications/Proceedings Team, The Second Annual Emerging Information Technology Conference (EITC), 2002.
• Referee for journals and conferences including Journal of Computational Biology, Mathematical Biology, Systematic Biology, WABI, RECOMB, COCOON.

Grants

• 1/2009–12/2010Co-Principal Investigator,
  Genome-wide Analysis of the Double-Stranded RNA Component of Eukaryotic Transcriptomes
  . Penn Genome Frontiers Institute (PGFI) Pilot Grant, total amount: $120,000 (PI: Brian Gregory).
• 01/2008–12/2008Principal Investigator,
  Novel Bioinformatic Approaches for Modeling Age-Correlated Gene Expression Progression.
  University of Pennsylvania Research Foundation Pilot Grant, total amount: $24,378.
• 07/2007/06/2008Principal Investigator,
  The role of G-quadruplexes in senescence through RecQ-dependent pathways.
  University of Pennsylvania Institute on Aging Pilot Grant, total amount: $50,000.

Publications

(complete list here)

Featured Talks

(complete list here)

1. "Regulatory Module Discovery With Heterogeneous Data by Multipartite Coclustering," 39th Symposium on the Interface: Computing Science and Statistics: Systems Biology, May 25, 2007.
2. "Clustering in the Space of Phylogenies," Department of Computer and Information Science and Interdisciplinary Faculty Seminar on Biomedical Informatics, Fordham University, February 22, 2007.
3. "Phylogenetic Estimation for Complex Evolutionary Processes," Institute of Information Science, Academia Sinica (Taiwan), January 4, 2007.
4. "Phylogenetic Estimation for Complex Evolutionary Processes," Department of Computer Science and Information Engineering, National Taiwan University, December 22, 2006.
5. "Interaction and Progression Modeling from Functional Genomics Data," Institute on Aging and Department of Pathology and Laboratory Medicine, University of Pennsylvania, April 20, 2006.
6. "Phylogenetic Estimation for Complex Evolutionary Processes," School of Computer Science, University of New Mexico, March 30, 2006.
7. "Phylogenetic Estimation for Complex Evolutionary Processes," School of Computer Science, McGill University, March 22, 2006.
8. "Phylogenetic Estimation for Complex Evolutionary Processes," Department of Computer Science, University of Pittsburgh, February 28, 2006.
9. "Phylogenetic Estimation for Complex Evolutionary Processes," Department of Biology, Virginia Polytechnic Institute and State University, February 16, 2006.
10. "Genome Rearrangement Phylogeny," Department of Computer Science, Virginia Polytechnic Institute and State University, December 13, 2005.
11. "Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony," conference presentation, IEEE Fifth Symposium on Bioinformatics and Bioengineering (BIBE'05), University of Minnesota at Twin Cities, October 20, 2005.
12. "Enhanced position weight matrices using mixture models," conference presentation, Thirteenth International Conference on Intelligent Systems for Molecular Biology (ISMB'05), Detroit, USA, June 28, 2005.
13. "Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony," Biocomplexity Workshop, University of Texas at Austin, April 29, 2005.
14. "Genome Rearrangement Phylogeny," Department of Mathematics, Lehigh University, April 27, 2005.
15. "Genome Rearrangement Phylogeny," Department of Computer Science, University of Illinois at Urbana Champaign, April 4, 2005.
16. "Phylogenetic and Functional Analyses at the Genomic Scale," Department of Biostatistics and Medical Informatics, University of Wisconsin at Madison, March 9, 2005.
17. "Phylogenetic and Functional Analyses at the Genomic Scale," Department of Biomedical Informatics, Ohio State University, February 28, 2005.
18. "Semi-Parametric Gene Ranking for Microarray Experiments," the Fourth Annual Emerging Information Technology Conference (EITC), Princeton University, October 28, 2004.
19. "Distance-Based Genome Rearrangement Phylogeny," the Third Annual Emerging Information Technology Conference (EITC), Princeton University, October 31, 2003.
20. "Distance-Based Genome Rearrangement Phylogeny," IMA/RECOMB Satellite Workshop on Comparative Genomics, University of Minnesota, October 20-24, 2003.
21. "Distance-Based Genome Rearrangement Phylogeny," Workshop on New Trends in Phylogenetics and Genomics, University of Tuebingen, Germany, July 1-4, 2003.
22. "A Simulation Study for Genome Rearrangement Phylogeny Using Beta-Splitting Models," Biocomplexity Workshop, University of Texas at Austin, April 12, 2003.
23. "Markovian Models for Genome Rearrangements," Mathematics of Evolution and Phylogeny Workshop, Institut Henri Poincare, France, June 16-19, 2003.
24. "Distance-Based Genome Rearrangement Phylogeny Reconstruction," Department of Com- puter Science, Virginia Institute of Technology, April 30, 2003.
25. "Genome Rearrangement Phylogeny,"DIMACS Tree of Life Workshop, Rutgers University, March 11-14, 2003.
26. "Distance-Based Genome Rearrangement Phylogeny," Department of Zoology, University of Chicago, January 30, 2003.
27. "Distance-Based Genome Rearrangement Phylogeny Reconstruction," Whitehead Insti- tute, Massachusetts Institute of Technology, January 9, 2003.
28. "Genome Rearrangement Phylogeny Using Weighbor," conference presentation, Second Workshop on Algorithms in Bioinformatics (WABI'02), Rome, Italy, September 17, 2002.
29. "Postprocessing of Phylogenetic Analysis Using Clustering," conference presentation, Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB'02), Edmonton, Canada, August 7, 2002.
30. "Computational Methods for Genome Rearrangement Phylogeny," Biocomplexity Workshop , University of Texas at Austin, April 12, 2002.
31. "Genome Rearrangement Phylogeny Estimation," the Colloquium on Biosystematics and Evolution Biology, hosted by Department of Biology, Stanford University and California Academy of Sciences, March 15, 2002.
32. "Fast Methods for Genome Rearrangement Phylogeny Estimation," Department of Ecology and Evolutionary Biology, Yale University, February 18, 2002.
33. "Clustering and Consensus for Phylogenetic Analysis," DIMACS Bioconsensus 2 Workshop, Rutgers University, October 4-7, 2001.
34. "New Polynomial Time Methods for Whole Genome Phylogeny Reconstruction," DIMACS Whole Genome Comparison Workshop, Rutgers University, February 28-March 2, 2001.

Skills (click)