Dogrusoz, U. - A Web Based Annotated Bibliography - Aigaion 2.0

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First name(s):	U.
Last name(s):	Dogrusoz

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., 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)

Dilek, A., Belviranli, M.E. and Dogrusoz, U., VISIBIOWeb: visualization and layout services fro BioPAX pathway models (2011), in: Nucleic Acids Research, 38(150-154)

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)

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., 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)

Sahinalp, S.C., Dogrusoz, U. and Muthukrishnan, S., Preface to special issue on Combinatorial Pattern Matching (2008), in: Theoretical Computer Science, 368(195)

Dogrusoz, U., Kakoulis, K.G., Madden, B. and Tollis, I.G., On Labeling in Graph Visualization (2007), in: Information Sciences, 177(2459-2472)

Genc, B. and Dogrusoz, U., A constrained, force-directed layout algorithm for biological pathways (2006), in: Lecture Notes in Computer Science, 2912(314-319)

Dogrusoz, U. and Genc, B., A Multi-Graph Approach to Complexity Management in Interactive Graph Visualization (2006), in: Computers and Graphics, 30(86-97)

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)

Genc, B. and Dogrusoz, U., A Layout Algorithm for Signaling Pathways (2005), in: Information Sciences, 176(135-149)

Dogrusoz, U. and Genc, B., A Framework for Complexity Management in Graph Visualization (2004), in: Lecture Notes in Computer Science, 2528(368-369)

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., 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)

Freivalds, K., Dogrusoz, U. and Kikusts, P., Disconnected graph layout and the polyomino packing approach (2004), in: Lecture Notes in Computer Science, 2265(378-391)

Dogrusoz, U., Kakoulis, K.G., Madden, B. and Tollis, I.G., Edge labeling in the graph layout toolkit (2004), in: Lecture Notes in Computer Science, 1547(356-363)

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)

Dogrusoz, U., Two-dimensional packing algorithms for layout of disconnected graphs (2002), in: Information Sciences, 143(147-158)

Dogrusoz, U., Feng, Q., Madden, B., Doorley, M. and Frick, A., Graph Visualization Toolkits (2002), in: IEEE Computer Graphics and Applications, 22(30-37)

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