Publications, Presentations, and Tutorials

• Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gokhan Yavas, Steve Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu. PathCase Pathways Database System. Bioinformatics, 24(21):2526-2533, November 2008.
• Ali Cakmak, Gultekin Ozsoyoglu. Discovering Gene Annotations in Biomedical Text Databases. BMC Bioinformatics 9:143, March 2008.
• Ali Cakmak, Gultekin Ozsoyoglu. Mining Biological Networks for Unknown Pathways. Bioinformatics, Vol. 23(20): 2775-2783, October 2007.
• Z. Meral Özsoyoglu, Gultekin Özsoyoglu, Joseph Nadeau. Genomic Pathways Database and Biological Data Management. Animal Genetics; 37 Suppl 1:41-7, August 2006.
• Z. Meral Özsoyoglu, Joseph Nadeau, Gultekin Özsoyoglu, Murat Tasan. Towards an Integrated Software System for Biological Pathways. IEEE Data Eng. Bull. 27(4): 53-60, 2004
• Lakshmi Krishnamurthy, Joseph H. Nadeau, Gultekin Özsoyoglu, Z. Meral Özsoyoglu, Greg Schaeffer, Murat Tasan, Wanhong Xu. Pathways Database System: An Integrated System for Biological Pathways. Bioinformatics 19(8): 930-937, 2003.
• Z. Meral Ozsoyoglu, Joseph Nadeau, Gultekin Ozsoyoglu. Pathways Database System. OMICS 7(1):123-5, Spring 2003.

• Ali Cakmak, Gultekin Ozsoyoglu, Richard W. Hanson. Managing and Querying Mammalian Metabolic Networks: A Metabolism Query Language and Its Query Processing. 8th International Conference on Computational Systems Bioinformatics (CSB), Stanford, California, August 10-13, 2009.
• Ali Cakmak, Arun Dsouza, Richard W. Hanson, Meral Ozsoyoglu, Gultekin Ozsoyoglu. A Web-Based Data Source for Metabolomics. 24th International Symposium on Computer and Information Sciences (ISCIS), Guzelyurt, Northern Cyprus, September 14-16, 2009.
• Mustafa Kirac, Gultekin Ozsoyoglu. Protein Function Prediction Based on Patterns in Biological Networks. 12th Annual Internation Conference on Research in Computational Molecular Biology (RECOMB), Singapore, March 30-April 2, 2008.
• Ali Cakmak, Gultekin Ozsoyoglu. Taxonomy-Superimposed Graph Mining. 11th International Conference on Extending Database Technology (EDBT), Nantes, France, March 25-30, 2008.
• Ali Cakmak, Mustafa Kirac, Marc Reynolds, Meral Özsoyoglu, Gultekin Özsoyoglu. Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. 19th International Conference on Scientific and Statistical Databases (SSDBM), Banff, Canada, 2007.
• Ali Cakmak, Gultekin Özsoyoglu. Annotating Genes Using Textual Patterns. 12th Pacific Symposium on Biocomputing (PSB), Hawaii, USA, 2007.
• Mustafa Kirac, Gultekin Özsoyoglu, Jiong Yang. Annotating Proteins by Mining Protein Interaction Networks. 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 2006.
• Mustafa Kirac, Ali Cakmak, Gultekin Özsoyoglu. Task-Oriented Integrated Use of Biological Web Data Sources. 18th International Conference on Scientific and Statistical Databases (SSDBM), Vienna, Austria, 2006.
• Nattakarn Ratprasartporn, Ali Cakmak, Gultekin Özsoyoglu. On Data and Visualization Models for Signaling Pathways. 18th International Conference on Scientific and Statistical Databases (SSDBM), Vienna, Austria, 2006.
• Scott Newman, Meral Ozsoyoglu. A Tree-Structured query interface for Querying Semi-Structured Data. 16th International Conference on Scientific and Statistical Databases (SSDBM), Santorini Island, Greece, 2004.
• Wanhong Xu, Lakshmi Krishnamurthy, Murat Tasan, Gultekin Özsoyoglu, Joseph H. Nadeau, Z. Meral Özsoyoglu, Greg Schaeffer. Pathways Database System: An Integrated Set of Tools for Biological Pathways. ACM Symposium on Applied Computing (SAC), 2003.
• Wei Yu, Z. Meral Özsoyoglu, Gultekin Özsoyoglu. XML Restructuring and Integration for Tabular Data. Database and Expert Systems Applications (DEXA), 2003.

• Yuan Wang. Familiar Layouts Generation for Metabolic Pathway Graph Visualization. MS Thesis, Case Western Reserve University, Computing and Information Science, 2008.
• Stephen F. Mayes. Advanced Interface for Querying Graph Data. MS Thesis, Case Western Reserve University, Computing and Information Science, 2007.
• Marc Reynolds. Visualizing, Querying, and Mining Biomedical Ontologies. MS Thesis, Case Western Reserve University, Computing and Information Science, 2006.
• Nattakarn Ratprasartporn. Java-Based Metabolic and Signaling Pathway Viewer. MS Thesis, Case Western Reserve University, Computing and Information Science, 2004.
• Scott W. Newman. A tree structured interface for querying semi-structured data. MS Thesis, Case Western Reserve University, Computing and Information Science, 2004.
• Z. M. Ozsoyoglu, J. Nadeau, G. Ozsoyoglu, M. Tasan, S. Newman, Yu Mei. Towards a System for Biological Pathways. Technical Report, EECS Department, CWRU, January 2004.
• Maneesha Rede. Pathway Viewer: A Biochemical Pathways Visualization Tool. MS Project Report, EECS Dept, CWRU, May 2003.
• Baoxin Zhang. Pathway Editor : A Tool for Creating and Editing Biological Pathways Data. MS Project, EECS Department, CWRU, July 2003.
• Lakshmi Krishnamurthy. Pathways Database System: An Integrated Toolset to Work with Biological Pathways. MS. Thesis, EECS Department, CWRU, May 2002

• [Tutorial] PathCase: A Web-Based Exploratory Querying and Visualization Tool for Biological Pathways. Ohio Collaborative Conference on Bioinformatics, June 2, 2008, Toledo, Ohio, USA. [File Size: ~20 MB]
• PathCase: A Web-Based Exploratory Querying and Visualization Tool for Biological Pathways. Medical College of Wisconsin, April 3, 2007, Milwaukee, Wisconsin, USA. [File Size: ~13 MB]
• PathCase: A Web-Based Exploratory Querying and Visualization Tool for Biological Pathways. 4th International Conference on Pathways, Networks, and Systems (PNAS). Royal Myconian Conference Center, October 8-13, 2006, Mykonos, Greece. [File Size: ~9 MB]

• PathCase: Pathways Database System. 12th Pacific Symposium on Biocomputing (PSB), Maui, Hawaii, USA, 2007.
• PathCase: Pathways Database System. Research ShowCASE'07, Case Western Reserve University, Cleveland, OH, USA, 2007.