PhD Student
Molecular and Computational Biology
Department of Biological Sciences
University of Southern California

1050 Childs Way, RRI416F
Los Angeles, CA 90089-2910
Email: xitingya at usc dot edu
Phone: (213) 821-3980

Education

• University of Southern California                           2005-present
  Molecular and Computational Biology Program
  Department of Biological Sciences
  Ph.D. in Computational Biology (expected in Summer 2009)
  Dissertation Title: "Probabilistic and Statistical Modeling
  of Various Biological Data to Reconstruct Regulatory Networks
  Advisor: Fengzhu Sun
• Peking University                                                   2001-2006
  Department of Probability and Statistics
  School of Mathematical Sciences
  Ph.D. in Probability and Statistics
  Dissertation Title: Identifying Phenotype Associated Genes
  from Gene Expression Microarray Data
  Advisor: Minping Qian
• Peking University                                                   1997-2001
  Department of Probability and Statistics
  School of Mathematical Sciences
  B.S. in Probability and Statistics with honors, Minor in Economics

Research Interests

• Probabilistic and Statistical Models in Biological Data
• Computational Biology and Bioinformatics
• Applied Statistics
• Gene Expression Analysis
• Gene Regulatory Network Analysis
• System Biology

Publications and Manuscripts

1. Yan, X., Sun, F. and Chen, T. TranSEQ: Estimating Expression Levels of Alternatively Spliced Transcripts using mRNA-seq Data. Submitted to Genome Research. [Supplementary Site]
2. Duan, S., Wan, L., Fu, W.J., Pan, H., Ding, Q., Chen, C., Han, P., Zhu, X., Du, L., Liu, H., Chen, Y., Liu, X.,Yan, X., Deng, M., Qian, M. Nonlinear cooperation of p53-ING1-induced bax expression and protein S-nitrosylation in GSNO-induced thymocyte apoptosis: a quantitative approach with cross-platform validation. Apoptosis. 2008, In press. [Pubmed]
3. Yan, X. and Sun, F. Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics. 2008, 9:362. [Pubmed] [Supplementary Site]
4. Jia, L., Berman, B.P., Jariwala, U., Yan, X., Cogan, J.P., Walters, A., Chen, T., Buchanan, G., Frenkel, B. and Coetzee, G.A. Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. PLoS ONE. 2008, 3(11):e3645. [Publisher Site]
5. Pregizer, S., Baniwal, S.K., Yan, X., Borok, Z. and Frenkel, B. Progressive recruitment of Runx2 to genomic targets despite decreasing expression during osteoblast differentiation. J Cell Biochem. 2008, 105(4):965-70.[Pubmed]
6. Cheng, C.*, Yan, X.*, Sun, F. and Li, L.M. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics. 2007, 8:452.[Pubmed] [Supplementary Site]
   * Equally Contribute

7. Cheng, C., Ma, X., Yan, X., Sun, F. and Li, L.M. MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics. 2006, 22(21):2650-7. [Pubmed] [Supplementary Site]
8. Yan, X., Deng, M., Fung, W.K., Qian, M. Detecting differentially expressed genes by relative entropy. J Theor Biol. 2005, 234(3):395-40. [Pubmed] [Supplementary Site]
9. Feng, X., Qian, M., Deng, M., Ma, X., Yan, X. Application of hidden semi-Markov model to 3-prime splice sites identification. Progress in Biochemistry and Biophysics, 2004, 31(5):455-458. [Publisher Site]

Teaching

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California

• Teaching Assistant, Computational Genome Analysis                     Summer 2008
  Lead discussion sessions, graded homework, and hold
  weekly office hours.


• Teaching Assistant, Computational Genome Analysis                     Summer 2007
  Lead discussion sessions, graded homework, and hold
  weekly office hours.


• Teaching Assistant, Introduction to Statistics for Biologists             Fall 2006
  Lead discussion sessions, graded homework, and hold
  weekly office hours.