To infinity ... and beyond!    -- Buzz Lightyear, Buzz Lightyear of Star Command: The Adventure Begins.

Wei Li

Permanent Head Damaged (PHD) student

Algorithm and Computational Biology Lab, University of California, Riverside

Contact: liw AT cs(dot)ucr(dot)edu OR wei_li3 AT dfci(dot)harvard(dot)edu


My Short Story

I am Wei Li (David), now a 4th-year Ph.D candidate in UCR under the supervision of Dr. Tao Jiang. My research interest focuses on designing tools and algorithms for the next generation sequencing (NGS) data, especially RNA-Seq data. Since September 2012, I'm a postdoc researcher in Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute and Harvard School of Public Health.

Before coming to UCR, I received a Bachelor and Master degree of Computer Science in Tsinghua University, Beijing, China.

You can find my CV here.


Research and Softwares

A short summary of my research experience can be found here.

Several softwares are developed by me and my colleagues, including IsoLasso, CEM, ISP, IsoInfer, and so on. 

I also provide some useful tools, including a RNA-Seq read simulator, and a collection of useful scripts written by me. Feel free to use them and contact me if you have questions.


Publications

Conference publications

5. Wei Li, Jianxing Feng and Tao Jiang. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), Lecture Notes in Computer Science, 6577:167-188, Springer Berlin/Heidelberg, 2011.

4. Wei Li, Paul M. Ruegger, James Borneman and Tao Jiang. Polony Identification Using the EM Algorithm Based on a Gaussian Mixture Model. Proc. 10th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2010), Philadelphia, PA, May 31 - June 3, 2010, pp. 220-225.

3. Jianxing Feng, Wei Li and Tao Jiang. Inference of Isoforms from Short Sequence Reads (Extended Abstract). 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lecture Notes in Computer Science, 6044:138-157, Springer Berlin/Heidelberg, 2010.

2. Wei Li, Yannan Zhao, Yixu Song and Zehong Yang. COX-2 Activity Prediction in Chinese Medicine Using Neural Network Based Ensemble Learning Methods. The 2008 International Joint Conference on Neural Networks (IJCNN 2008). pp. 1853-1858.

1. Wei Li, Yannan Zhao, Yixu Song and Zehong Yang. SVM Feature Selection and Sample Regression for Chinese Medicine Research. The 2008 International Conference on Information and Antomation (ICIA 2008). pp. 1773-1777.

Journals

4. Paul M. Ruegger, Elizabeth Bent, Wei Li, Daniel R. Jeske, Xinping Cui, Jonathan Braun, Tao Jiang, James Borneman. Improving Oligonucleotide Fingerprinting of rRNA Genes by Implementation of Polony Microarray Technology. Journal of Microbiological Methods (2012) 90(3):235-240.

3. Wei Li and Tao Jiang. Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads. Bioinformatics (2012) 28(22): 2914-2921.

2. Wei Li, Jianxing Feng and Tao Jiang. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. Journal of Computational Biology, 18(11): 1693-1707, Nov. 2011. (Journal version of the RECOMB paper)

1. Jianxing Feng, Wei Li and Tao Jiang. Inference of Isoforms from Short Sequence Reads. Journal of Computational Biology, 18(3):305-321, Mar. 2011. (Journal version of the RECOMB paper)

Talks

2. Wei Li and Tao Jiang. Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads. IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2012). Las Vegas, NV. Mar. 2012.

1. Wei Li, Jianxing Feng and Tao Jiang. Transcriptome assembly from RNA-Seq data: Objectives, algorithms and challenges. IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2011). Orlando, FL. Feb. 2011.

Activities & Awards

IEEE ICCABS conference Travel Award, 2012
Graduate Division Fellowship Award, University of California, Riverside, 2008-2009
Tsinghua University Student Art Group Fellowship, 2005
Tsinghua University Academic Career Fellowship, 2004
Captain, Tsinghua University Military Band Freshman Division, 2006-2007
Vice-Captain, Tsinghua University Military Band, 2004-2005
1st Prize of Freshman Excellency Scholarship of Tsinghua University, 2002 (college entrance exam "Champion", rank top 0.003% (around 7/200,000) in Canton province)


TA

I have been TA for various classes, including CS005 (Introduction to Computer Programming), CS008 (Introduction to Computing), CS150 (The Theory of Automata and Formal Languages), and CS229 (Machine Learning) in UCR CSE department.


RA

I am involved in many research projects beginning from 2005. These projects include soccer robots, traditional Chinese medicine, microbiology, high-throughput sequencing, and so on. For all research projects I'm involved, please refer to the research webpage.

| 2012 davidliwei