Bio

I moved to the Robert Darnell lab at Rockefeller University as a PostDoc very recently. The homepage will be updated soon.

*****

I am a fourth year Ph.D. student at Cold Spring Harbor Laboratory & Dept. Biomedical Engineering of SUNY at Stony Brook. I work with Profs. Michael Q. Zhang and Adrian Krainer. The homepage of the Zhang lab.

I got my Bachelor's Degree of Engineering (B.E.) at Department of Automation, Tsinghua University in 2002. Then, I worked in the Institute of Bioinformatics, Tsinghua University with Dr. Xuegong Zhang for two years. I was also an intern student of the visual computing group at Microsoft Research Asia before I came to US.

I got Master's Degree of Science (M.S.) at SUNY at Stony Brook in May 2006. I advanced to my candidacy in Feb, 2007. Now I am in the last year of my Ph.D. study.

In the summer of 2006, I had a great research internship at Rosetta Inpharmatics, LLC, Seattle, WA.

A complete CV can be reached here.
 

Research Interests

My long-term research interest is to understand gene expression regulation in mammalian systems and its implications in human diseases, mainly through computational approaches in collaboration with bench biologists. My Ph.D. thesis research focuses on fidelity and regulation of pre-mRNA splicing and alternative splicing.  I am also interested in developing and applying statistical machine learning and data mining methods.

Here is a brief list of projects I am working on:

• Predicting and characterizing Fox-1(A2BP1) and Fox-2(RBM9) targets.

• Developing a statistical framework to uncover splicing motifs from splicing microarray data and genomic sequences.

• Exploring evolutionary characteristics related to alternative splicing.

I maintain several tools and databases developed by our lab, including

• dbCASE: database of classified alternative splicing events

• ESEfinder: an online tools to predict exonic splicing enhencer.

• AEDB: Alternative exon database

• TRED: transcriptional regulatory element database

• CpG_promoter: human promoter mapping using CpG islands

A few past projects:

• Identification of signature splicing events in prostate cancer by isoform sensitive microarray essays, collaborating with Fu lab at UCSD. [completed/published]

• Transcription factor binding site identification and pattern analysis, laboratory rotation in Mandel lab, HHMI & Dept of Neurobiology and Behavior, SUNY at Stony Brook. [completed/published]
   

• Differential methylation pattern in breast cancer with CpG island microarrays, collaborating with Duffy lab, SUNY at Stony Brook.

Links

My wife Shu's homepage at Columbia and old homepage

Friends:
Xiaodan Fan, Department of Statistics, Harvard University
Yan Lin, Electronical Engineering Department, University of California, Los Angeles
Bo Lu, Nuclear Engineering, University of Tennessee
Tao Peng, Department of Biomedical Engineering, SUNY at Stony Brook
Jue Wang, Department of Electrical Engineering, University of Washington
Yuan Yuan, Department of Statistics, Harvard University
Meng Zhang, Department of Biomedical Engineering, SUNY at Stony Brook