Young-Rae Cho (Youngrae Cho), The State University of New York at Buffalo

Young-Rae Cho

Bioinformatics Research Group
Department of Computer Science and Engineering
State University of New York at Buffalo
ycho8[at]cse.buffalo.edu

Current Interest

Bioinformatics and Computational Biology:
Functional Genomics, Systems Biology, Protein Interaction Network Analysis
Data Mining and Data Management:
Frequent Pattern Mining, Classification and Clustering, Data Integration

Papers

Journal Papers
	2008
	Young-Rae Cho, Lei Shi and Aidong Zhang. "Functional module detection by functional flow pattern minining in potein interaction networks". BMC Bioinformatics, 9(Suppl 10):O1.
	Young-Rae Cho, Lei Shi, Murali Ramanathan and Aidong Zhang. "A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge". BMC Bioinformatics, 9:392.
	Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. "CASCADE: a novel quasi all path-based network analysis algorithm for clustering biological interactions". BMC Bioinformatics, 9:64.
	2007
	Young-Rae Cho, Woochang Hwang, Murali Ramanathan and Aidong Zhang. "Semantic integration to identify overlapping functional modules in protein interaction networks". BMC Bioinformatics, 8:265.
	2006
	Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. "A novel functional module detection algorithm for protein-protein interaction networks". Algorithms for Molecular Biology, 1:24.
Conference Papers
	2008
	Young-Rae Cho and Aidong Zhang. "Discovering frequent patterns of functional associations in protein interaction networks for function prediction". IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), November 3-5, 2008, Philadelphia, PA.
	2007
	Young-Rae Cho, Xian Xu, Woochang Hwang and Aidong Zhang. "Feature extraction from microarray expression data by integration of semantic knowledge". IEEE International Conference on Machine Learning and Application (ICMLA 2007), December 13-15, 2007, Cincinnati, OH.
	Young-Rae Cho, Woochang Hwang and Aidong Zhang. "Assessing reliability of protein-protein interactions by semantic data integration". IEEE ICDM 2006 Workshop on Mining and Management of Biological Data (MMBD 2007), October 28-31, 2007, Omaha, NE.
	Young-Rae Cho, Woochang Hwang and Aidong Zhang. "Optimizing flow-based modularization by iterative centroid search in protein interaction networks". IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2007), October 14-17, 2007, Boston, MA.
	Woochang Hwang, Taehyong Kim, Young-Rae Cho, Aidong Zhang and Murali Ramanathan. "SIGN: reliable protein interaction identification by integrating the similarity in GO and the similarity in protein interaction networks". IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2007), October 14-17, 2007, Boston, MA.
	Young-Rae Cho, Woochang Hwang, and Aidong Zhang. "Modularization of protein interaction networks by incorporating Gene Ontology annotations". IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007), April 1-5, 2007, Honolulu, Hawaii.
	2006
	Young-Rae Cho, Woochang Hwang, and Aidong Zhang. "Identification of overlapping functional modules in protein interaction networks: information flow-based approach". IEEE ICDM 2006 Workshop on Data Mining in Bioinformatics (DMB 2006), December 18, 2006, Hong Kong, China.
	Young-Rae Cho, Woochang Hwang, and Aidong Zhang. "Efficient modularization of weighted protein interaction networks using k-hop graph reduction". IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE 2006), October 16-18, 2006, Washington DC.
	Woochang Hwang, Young-Rae Cho, Aidong Zhang, and Murali Ramanathan. "Signal transduction model based functional module detection algorithm for protein-protein interaction networks". 6th SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2006), August 20, 2006, Philadelphia, PA.
Poster Abstracts
	2006
	Young-Rae Cho, Woochang Hwang, Aidong Zhang, and Murali Ramanathan. "Assessing hierarchical modularity in protein interaction networks". LSS Computational Systems Bioinformatics Conference (CSB 2006), August 14-18, 2006, Stanford, CA, USA.
Book Chapter
	Chuan Lin, Young-Rae Cho, Woochang Hwang, Pengjun Pei, and Aidong Zhang. "Clustering Methods In Protein-Protein Interaction Network". in Xiaohua Hu and Yi Pan (eds.), Knowledge Discovery in Bioinformatics: Techniques, Methods and Application., John Wiley & Sons Inc.

Talks

Conference Presentation
	2007
	Feature Extraction from Microarray Expression Data by Integration of Semantic Knowledge. (ICMLA 2007) Optimizing Flow-based Modularization by Iterative Centroid Search in Protein Interaction Networks. (BIBE 2007)
	2006
	Identification of Overlapping Functional Modules in Protein Interaction Networks: Information Flow-based Approach. (DMB 2006) Efficient Modularization of Weighted Protein Interaction Networks using k-Hop Graph Reduction. (BIBE 2006)
Poster Presentation
	2006
	Assessing Hierarchical Modularity in Protein Interaction Networks. (CSB 2006)
Seminar Presentation
	2006
	Survey: Clustering of Biological Networks - Functional Module Detection.
	2005
	Survey: Prediction of Protein-Protein Interactions.
	2003
	Decision Tree Classification - RainForest. Introduction to Data Integration Systems.

Codes

Java codes for Cho et al., "Semantic integration to identify overlapping functional modules
in protein interaction networks", BMC Bioinformatics, 2007.

Patents

Method for identifying drug targets in biological networks
Inventors: Murali Ramanathan, Aidong Zhang, Woochang Hwang, Young-Rae Cho
In progress
Bridging Centrality: a concept and formula to identify bridging nodes in scale-free networks
Inventors: Aidong Zhang, Murali Ramanathan, Woochang Hwang, Young-Rae Cho
Patent No.: US 20070286218
Issue Date: Dec. 12, 2007
Method for manufacturing semiconductor package containing cylindrical type Bump Grid Array
Inventors: Young-Rae Cho, Wook-yeol Ryu, Sang-kyun Lee
Patent No.: US 6,352,915 B1
Issue Date: Mar. 5, 2002
Chip-size packages assembled using mass production techniques at the wafer-level
Inventors: Sam-Il Kim, Young-Rae Cho
Patent No.: US 6,004,867
Issue Date: Dec. 21, 1999

Courseworks

2004, Bioinformatics by Dr. Aidong Zhang

2003, Data Mining by Dr. Jiawei Han

2003, Data Integration by Dr. Anhai Doan

Knowledge Intensive Approach to Schema Matching

Personal History

2004~ :	Ph.D. candidate of Computer Science and Engineering at State Univ. of New York - Buffalo, NY Research Area: Bioinformatics, Systems Biology and Functional Genomics
2002~2004:	MCS (Master of Computer Science) degree at Univ. of Illinois - Urbana-Champaign, IL Research Area: Data Mining, Data Integration and Database Systems
2000~2002:	BA degree of Computer and Information Science at Ohio State Univ. - Columbus, OH Magna Cum Laude (3.87/4.0)
1997~2000:	Assistant Manager at Lead-Frame Research Lab, Samsung Aerospace - Yongin, Korea Research Area: Advanced Semiconductor Packaging (HBGA, TBGA)
1994~1997:	Research Engineer at Package Development Team, Samsung Electronics - Seoul, Korea Research Area: Advanced Semiconductor Packaging (PBGA, COB for Smart Card)
1988~1993:	BS degree of Material Science and Engineering at Yonsei University - Seoul, Korea
1990~1991:	Korean Army at Transportation Battalion in Korean National Defense - Seoul, Korea

My Family & Church

Married Na-young at Seoul, Korea in 1998.

My first child, Justin (Wonho), born at Columbus, OH in 2001.

My second child, Brandon (Hyunsoo), born at Iowa City, IA in 2008.

Served at Zion Choir in NHPC (New Hope Presbyterian Church), Buffalo, NY, in 2005.

Leader of Bible Reading Club (BiMac) in 2005 and 2006.

Leader of System Management Team in Computer Mission Division in NHPC in 2006 and 2007.

Last Updated 11/10/2008