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Jul 25, 2008 With the dissertation submitted to the graduate division, I am now officially gradulated from UCR.

Jun 16, 2008 I attended the UCR's 54th commencement and was hooded by Dr. Close. Ni Li was the only family member who witnessed the event.

Jun 13, 2008 I officially received the M.S. degree in statistics.

Jun 6, 2008 I successfully defended my thesis titled "on the accurate construction of genetic linkage maps".

May 21, 2008 I passed the written qualifying exam for the M.S. degree in statistics.

May 5, 2008 Our paper titled "On the acurate construction of consensus genetic maps" was accepted by CSB 2008.

Yonghui Wu

Ph.D Candidate
Algorithms and Computational Biology Lab
Department of Computer Science and Engineering
University of California - Riverside
Riverside, CA 92521
Lab: Engineering Building II, Room 362
email: yonghui@cs.ucr.edu


Ph.D Computer Science
University of California, Riverside
Sep, 2004 ~ Jul, 2008
M.S. Statistics
University of California, Riverside
Sep, 2005 ~ Jun, 2008
B.S. Computer Science
Nanjing University, Nanjing, P.R.China
Sep, 1997 ~ Jun, 2001

Working Experience:

Software Engineer Intern
Google, Mountain View, CA
Jun, 2007 ~ Sep, 2007
Database Support Engineer
Microsoft, Shanghai, P.R.China
Jul, 2001 ~ Aug, 2004
My primary research interest is in algorithms and computational biology. I am also interested in data compression, data mining and machine learning. My advisor is Prof. Stefano Lonardi.

Research Projects:

  • Genetic Linkage Mapping: This is a collaborative projects with my advisor Dr. Lonardi, Prof. Timothy J. Close from the Botany and Plant Sciences department who is also the PI of this project, and Prasanna Bhat who is a post-doc in Dr. Close's lab. The main purpose of this project on my side is to build a consensus genetic linkage map for Barley. Along the way of building such a consensus map, we have developed two new software tools, i.e. MSTMap and MergeMap, which can be applied to other organisms in general. MSTMap can be downloaded from http://www.cs.ucr.edu/~yonghui/mstmap.html. MergeMap can be downloaded from http://www.cs.ucr.edu/~yonghui/mgmap.html.
  • Genome-Wide TagSNP Selection: In this project, we aimed to select a smallest set of tagging Snips for a set of Snips under consideration. We developed a new software tool named LRTag, which can be accessed on-line at http://www.cs.ucr.edu/~yonghui/LRTag.html. The collaborators of this project are Dr. Liu, Dr. Lonardi and Dr. Jiang.
  • BAC-gene Deconvolution: The objective of this project is to deconvolute the relationships between BACs and genes, i.e. to figure out which BAC contains which gene. We have proposed a new method which combines the outcomes of a light-weight combinatorial pooling and the physical map of the underlying BACs for the deconvolution of BAC-gene relationships. The python script that performs the actual deconvolution can be downloaded from http://www.cs.ucr.edu/~yonghui/BAC_gene_deconvolution.tar.gz
  • Error-Resilient LZW: In this project, we identified a new way of embedding error-detection and/or error-correction bits into the LZW data streams. The prototype implementation of the newly proposed LZW scheme can be downloaded from http://www.cs.ucr.edu/~yonghui/error_resillientLZW.tar.gz

Conference Publications:

Journal Publications:

I have been a TA for the following courses so far:
  • Winter 2005, CS010: Introduction to Computer Science for Science, Mathematics, and Engineering I
  • Spring 2005, CS010: Introduction to Computer Science for Science, Mathematics, and Engineering I
  • Fall 2005, CS141: Intermediate Data Structures and Algorithms
  • Winter 2006, CS141: Intermediate Data Structures and Algorithms
  • Spring 2006, CS150: The Theory of Automata and Formal Languages
I received The Outstanding Teaching Assistant Award by University of California, Riverside Graduate Division in 2005-2006 academic year.
Professional Service
I reviewed papers for the following conferences:
  • WABI'08: Workshop on Algorithms in Bioinformatics, University of Karlsruhe, Germany.
  • CSB'08: Computational Systems Bioinformatics Conference, Stanford, CA.
  • SDM'08: SIAM Conference on Data Mining, Atlanta, GA.
  • CPM'08: 19th Annual Symposium on Combinatorial Pattern Matching, University of Pisa, Italy.
  • WABI'07: Workshop on Algorithms in Bioinformatics, Philadelphia, PA.
  • CPM'06: 17th Annual Symposium on Combinatorial Pattern Matching, Technical University of Catalonia in Barcelona, Spain.
  • SPIRE'06: String Processing and Information Retrieval
  • ICTAI'05: International Conference on Tools with Artificial Intelligence, Hong Kong
Last updated on Jun 20 2008