Computer Science Engineer
Resume:
Yiqun Eddie Cao
Riverside, CA 92507
PhD Candidate, Computer Science, UC Riverside abpo6e@r.postjobfree.com
http://www.cs.ucr.edu/~ycao/
Objective
A computer science and computer engineer career, preferably in interdisciplinary areas of
scienti c computing, bioinformatics, and cheminformatics; to develop novel
computational systems and approaches that better people s health and life.
Experience
Graduate Student Researcher, Bioinformatics Lab, University of California, Riverside 2006-present
Performed database and machine learning study on chemical compound structure and
activity data. Proposed new algorithms to process large scale structural/graph data and
built implementations with C, C++, R, Python and Web Application technologies.
Proposed and implemented a Maximum Common Substructure-based (MCS) algorithm for searching
chemical structures and performing ligand-based virtual screening.
Designed and implemented a general method to greatly accelerate chemical structural similarity search.
Created a software package for calculating structural descriptors and similarities.
Co-authored ChemMine, a web-based compound mining environment.
Co-authored ChemmineR, a chemoinformatics framework using R programming environment.
Authored the Bioactivity and Phenotype Database (BAPDB), a database for exploring the biological and
molecular functions of genes based on available phenotype and screening data.
Authored the EI website, a gateway for accessing tens of millions of PubChem compounds, which provides
ultra-fast highly-accurate similarity search and high-quality clustering results.
Visiting Student, Shoichet s Lab, University of California, San Francisco Jan. 2007-Apr. 2007
Conducted research on automated receptor-based virtual screening.
Studied large-scale automated molecular docking and consensus scoring in molecular docking.
Built a prototype database for automated docking runs using the whole PDB.
Built systems to simplify the use of Protein Ligand Optimization Program (PLOP) and to facilitate single-mode
DOCK run.
Graduate Student Researcher, National University of Singapore Jan. 2004-Jul. 2005
Conducted research on distributed and parallel computing, with applications in
computational biomedical applications.
Undergraduate Student Researcher, Tsinghua University, Beijing, China Nov. 2001-Jun. 2003
Worked on embedded system and system and network programming.
Worked on an embedded Bluetooth-based wireless communication system.
Conducted research on a network-facilitated anti-virus system (similar to today's Microsoft SpyNet).
Freelance Author Jun. 2001-Dec. 2001
Co-authored Advanced PHP Programming (in Chinese) (ISBN 7-302-05344-8).
Freelance Web Developer - Mar. 2005-Aug. 2005
Designed a website and CMS for Party World KTV Pte Ltd Singapore using PHP.
Publications
Yiqun Cao, Tao Jiang, Thomas Girke. A maximum common substructure-based algorithm for
searching and predicting drug-like compounds. ISMB 2008. Also appeared on Bioinformatics, 24(13).
doi:10.1093/bioinformatics/btn186
Yiqun Cao, Anna Charisi, Li-Chang Cheng, Tao Jiang, Thomas Girke. ChemmineR: a compound
mining framework in R. Bioinformatics 24(15). doi:10.1093/bioinformatics/btn307
John J. Irwin, Brian K. Shoichet, Michael M. Mysinger, Niu Huang, Francesco Colizzi, Pascal Wassam,
Yiqun Cao. Automated Docking Screens: A Feasibility Study. J Med Chem 52(18). doi: 10.1021/
jm9006966
Yiqun Cao, Tao Jiang, Thomas Girke. Accelerated Similarity Searching and Clustering of Large
Compound Sets by Geometric Embedding and Locality Sensitive Hashing. Bioinformatics 26(7). doi:
10.1093/bioinformatics/btq067
Education
Univ. of California, Riverside, CA PhD in Computer Science, 2010 (expected)
National Univ. of Singapore Master of Engineering in Electrical & Computer Engineering, 2005
Tsinghua Univ., Beijing, P.R.China B.S in Electrical Engineering, 2003
Skills
Have experience in parallel and concurrent programming, object-oriented programming and functional
programming. Have extensive skills in client- and server-side web application development. Have basic
backgrounds in computer architecture, distributed system, operating system, arti cial intelligence, data
mining, machine learning, database, computer networks, network programming, programming language
concepts, theory of computation, algorithm design and analysis, parallel algorithms, sequence analysis,
discrete event simulation, and numerical analysis.
C/C++ 9+ years of programming experience in general problem solving, UNIX system programming, multithread
and parallel programming, and mixed language programming.
Java 2+ years of experience in web application contexts (Servlet, JSP, and Struts).
Python 3+ years of experience, especially in web application development (CherryPy, Kid, Paste, Django, and
Google App Engine).
Other Languages R (S PLUS); XML; JavaScript, XHTML/HTML, CSS; MATLAB; SQL; AWK; LaTeX; Bash.
OS & Tools GNU/Linux (6+ years), Mac OS X (3+ years); Vim, Autotools, gcc, gdb, Eclipse; OpenBabel, JOELib;
DOCK, PLOP, DockBlaster.
Honors
Integrative Graduate Education and Research Traineeship (IGERT) Fellowship at Center for for Plant
Cell Biology (CEPCEB) of UCR 2007-present
Dean's Distinguished Fellowship Award at UCR 2005-2007
Graduate Research Scholarship, National University of Singapore 2003-2005
Academic Excellence Scholarship, Tsinghua University, Beijing, China 2000-2002
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