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case western reserve university

Database and Bioinformatics Lab

Publications

 

2013



Cicek A.E., Bederman I., Henderson L., Ozsoyoglu G. "ADEMA: An Algorithm to Determine Expected Metabolite Level Changes Using Mutual Information". PLoS Computational Biology 2013, 9(1) : e1002859.

Johnson S.R., Qi X., Cicek A.E., Ozsoyoglu G. "iPathCase-KEGG: An iPad Interface for KEGG Data". Health Information Sciences and Systems 2013, 1:4

2012



Coskun S.A., Qi X., Cakmak A., Cheng E., Cicek A.E., Yang L., Jadeja R., Dash R., Lai N., Ozsoyoglu G. Ozsoyoglu Z.M. "PathCase-SB User Interfaces: Computational Tools for Systems Biology". BMC Systems Biology 2012, 6:67

Cakmak A., Qi X., Cicek, A.E., Ozsoyoglu, G., "A New Metabolomics Analysis Technique: Steady State Metabolic Network Dynamics Analysis", Journal of Bioinformatics and Computational Biology (JBCB), 10:(1), 1240003, 2012.

Qi X., Coskun S.A., Cakmak A., Cheng E., Cicek A.E., Das M., Yang L., Jadeja R., Syed S., Dash R.K., Lai N., Özsoyoğlu G., Özsoyoğlu Z.M. "PathCase-SB: Database-Enabled Tools for Regulatory Metabolic Networks". ACM SigBioinformatics Record 2012, 3(2).

Cicek, A.E., Ozsoyoglu, G., "Observation Conflict Resolution in Steady-State Metabolic Network Dynamics Analysis", Journal of Bioinformatics and Computational Biology (JBCB), 10:(1), 1240004, 2012.

2011



Cakmak A., Qi X., Coskun S.A., Das M., Cheng E., Cicek A.E., Lai N., Ozsoyoglu Z.M., Ozsoyoglu G., "PathCase-SB Architecture and Database Design", BMC Systems Biology 2011, 5:188doi:10.1186/1752-0509-5-188 doi:10.1186/1752-0509-5-188.

Cicek, A.E., Ozsoyoglu, G., "Resolving Observation Conflicts in Steady-State Metabolomics Dynamics Analysis", Proceedings of  2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM BCB 2011),  Aug 1 -3, Chicago, IL.

Cakmak A., Qi X., Cicek, A.E., Ozsoyoglu, G., "Computational Interpretation of Metabolomics Measurements: Steady-State Metabolic Network Dynamics Analysis", Proceedings of  2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM BCB 2011),  Aug 1 -3, Chicago, IL.

Yang L., Cheng E., Ozsoyoglu Z. M., Using Compact Encodings for Path-based Computations on Pedigree Graphs, ACM International Conference on Bioinformatics and Computational Biology, (BCB2011): 235-244.

Cicek, A.E., Qi X., Cakmak A., Ozsoyoglu Z.M., Ozsoyoglu, G., "Steady-State Metabolomics Dynamics Analysis Tool", Poster, Great Lakes Bioinformatics Conference 2011 (GLBIO 2011), Athens, OH.

2010


1. Manilich, E., Ozsoyogu, Z.M., Trubachev, V., Radivoyevitch, " Classification of Large Microarray Datasets using Fast Random Forest Construction", 9th Annual International Conference on Computational Systems Bioinformatics (CSB 2010), August 2010.

2. Cakmak, A., Dsouza, A., Hanson, R.W., Ozsoyoglu, Z. M., "Analysing metabolite measurements for Automated Prediction of Underlying Biological mechanisms", ACM Bionformatics and Computational Biology (BCB) Conference, Aug. 2010.

3. Cheng, E., Cakmak, A., Ozsoyoglu, Z.M., "Efficient Query evaluation for DAG-Shaped Hierarchies", ACM BCB Conference, Poster, Aug. 2010.

4. Cakmak, Ozsoyoglu, G., Hanson, R., “Querying Metabolism under Different Physiological Conditions”, Journal of Bioinformatics and Computational Biology, April 2010.

5. Elliott, B., Mayes, S., Cakmak, A., Ozsoyoglu, G., Ozsoyoglu, Z. M., “Advanced Querying Interface for Biochemical Network Databases”, 25th ACM Symposium on Applied Computing, March 2010.

6. Yavas, G. Koyuturk, M., Ozsoyoglu, Z.M., Gould, M., Laframboise, T, “Cokgen: A Software for Identification of Rare Copy Number Variation from SNP Microarrays”, 15th Pacific symposium of Biocomputing (PSB 2010), January 4-8, 2010, Hawaii.

2009


7. Elliot, B., Cheng, E. Mayes, S., Ozsoyoglu, Z.M., “Efficiently Computing Inbreeding on Large Pedigrees”, Information Systems, Vol. 34, No. 6, 469-576, September 2009.

8. Gupta, C., Ozsoyoglu, G., Ozsoyoglu, Z.M., “Efficient K-word Proximity Search”, 24th International Symposium on Computer and Information Sciences (ISCIS), Cyprus, September 14-16, 2009.

9. Elliott, B., Cheng, E., Chimezie, T-O, Ozsoyoglu, Z.M., A Complete Translation from SPARQL into Efficient SQL, IDEAS 2009 Conference, Calabria, Italy, September, 2009.

10. Yavas, G. Koyuturk, M., Ozsoyoglu, Z.M., Gould, M., Laframboise, T, “An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data”, Genome Biology Journal, Vol. 10, no. 10, October 2009.

11. Cheng, E., Elliott, B., Ozsoyoglu, Z.M., Efficient Computation of Kinship and Identity Coefficients on Large Pedigrees, Journal of bioinformatics and Computational Biology (JBCB), Vol.7, No. 3, pp. 429-453, 2009.

12. Ratprasartporn, N., Po, J., Cakmak, A., Bani-Ahmad, S., Ozsoyoglu, G., “Context-based Literature Digital Collection Search”, VLDB Journal, Vol. 18, Issue 1, 2009.

13. Bani-Ahmad, S., Ozsoyoglu, G., “On popularity quality: Growth and decay phases of publication popularities”, Innovations’09 Conf., Dec. 2009.

14. Luo, C., Jiang, J., Hou, W-C., Ozsoyoglu, G., “Progressive evaluation of XML queries for online aggregation and progress indicator”, 20th DEXA Conf., Linz, Austria, 2009.

15. Gupta, C., Ozsoyoglu, G., Ozsoyoglu, Z.M., “Efficient k-Word Proximity Search”, ISCIS Conference, Sept. 2009.

16. Cakmak, A., Kirac, M., Ozsoyoglu, G., “PopulusLog: People Information Database”, ISCIS Conference, Sept. 2009.

17. Cakmak, A., Dsouza, A., Hanson, R., Ozsoyoglu, G., Ozsoyoglu, M., “A Web-Based Data Source for Metabolomics”, ISCIS Conference, Sept. 2009.

18. Cakmak, A., Ozsoyoglu, G., Hanson, R.W., "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.

2008


19. Cakmak, A., Ozsoyoglu, G., “Discovering Gene Annotations in Biomedical Text Databases”, BMC Bioinformatics 2008, 9:143.

20. Elliott, B., Kirac, M., Cakmak, A., Yavas, G., mayes, S., Cheng, E., Wang, Y., Gupta, C., Ozsoyoglu, G., Ozsoyoglu, Z.M., “PathCase: Pathways Database System”, Bioinformatics Journal, Nov. 2008, Vol. 24, No. 21, pp. 2526-2533.

21. Cheng, E., Elliott, B., and Ozsoyoglu, Z.M., “Scalable Computation of Kinship and Identity Coefficients on Large Pedigrees”, 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008), August 2008.

22. Elliott, Brendan, and Ozsoyoglu, Z.M., “Annotation Suggestion and Search for Personal Multimedia Objects on the Web", ACM International Conference on Image and Video Retrieval, July 2008, Canada.

23. Kirac, M., Ozsoyoglu, G., “Protein Function Prediction Based on Patterns in Biological Networks”, 12th Annual Int. Conf. on Research in Computational Molecular Biology (RECOMB), March 30-April 2, 2008.

24. Bani-Ahmad, S., Ozsoyoglu, G., “On Content-Driven Search-Keyword Suggesters for Literature Digital Libraries”, JCDL Conf., June 15, 2008.

25. Bani-Ahmad, S., Ozsoyoglu, G., “elGiza, A Research-Pyramid-Based Search Tool for Vertical Literature Digital Libraries”, DBRank Workshop, April 2008.

26. Cakmak, A., Ozsoyoglu, G, ““Taxonomy-Superimposed Graph Mining”, 11th International Conference on Extending Database Technology (EDBT), Nantes, France, March 25-30, 2008.

2007


27. Elliott, B., and Ozsoyoglu, Z.M., “ A Comparison of Methods for Semantic Photo Annotation Suggestion”, Proceedings of International Symposium on Computer and Information Systems (ISCIS) 2007, Nov. 2007, Ankara, Turkey

28. Cakmak, A., Ozsoyoglu, G., “Mining Biological Pathways for Unknown Pathways”, Bioinformatics Journal, 23(20): 2775-2783, October 15, 2007.

29. Cakmak, A., Kirac, M., Reynolds, M., Ozsoyoglu, Z.M., Ozsoyoglu, G., “Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways”, 19th Int. Conf. on Scientific and Statistical Database Management (SSBM), Alberta, Canada, July 2007.

30. Ratprasartporn, N., Ozsoyoglu, G., “Finding Related Papers in Literature Digital Libraries”, 11th European Conf. for Digital Libraries (ECDL), Budapest, Hungary, Sept. 2007.

31. Bani-Ahmad, S., Ozsoyoglu, G., “Improved Publication Scores for Online Digital Libraries via Research Pyramids”, 11th ECDL Conf., Budapest, Hungary, Sept. 2007.

32. Elliott, B., Akgul, S.F., Mayes, S., Ozsoyoglu, Z.M., “Efficient Evaluation of Inbreeding Queries on Pedigree Data”, International Scientific and Statistical Database Conference, Banff, Alberta, Canada, July 2007.

33. Ratprasartporn, N., Bani-Ahmad, S., Cakmak, A., Po, J., Ozsoyoglu, G., “Evaluating Utility of Different Score Functions in a Context-Based Environment”, IEEE DBRank Workshop, April 2007.

34. Cakmak, A., Ozsoyoglu, G., “Annotating Genes by Mining PubMed”, Pacific Symposium on Biocomputing (PSB) Conf., Hawaii, Jan. 2007.

2006


35. Ozsoyoglu, Z.M., Ozsoyoglu, G., Nadeau, J., “Genomic Pathways Database and Biological Data Management”, Journal of Animal Genetics, Aug. 2006.

36. Kirac, M., Ozsoyoglu, G., Yang, J., “Annotating Proteins by Mining Protein Interaction Networks”, Bioinformatics, 15 July 2006, 22: e360- e270

37. Kirac, M., Ozsoyoglu, G., Yang, J., “Annotating Proteins by Mining Protein Interaction Networks”, 14th Int. Conf. on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, Aug. 6, 2006.

38. Kirac, M., Cakmak, A., Ozsoyoglu, G., “Task-Oriented Integrated Use of Biological Data Resources”, 18th Int. Conference on Scientific and Statistical Database Management, July 2006.

39. Elliott, B., Akgul, S.F., Ozsoyoglu, Z.M., Manilich, E., “A Framework for Querying Pedigree Data”, International Scientific and Statistical Database Conference, Vienna, Austria, July 2006

40. Ratprasartporn, N., Ozsoyoglu, G., “On Data and Visualization Models for Signaling Pathways”, 18th Int. Conference on Scientific and Statistical Database Management, July 2006.

41. Chung, S. S., Ozsoyoglu, G., “Anti-Tamper Databases: Processing Aggregate Queries over Encrypted Databases”, IEEE Workshop on Privacy Data Management, April 8, 2006.