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Publications, Presentations, and Tutorials

PathCase:
  • Cicek A.E., Bederman I., Henderson L., Ozsoyoglu • 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. HISS 2013, 1:4
  • 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
  • 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 3(2)
  • 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, 5:188
  • Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Ozsoyoglu. A New Metabolomics Analysis Technique: Steady State Metabolic Network Dynamics Analysis.Journal of Bioinformatics and Computational Biology (JBCB) 10:(1),1240003 2012.
  • A. Ercument Cicek, Gultekin Ozsoyoglu. Observation Conflict Resolution in Steady-State Metabolomics Dynamics Analysis.Journal of Bioinformatics and Computational Biology (JBCB) 10:(1) 1240004, 2012.
  • A. Ercument Cicek, Gultekin Ozsoyoglu. Resolving Observation Conflicts in Steady-State Metabolomics Dynamics AnalysisProceedings of  2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM BCB 2011),  Aug 1 -3, Chicago, IL.
  • Ali Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Ozsoyoglu. 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.
  • Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Ozsoyoglu. Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms. ACM Conference on Bioinformatics and Computational Biology (ACM BCB), August 2010.
  • Ali Cakmak, Gultekin Ozsoyoglu, Richard W. Hanson. Querying Metabolism under Different Physiological Constraints. Journal of Bioinformatics and Computational Biology, 8:(2) pp. 247-293, April 2010.
  • Brendan Elliott, Steve Mayes, Ali Cakmak, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu. Advanced Querying Interface for Biochemical Network Databases. 25th ACM Symposium On Applied Computing (SAC), Sierre, Switzerland, March 22 - 26, 2010.
  • 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.
  • 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.
  • 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 Journal, 24(21):2526-2533, November 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.
  • 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, July 2006.
  • 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.
  • 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.
  • 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.

Pedigrees:
  • 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.
  • En Cheng, Brendan Elliott, Z. Meral Ozsoyoglu. Efficient Computation of Kinship and Identity Coefficients on Large Pedigrees. Journal of Bioinformatics and Computational Biology (JBCB), Vol. 7(3):429-453, 2009.
  • Brendan Elliott, En Cheng, Steve Mayes, Z. Meral Ozsoyoglu. Efficiently Computing Inbreeding on Large Pedigrees. Information Systems, Vol. 34(6):469-576, September 2009.
  • En Cheng, Brendan Elliott, Z. Meral Ozsoyoglu. Scalable Computation of Kinship and Identity Coefficients on Large Pedigrees. 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008), August 2008.
  • Brendan Elliott, S.F. Akgul, S. Mayes, Z. Meral Ozsoyoglu. Efficient Evaluation of Inbreeding Queries on Pedigree Data. 19th International on Conference Scientific and Statistical Database (SSDBM), Banff, Canada, July 2007.
  • Brendan Elliott, S.F. Akgul, Z. Meral Ozsoyoglu, E. Manilich. A Framework for Querying Pedigree Data. 18th International Conference on Scientific and Statistical Databases (SSDBM), Vienna, Austria, July 2006.

Bioinformatics:
  • Manilich, E., Ozsoyoglu, 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.
  • G. Yavas, M. Koyuturk, Z. Meral Ozsoyoglu, M. Gould, T. Laframboise. Cokgen: a Software for Identification of Rare Copy Number Variation from SNP Microarrays. 15th Pacific Symposium of Biocomputing (PSB 2010), Hawaii, January 4-8, 2010.
  • G. Yavas, G. Koyuturk, Z. Meral Ozsoyoglu, M. Gould, T. Laframboise. An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data. Genome Biology Journal, Vol. 10(10), October 2009.
  • Ali Cakmak, Gultekin Ozsoyoglu. Discovering Gene Annotations in Biomedical Text Databases. BMC Bioinformatics 9:143, March 2008.
  • 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, Gultekin Ozsoyoglu. Mining Biological Networks for Unknown Pathways. Bioinformatics, Vol. 23(20): 2775-2783, October 15, 2007.
  • M. Kirac, Gultekin Ozsoyoglu, J. Yang. Annotating Proteins by Mining Protein Interaction Networks. Bioinformatics, 22:e360-e270, July 15, 2006.
  • Ali Cakmak, Gultekin Özsoyoglu. Annotating Genes Using Textual Patterns. 12th Pacific Symposium on Biocomputing (PSB), Hawaii, USA, January 2007.
  • Ali Cakmak, Gultekin Ozsoyoglu. Annotating Genes by Mining PubMed. 12th Pacific Symposium on Biocomputing (PSB), Hawaii, USA, January 2007.
  • M. Kirac, Gultekin Ozsoyoglu, J. Yang. Annotating Proteins by Mining Protein Interaction Networks. 14th International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, August 6, 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, July 2006.

Systems Biology:
  • A. Hernandez, J. McDonald, N. Lai, L.B. Gladden. A Prior Bout of Contractions Speeds VO2 and Blood Rlow On-kinetics and Reduces the VO2 Slow Component Amplitude in Canine Skeletal Muscle Contracting in Situ. J Appl Physiol., 108: 1169-1176, 2010.
  • A. Hernandez, M.L. Goodwin, N. Lai, M.E. Cabrera, J.R. McDonald, L.B. Gladden. Contraction-by-contraction VO2 and Computer-controlled Pump-perfusion as Novel Techniques to Study Skeletal Muscle Metabolism in Situ. J Appl Physiol., 108(3):705-712, 2010.
  • J. Spires, N. Lai, H. Zhou, G.M. Saidel. Hemoglobin and Myoglobin Contributions to Skeletal Muscle Oxygenation in Response to Exercise. Adv Exp Med Biol., (In Press), 2010.
  • H. Zhou, N. Lai, G.M. Saidel, M.E. Cabrera. Multi-scale Modeling of Respiration: Linking External to Cellular Respiration During Exercise. IEEE Enginerring in Medicine and Biology, 28(3):34-40, 2009. PMID: 19457732.
  • N. Lai, G.M. Saidel, M. Iorio, M.E. Cabrera. Non-invasive Estimation of Metabolic Flux and Blood in Working Muscle: Effect of Blood-tissue Distribution. Adv Exp Med Biol., 645:155-160, 2009. PMID: 19227465.
  • N. Lai, H. Zhou, G.M. Saidel, M. Wolf, K. McCully, L.B. Gladden, M.E. Cabrera. Modeling Oxygenation in Venous Blood and Skeletal Muscle in Response to Exercise using Near-infrared Spectroscopy. J Appl Physiol., 106(6):1858-1874, 2009. PMID: 19342438.
  • N. Lai, L.B. Gladden, P.G. Carlier, M.E. Cabrera. Models of Muscle Contraction and Energetics. Drug Discovery Today: Disease Models, 5(4):273-288, 2009.
  • H. Zhou, N. Lai, G.M. Saidel. Evaluation of Muscle Adaptation to Endurance Training in Humans. Biomedical Engineering Society, Annual Meeting, Pittsburg, Pennsylvania, 2009.
  • J. Spires, N. Lai, H. Zhou, G.M. Saidel, M.E. Cabrera. Hemoglobin and Myoglobin Contribution to Skeletal Muscle Oxygenation by NIRS in Response to Exercise. Biomedical Engineering Society, Annual Meeting, Pittsburg, Pennsylvania, 2009.

Presentations and Tutorials:
  • [Slides] Pedigree Data Management and Querying, Z.M. Ozsoyoglu, University of Calabria, Cosenza, Italy, June 2010.
  • [Slides] Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms, G. Ozsoyoglu, Univ. of Calabria, Italy, June 2010.
  • Microsoft Research Channel Video Library, Analyzing Metabolomics Data, available at http://www.researchchannel.org/
  • [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]

Demostrations and Posters:
  • A.Ercument. Cicek, Xinjian Qi, Ali Cakmak, Meral Ozsoyoglu, Gultekin Ozsoyoglu, Steady-State Metabolomics Dynamics Analysis Tool, Great Lakes Bioinformatics Conference 2011 (GLBIO 2011), Poster presentation, Athens, OH.
  • En Cheng, Ali Cakmak, Z. Meral Ozsoyoglu. Efficient Query Evaluation for DAG-Shaped Hierarchies. ACM Conference on Bioinformatics and Computational Biology (BCB), Poster presentation, August 2010.
  • En Cheng, Brendan Elliott, Robert C. Elston, Z. Meral Özsoyoğlu. On Efficient Computation of Kinship and Identity Coefficients, Case Research ShowCASE'10, Poster presentation, Case Western Reserve University, Cleveland, OH, USA, April 2010.
  • Ercument Cicek, Xinjian Qi, Sarp Coskun, Eric Coopey, D. Babuji, Richard hanson, Z. Meral Ozsoyoglu, Gultekin Ozsoyoglu. PathCase-MAW: PathCase Metabolomics Workbench, Poster presentation, OCCBIO Conference, Columbus Ohio, June 2010. [File Size: ~951 KB]
  • Sarp Coskun, En Cheng, Xinjian Qi, R. Jajeda, Ercument Cicek, Sarmila Syed, Zhufou Bai, Nicola Lai, Ranjan Dash, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu.PathCase-SysBio: Database Enabled Tools for regulatory Metabolic networks, Poster presentation, OCCBIO Conference, Columbus Ohio, June 2010. [File Size: 1.6 MB]
  • Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Ozsoyoglu, Gultekin Ozsoyoglu Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms, Metabolomics Conference, Boston, August 2008. [File Size: ~1.2 MB]
  • Mustafa Kirac and Gultekin Ozsoyoglu. Annotating Proteins via Biological Networks, Poster presentation, Aegean Conference on Pathways, Greece, July 2007. [File Size: ~897 KB]
  • PathCase: Pathways Database System. 12th Pacific Symposium on Biocomputing (PSB), Poster presentation, Maui, Hawaii, USA, 2007.
  • PathCase: Pathways Database System. Research ShowCASE'07, Case Western Reserve University, Poster presentation, Cleveland, OH, USA, April 2007.
  • Visualizing and Querying Biomedical Ontologies. Marc R. Reynolds 2006 [File Size: ~461 KB]
  • Z.M. Ozsoyoglu, J. Nadeau, G. Ozsoyoglu, A. Cakmak, B. Elliott, M. Kirac, G. Strnad, G. Yavas. PathCase: Pathways Database System. 2006 [File Size: ~727 KB]