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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.
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Education:
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Ph.D Computer Science
University of California, Riverside
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Sep, 2004 ~ Jul, 2008
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M.S. Statistics
University of California, Riverside
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Sep, 2005 ~ Jun, 2008
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B.S. Computer Science
Nanjing University, Nanjing, P.R.China
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Sep, 1997 ~ Jun, 2001
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Working Experience:
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Software Engineer Intern
Google, Mountain View, CA
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Jun, 2007 ~ Sep, 2007
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Database Support Engineer
Microsoft, Shanghai, P.R.China
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Jul, 2001 ~ Aug, 2004
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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. .
Research Projects:
- Genetic Linkage Mapping: This is a collaborative projects with
my advisor Dr. Lonardi, Prof. 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
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MergeMap can be downloaded from
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- 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 . The collaborators of this project are
,
Dr. Lonardi and .
- 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
- 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
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Conference Publications:
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Y. Wu, T.J. Close, S. Lonardi,
On the Accurate Construction of Consensus Genetic Maps.
CSB 2008 - Computational Systems Bioinformatics Conference , to appear, Stanford, CA, 2008.
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Y. Wu, S. Lonardi,
A Linear-Time Algorithm for Predicting Functional Annotations from Protein-Protein Interaction Networks.
BIOKDD 2007 - 7th International Workshop on Data Mining in Bioinformatics, 35-41, San Jose, 2007.
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Y. Wu, P. Bhat, T. J Close, S. Lonardi,
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data.
WABI 2007 - Workshop on Algorithms in Bioinformatics, LNBI 4645, pp.395-406, Philadelphia PA, 2007.
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L. Liu, Y. Wu, S. Lonardi, T. Jiang,
Efficient Algorithms for Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion.
CSB 2007 - Computational Systems Bioinformatics Conference, 67-78, San Diego CA, 2007.
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Y. Wu, L. Liu, T. Close, S. Lonardi,
Deconvoluting the BAC-Gene Relationships Using a Physical Map.
CSB 2007 - Computational Systems Bioinformatics Conference, 203-214, San Diego CA, 2007.
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S. Sirowy, Y. Wu, S. Lonardi, F. Vahid,
Two Level Microprocessor-Accelerator Partitioning.
DATE 2007 - Design, Automation and Test in Europe, pp.313-318, Nice, France, 2007.
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S. Sirowy, Y. Wu, S. Lonardi, F. Vahid,
Clock-Frequency Assignment for Multiple Clock Domains Systems-on-a-chip.
DATE 2007 - Design, Automation and Test in Europe, pp.397-402, Nice, France, 2007.
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Y. Wu, S. Lonardi, W. Szpankowski,
Error-Resilient LZW Data Compression.
DCC 2006 - IEEE Data Compression Conference, 193-202, Snowbird, Utah, 2006.
Journal Publications:
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L. Liu, Y. Wu, S. Lonardi, T. Jiang,
Efficient algorithms for genome-wide tagSNP selection across populations via the linkage disequilibrium criterion
Journal of Computational Biology, to appear, 2010.
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T.J. Close, P.R. Bhat, S. Lonardi, Y. Wu, et. al.,
Development and implementation of high-throughput SNP genotyping in barley
BMC Genomics, 2009.
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Y. Wu, P. Bhat, T.J. Close, S. Lonardi,
Efficient and Accurate Construction of Genetic Linkage Maps from Minimum Spanning Tree of a Graph
Plos Genetics, 2008.
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Y. Wu, S. Lonardi,
A Linear-Time Algorithm for Predicting Functional Annotations from Protein-Protein Interaction Networks.
Journal of Bioinformatics and Computational Biology, () to appear, 2008.
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N. G. Portney, Y. Wu, L. K. Quezada, S. Lonardi, M. Ozkan,
Length-based Encoding of Binary Data in DNA.
Langmuir, (): to appear, 2008.
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Y. Wu, L. Liu, T. Close, S. Lonardi,
Deconvoluting BAC-gene Relationships Using a Physical Map.
Journal of Bioinformatics and Computational Biology, 603-622, 2008.
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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.
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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
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