Bo Li

Ph.D. Candidate,
Department of Computer Sciences,
University of Wisconsin-Madison

5745 Medical Sciences Center,
1300 University Ave,
Madison, WI 53706-1510

Curriculum Vitae

Email: bli [at] cs [dot] wisc [dot] edu

Education

• 2008.9 ~ present        Computer Sciences Department, University of Wisconsin-Madison
• 2004.9 ~ 2008.7         ACM Honor Class, Department of Computer Science and Engineering, Shanghai Jiao Tong University

Research

My research interests are machine learning, computational biology and NGS(Next Generation Sequencing) data analysis. My advisor is Prof. Colin Dewey.

Publications

• Li, B. and Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 12:323.


• Chung, D., Kuan, P. F., Li, B., Sanalkumar, R., Liang, K., Bresnick, E., Dewey, C. N., Keles, S. (2011). Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-seq data. PLoS Computational Biology, 7:e1002111.


• Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A., Dewey, C. N. (2010). RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26(4), 493-500.

Software

• RSEM(RNA-Seq by Expectation-Maximization): Accurate gene and isoform expression levels quantification from RNA-Seq data with or without a reference genome.


• CSEM(ChIP-Seq multi-read allocation using Expectation-Maximization): A ChIP-Seq multi-read allocator which allows multi-reads to be utilized by peak callers.

Miscellaneous