Demir, E. - A Web Based Annotated Bibliography - Aigaion 2.0

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First name(s):	E.
Last name(s):	Demir

Demir, E., Cary, M., Paley, S., Fukuda, K., .., Dogrusoz, U., Sander, C. and Bader, G., The BioPAX community standard for pathway data sharing (2011), in: Nature Biotechnology, 28(935-942)

Babur, O., Demir, E., Gonen, M., Sander, C. and Dogrusoz, U., Discovering Modulators of Gene Expression (2011), in: Nucleic Acids Research, 38(5648-5656)

Demir, E. and Aykanat, C., Efficient Successor Retrieval Operations for Aggregate Query Processing on Clustered Road Networks (2011), in: Information Sciences, 180(2743-2762)

Demir, E., Aykanat, C. and Barla-Cambazoglu, B, A link-based storage scheme for efficient aggregate query processing on clustered road networks (2010), in: Information systems, 35(75-93)

Babur, O., Dogrusoz, U., Demir, E. and Sander, C., chiBE: Iterative visualization and manipulation of BioPAX pathways models (2010), in: Bioinformatics, 26(429-431)

LeNovere, N, Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M.I., Wimalaratne, S.M., Bergman, F.T., Gauges, R., Ghaza, P., Kawaji, H., Li, L., Matsuoka, Y, .., Dogrusoz, U., Freeman, T., Funahashi, A. and Kitano, H., The Systems Biology Graphical Notation (2010), in: Nature Biotechnology, 27(735-741)

Dogrusoz, U., Cetintas, A., Demir, E. and Babur, O., Algorithms for effective querying of compound graph-based pathway databases (2010), in: BMC Bioinformatics, 10(376--1-16)

Dogrusoz, U., Giral, E., Cetintas, A., Civril, A. and Demir, E., A Layout Algorithm for Undirected Compound Graphs (2009), in: Information Sciences, 179(980-994)

Babur, O., Colak, R., Demir, E. and Dogrusoz, U., PATIKAmad: analysis of pathways using microarray data (2009), in: Proteomics, 8(2196-2198)

Dogrusoz, U., Erson, E.Z., Giral, E., Demir, E., Babur, O., Cetintas, A. and Colak, R., PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization (2006), in: Bioinformatics, 22(374-375)

Dogrusoz, U., Giral, E., Cetintas, A., Civril, A. and Demir, E., A Compound Graph Layout Algorithm for Biological Pathways (2005), in: Lecture Notes in Computer Science, 3383(442-447)

Can, F., Altingovde, I.S. and Demir, E., Efficiency and effectiveness of query processing in cluster-based retrieval (2005), in: Information Systems, 29(697-717)

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Ayaz, A., Gulesir, G., Nisanci, G. and Cetin-Atalay, R., An Ontology for Collaborative Construction and Analysis of Cellular Pathways (2004), in: Bioinformatics, 20(349-356)

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R. and Ozturk, M., PATIKA: An Integrated Visual Environment for Collaborative Construction and Analysis of Cellular Pathways (2003), in: Bioinformatics, 18(996-1003)

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R. and Ozturk, M., PATIKA: An integrated Visual environment for collaborative construction and analysis of cellular pathways (2003), in: Bioinformatics, 18(996-1003)

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R. and Ozturk, M., PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways (2003), in: Bioinformatics, 18(996-1003)

Altingovde, I.S., Demir, E., Can, F. and Ulusoy, O., Incremental Cluster-Based-Retrieval Using Compressed Cluster Skipping Inverted Files (2008), in: ACM Trans on Information Systems, 26

Altingovde, A., Demir, E., Can, F. and Ulusoy, O., Incremental Cluster-Based Retrieval Using Compressed Cluster-Skipping Inverted Files (2008), in: ACM Trans on Information Systems, 26(15-1--36)

Demir, E., Aykanat, C. and Cambazoglu, B.B., Clustering Spatial Networks for Aggregate Query Processing, a Hypergraph Approach (2008), in: Information Systems, 33(1-17)

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Ayaz, A., Gulesir, G., Nisanci, G. and Cetin-Atalay, R., An ontology for collaborative construction and analysis of cellular pathways (2004), in: Bioinformatics, 20(349-356)

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