Education:

Working Experience:

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 CMap, which can be applied to other organisms in general. MSTMap can be downloaded from http://www.cs.ucr.edu/~yonghui/mstmap.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:

• A Linear-Time Algorithm for Predicting Functional Annotations from Protein-Protein Interaction Networks. Y. Wu, S. Lonardi BIOKDD 2007 - 7th International Workshop on Data Mining in Bioinformatics, 35-41, San Jose, 2007.
   
• Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. Y. Wu, P. Bhat, T. J Close, S. Lonardi WABI 2007 - Workshop on Algorithms in Bioinformatics, LNBI 4645, pp.395-406, Philadelphia PA, 2007.
   
• Efficient Algorithms for Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. L. Liu, Y. Wu, S. Lonardi, T. Jiang CSB 2007 - Computational Systems Bioinformatics Conference, 67-78, San Diego CA, 2007.
   
• Deconvoluting the BAC-Gene Relationships Using a Physical Map. Y. Wu, L. Liu, T. Close, S. Lonardi CSB 2007 - Computational Systems Bioinformatics Conference, 203-214, San Diego CA, 2007.
   
• Two Level Microprocessor-Accelerator Partitioning. S. Sirowy, Y. Wu, S. Lonardi, F. Vahid DATE 2007 - Design, Automation and Test in Europe, pp.313-318, Nice, France, 2007.
   
• Clock-Frequency Assignment for Multiple Clock Domains Systems-on-a-chip. S. Sirowy, Y. Wu, S. Lonardi, F. Vahid DATE 2007 - Design, Automation and Test in Europe, pp.397-402, Nice, France, 2007.
   
• Error-Resilient LZW Data Compression. Y. Wu, S. Lonardi, W. Szpankowski DCC 2006 - IEEE Data Compression Conference, 193-202, Snowbird, Utah, 2006.
   

Journal Publications:

• A Linear-Time Algorithm for Predicting Functional Annotations from Protein-Protein Interaction Networks. Y. Wu, S. Lonardi Journal of Bioinformatics and Computational Biology, () to appear, 2008.
   
• Length-based Encoding of Binary Data in DNA. N. G. Portney, Y. Wu, L. K. Quezada, S. Lonardi, M. Ozkan Langmuir, (): to appear, 2008.
   
• Deconvoluting BAC-gene Relationships Using a Physical Map. Y. Wu, L. Liu, T. Close, S. Lonardi Journal of Bioinformatics and Computational Biology, () to appear, 2008.
   

• 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