Dr. William (Bill) Andreopoulos

I have been working as an Associate Research Scientist at Columbia University in New York since September 2010. I was a Post-Doctoral Research Scientist at the Biotechnologisches Zentrum, TU-Dresden, Germany till August 2010.

I obtained my PhD from the Department of Computer Science and Engineering of York University, Toronto, Canada, in 2006. I worked under the supervision of Professors Aijun An and Xiaogang (Steven) Wang. I was a course instructor at York University during 2003-2005.

I completed my M.Sc. in the Department of Computer Science at the University of Toronto (2001) and my B.Sc. (Honours with Dinstinction) in the Department of Computing and Software at McMaster University (1999).

e-mail: billa at ee dot columbia dot edu

Teaching

Summer 2005: ITEC3220 Using and Designing Database Systems, COSC1030 Introduction to Computer Science II
Winter 2005: COSC4413 Building e-Commerce Systems, COSC4301 Programming Language Design
Summer 2004: ITEC2010 Systems Analysis and Design, COSC3461 User Interfaces
Winter 2004: COSC4413 Building e-Commerce Systems, COSC4301 Programming Language Design
Fall 2003: COSC4413 Building e-Commerce Systems

Patent

Bill Andreopoulos, Frank Dressel, Dirk Labudde, Michael Schroeder (nanometis and TU Dresden). Automatic Analysis of bio-molecules. Filed Patent (European Patent Application Number EPO 9180269.4), 2009.

Refereed Journal Papers

Bill Andreopoulos, Dimitris Anastassiou. Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature. Cancer Informatics 2012:11 61-75.
Bill Andreopoulos, Dirk Labudde. Efficient unfolding pattern recognition in single molecule force spectroscopy data. Algorithms for Molecular Biology 2011, 6:16.
Bill Andreopoulos, Xiangji Huang, Aijun An, Dirk Labudde, and Qinmin Hu. Promoting Diversity in Top Hits for Biomedical Passage Retrieval. Springer Series on Studies in Computational Intelligence, Advances in Data Management, Volume 223/2009, Pages 371-393, July 2009.
Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder. Triangle network motifs predict complexes by complementing high-error interactomes with structural information. BMC Bioinformatics, 2009.
Bill Andreopoulos, Aijun An, Xiaogang Wang, Dirk Labudde. Efficient Layered Density-based Clustering of Categorical Data. Elsevier Journal of Biomedical Informatics, 2009.
Bill Andreopoulos, Aijun An, Xiaogang Wang, Michael Schroeder. A roadmap of clustering algorithms: finding a match for a biomedical application. Briefings in Bioinformatics, 2009.
Dimitra Alexopoulou*, Bill Andreopoulos*, Heiko Dietze, Andreas Doms*, Fabien Gandon, Joerg Hakenberg, Khaled Khelif*, Michael Schroeder, Thomas Waechter. Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinformatics, 2008.
Loic Royer, Matthias Reimann, Bill Andreopoulos and Michael Schroeder. Unraveling protein networks with power graph analysis. PLoS Computational Biology 4(7): e1000108. doi:10.1371/journal.pcbi.1000108. 2008.
Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos and Michael Schroeder. Clustering by common friends finds locally significant proteins mediating modules. Bioinformatics, Oxford University Press, 23(9): 1124-1131, 2007. Suppl.info MULIC clustering
Bill Andreopoulos, Dimitra Alexopoulou and Michael Schroeder. Word-Sense Disambiguation in Biomedical Ontologies with term co-occurrence analysis and document clustering. International Journal of Data Mining and Bioinformatics (IJDMB), Special Issue on Biomedical Text Retrieval and Mining.
Bill Andreopoulos, Aijun An and Xiaogang Wang. Finding Molecular Complexes through Multiple Layer Clustering of Protein Interaction Networks. International Journal of Bioinformatics Research and Applications (IJBRA), 3(1):65-85, 2007. Suppl.info MULIC clustering
Bill Andreopoulos, Aijun An, Vassilios Tzerpos and Xiaogang Wang. Clustering Large Software Systems at Multiple Layers. Elsevier Information and Software Technology (IST), 49(3):244-254, 2007.
Bill Andreopoulos, Aijun An and Xiaogang Wang. Bi-level Clustering of Mixed Categorical and Numerical Biomedical Data (38 pages). International Journal of Data Mining and Bioinformatics (IJDMB), 1(1):19-56, 2006.
Bill Andreopoulos, Aijun An, Xiaogang Wang. Clustering the Internet Topology at Multiple Layers. Transactions on Information Science and Applications, 10(2):1625-1634, 2005.

Refereed Conference Papers

Bill Andreopoulos, Aijun An, Xiangji Huang, Dirk Labudde. Integration of Gene Interactions, Protein Interactions and Other Biomedical Information on the Semantic Web. ER workshop on Conceptual Modelling in Life Sciences Applications (CMLSA), Barcelona, October 2008.
Loic Royer, Matthias Reimann, Bill Andreopoulos and Michael Schroeder. Visualising protein interaction networks with power graphs. BMC Systems Biology, 1(Suppl 1):51, 2007. From BioSysBio 2007: Systems Biology, Bioinformatics and Synthetic Biology. Manchester, UK, 11-13 January 2007.
Bill Andreopoulos, Aijun An and Xiaogang Wang. Hierarchical Density-based Clustering of Categorical Data and a Simplification. In Proceedings of the 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2007), Springer LNCS 4426/2007, pages 11-22, Nanjing, China, May 22-25, 2007. (full paper acceptance rate 4.66%).
Alexander Andreopoulos, Bill Andreopoulos, Aijun An and Xiaogang Wang. Translation and Rotation Invariant Mining of Frequent Trajectories: Application to Protein Unfolding Pathways. In Proceedings of PAKDD workshop on data mining for biomedical applications (BioDM 2007), Springer LNAI/LNCS, Nanjing, China, May 22-25, 2007.
Bill Andreopoulos, Aijun An, Vassilios Tzerpos and Xiaogang Wang. Multiple Layer Clustering of Large Software Systems. In Proceedings of the 12th IEEE Working Conference on Reverse Engineeering 2005 (WCRE 2005), pages 79-88, Pittsburgh PA (Carnegie Mellon), USA, November 2005.
Bill Andreopoulos, Aijun An, Xiaogang Wang. Clustering Mixed Numerical and Low Quality Categorical Data: Significance Metrics on a Yeast Example. In Proceedings of the ACM SIGMOD Workshop on Information Quality in Information Systems, IQIS 2005 statistics clustering session, pages 87-98, June 17th, Baltimore, MD, US. [slides]
Bill Andreopoulos, Aijun An, Xiaogang Wang. Clustering the Internet Topology at the AS-Level. In Proceedings of the WSEAS conference, Data Mining symposium, Corfu Greece, August 2005.
Bill Andreopoulos, Aijun An and Xiangji Huang. The IGIPI Ontological Framework: Integrating Gene Interaction with Protein Interactions. Oral communication paper. In Proceedings of Network Tools and Applications in Biology 2005, NETTAB 2005, Naples, Italy, October 2005. [slides]
Bill Andreopoulos. Knowledge-based Clustering of Numerical Data Sets Incorporating Confidence Values: Applications to Yeast Genomic Data Sets . In Proceedings of Network Tools and Applications in Biology 2004 (NETTAB 2004), Camerino, Italy, September 2004.
Bill Andreopoulos. Satisficing the Conflicting Software Qualities of Maintainability and Performance at the Source Code Level . In Proceedings of the Workshop on Requirements Engineering 2004 (WER 2004), Tandil, Argentina, December 2004.
Bill Andreopoulos. Achieving Software Quality Using the NFR Framework: Maintainability and Performance . In Proceedings of the 3rd International Conference on Computer Science, Software Engineering, Information Technology, e-Business, and Applications (CSITeA'04), Special Session on Object-oriented software engineering, Cairo, Egypt, December 27-29, 2004.

Book chapter

Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Joerg Hakenberg, Jan Moennich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Waechter, Matthias Zschunke and Michael Schroeder. GoPubMed: Exploring PubMed with Ontological Background Knowledge. In Stephen A. Krawetz, editor, Bioinformatics for Systems Biology. Humana Press, 2009.
GENE Expression Specification. Andreopoulos B. contributor. Object Management Group, February 2003.

Theses

Andreopoulos W. Clustering Algorithms for Categorical Data. PhD thesis, York University, Department of Computer Science and Engineering, 2006.
Committee examiners: Aijun An, Xiangji (Jimmy) Huang, Charles Ling, Minas Spetsakis, John Tsotsos, Bil Tzerpos, Xiaogang (Steven) Wang.
Andreopoulos W. Achieving Software Quality Through Heuristic Transformations: Maintainability and Performance. MSc thesis, University of Toronto, Department of Computer Science, 2001. [http://www.cse.yorku.ca/~billa/SIG/SIG.xml]

Links

Website online since September 10, 2004. Last updated: Nov 8, 2010.