Yang, Qiaofeng
Graduate Program in Genetics, Genomics & Bioinformatics
Department of Computer Science and Engineering
University of California, Riverside
Riverside, CA 92521, USA
Advisor: Dr. Stefano Lonardi
1998 B.S. in Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
1998 B.S. in Corporate Management, Shanghai Jiao Tong University, Shanghai, China.
2006 M.S. in Computer Science & Engineering, University of California, Riverside.
2006 Ph.D. in Bioinformatics, University of California, Riverside.
Computational Biology
Data Mining
Machine Learning
1996-1997 Renmin Scholarship, Shanghai Jiao Tong University, Shanghai, China.
1999 WanTong Scholarship, Shanghai Jiao Tong University, Shanghai, China.
2000-2005 Chancellor's Distinguished Fellowship Award, University of California, Riverside.
2005 GSA UCR Minigrant, University of California, Riverside.
Journal
Yang Q, Jiang H and Xu DQ. 1999. Changes in photosynthetic efficiency of flag leaves of wheat during development. Acta Phytophysiologica Sinica 25(4):408-412.(in Chinese with English abstract)
Swanson WJ, Nielsen R, and Yang Q. 2003. Pervasive adapative evolution in mammalian fertilization proteins. Mol. Biol. Evol. 20(1):18-20. Lonardi S, Szpankowski W and Yang Q. 2006. Finding biclusters by random projections. Theoretical Computer Science, 368(3):217-230.Yang Q and Lonardi S. 2007. A parallel edge-betweenness clustering tool for protein interaction networks. International Journal of Data Mining and Bioinformatics, 1(3):241-247. Wang C, Ding C, Yang Q, and Holbrook SR. 2007. Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biology, 8:R271. Pennycooke JC, Cheng H, Roberts SM, Yang Q, Rhee SY and Stockinger EJ. 2008. The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions and rearrangements. Accepted by Plant Molecular Biology.Conference
Lonardi S, Szpankowski W and Yang Q. 2004. Finding biclusters by random projections. In Proceedings of Symposium on Combinatorial Pattern Matching (CPM'04), LNCS 3109, p. 102-116, Istanbul, Turkey. Yang Q, Lonardi S and Melkman A. 2006. A compression-boosting transform for two-dimensional data. In Proceedings of the 2nd International Conference on Algorithmic Aspects in Information and Management (AAIM'06), LNCS 4041, p. 126-137, Hong Kong, China. Yang Q, Siganos G, Faloutsos M and Lonardi S. 2006. Evolution versus intelligent design: comparing the topology of protein-protein interaction networks to the Internet. In Proceedings of Computational Systems Bioinformatics Conference (CSB'06), p. 299-310, Stanford, CA. Yang Q and Lonardi S. 2007. A decomposition approach for discovering network building blocks. In Proceedings of 7th International Workshop on Data Mining in Bioinformatics ( BIOKDD'07), p. 50-59, San Jose, CA. Ding C, Wang C, Yang Q and Holbrook S. 2007. Computing Protein Interaction Modules via Clique Finding Based on Generalized Motzkin-Strauss Formalism. to appear in IEEE Workshop on High-Throughput Data Analysis for Proteomics and Genomics, Silicon Valley, CA. Cell, Molecular and Developmental Biology program spring retreat, February 2001. Oral presentation titled "DNA microarray data analysis".
Symposium at Lake Arrowhead, CA, March 2002. Poster presentation titled "Promoter recognition and clustering".
Symposium at Lake Arrowhead, CA, March 2003. Oral presentation titled " Biclustering of gene expression data".
IEEE Computational Systems Bioinformatics Conference (CSB'03), Stanford, CA, August 2003.
The Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB'04), San Diego, CA, March 2004. Poster presentation titled "Finding biclusters by random projections".
Arthur M. Sackler Colloquium on Frontiers in Bioinformatics: Unsolved Problems and Challenges, UCI, October 2004.
GGB Fall Orientation Symposium, October 2004. Oral presentation titled "Finding biclusters by random projections".
IEEE Computational Systems Bioinformatics Conference (CSB'05), Stanford, CA, August 2005. Poster presentation titled "A parallel algorithm for clustering protein-protein interaction networks".
Sequence Analysis toward System Biology, Institute of Pure & Applied Mathematics, UCLA, January 2006.
International Conference on Algorithmic Aspects in Information and Management (AAIM'06), Hong Kong, June 2006. Oral presentation titled "A compression-boosting transform for two-dimensional data".
IEEE Computational Systems Bioinformatics Conference (CSB'06), Stanford, CA, August 2006. Poster presentation titled "Evolution versus intelligent design: comparing the topology of protein-protein interction networks to the Internet".
The Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), Oakland, CA, April 2007.
The Seventh International Workshop on Data Mining in Bioinformatics (BIOKDD'07), San Jose, CA, August 2007. Oral presentation titled "A decomposition approach for discovering network building blocks".
The Thirteenth International Conference on Knowledge Discovery and Data Mining (KDD'07), San Jose, CA, August 2007.
2002 Spring, Teaching assistant, University of California, Riverside.
2005 Fall, Teaching assistant, University of California, Riverside.
2000-2006, Research assistant, University of California, Riverside.
A Parallel Edge Betweenness Clustering Tool for Protein Interaction Networks
Annotations for 29 5-cliques found in S. cerevisiae PPI network
C++ Standard Library
C++ STL
C++ Reference
Boost Graph Library
MATLAB
Programming Languages
Engineering Statistics Handbook
Stephen Spain (my husband's homepage :-) )