Ugur Dogrusoz - Research

Research

Interests	My research interests fall into the areas of information visualization (e.g. biological pathway and social network visualization), bioinformatics (pathway informatics), and graph algorithms (e.g. graph layout algorithms and query algorithms for graph-based knowledgebases) under the roofs of i-Vis Research Group and BCBI. My philosophy in research is to identify and tackle complex real-life problems and develop solutions of practical value. Such problems typically embrace challenging theoretical problems as well.
Selected Recent Publications	A.C. Villéger, M.P. van Iersel, T. Czauderna, S.E. Boyd, F.T. Bergmann, A. Luna, E. Demir, A. Sorokin, U. Dogrusoz, Y. Matsuoka, A. Funahashi, M.I. Aladjem, H. Mi, S.L. Moodie, H. Kitano, N. Le Novère, and F. Schreiber, "Software support for SBGN maps: SBGN-ML and LibSBGN", to appear in Bioinformatics. E. Cerami, J. Gao, U. Dogrusoz, B.E. Gross, S.O. Sumer, B.A. Aksoy, A. Jacobsen, C.J. Byrne, M.L. Heuer, E. Larsson, Y. Antipin, B. Reva, A.P. Goldberg, C. Sander, and N. Schultz, "The cBio Cancer Genomics Portal: An open source platform for exploring multi-dimensional cancer genomics data", Cancer Discovery, 2, pp. 401-404, May 2012. O. Babur, E. Demir, M. Gonen, C. Sander, and U. Dogrusoz, "Discovering Modulators of Gene Expression", Nucleic Acids Research, 38(17), pp. 5648-5656, 2010. E. Demir, M. Cary, S. Paley, K. Fukuda, C. Lemer, I. Vastrik, G. Wu, P. D'Eustachio, C. Schaefer, J. Luciano, F. Schacherer, I. Martinez-Flores, Z. Hu, V. Jimenez-Jacinto, G. Joshi-Tope, K. Kandasamy, A.C. Lopez-Fuentes, H. Mi, E. Pichler, I. Rodchenkov, A. Splendiani, S. Tkachev, J. Zucker, G. Gopinath, H. Rajasimha, R. Ramakrishnan, I. Shah, M. Syed, N. Anwar, O. Babur, M .Blinov, E. Brauner, D. Corwin, S. Donaldson, F. Gibbons, R. Goldberg, P. Hornbeck, A. Luna, P. Murray-Rust, E. Neumann, O. Ruebenacker, M. Samwald, M. van Iersel, S. Wimalaratne, K. Allen, B. Braun, M. Whirl-Carrillo, K. Cheung, K. Dahlquist, A. Finney, M. Gillespie, E. Glass, L. Gong, R. Haw, M. Honig, O. Hubaut, D. Kane, S. Krupa, M. Kutmon, J. Leonard, D. Marks, D. Merberg, V. Petri, A. Pico, D. Ravenscroft, L. Ren, N. Shah, M. Sunshine, R. Tang, R. Whaley, S. Letovsky, K. Buetow, A. Rzhetsky, V. Schachter, B. Sobral, U. Dogrusoz, S. McWeeney, M. Aladjem, E. Birney, J. Collado-Vides, S. Goto, M. Hucka, N. Le Novere, N. Maltsev, A. Pandey, P. Thomas, E. Wingender, P. Karp, C. Sander, and G. Bader, "The BioPAX community standard for pathway data sharing", Nature Biotechnology, 28, pp. 935-942, 2010. A. Dilek, M.E. Belviranli, and U. Dogrusoz, "VISIBIOweb: visualization and layout services for BioPAX pathway models", Nucleic Acids Research, 38(Suppl), pp. W150-154, 2010. O. Babur, U. Dogrusoz, E. Demir, and C. Sander, "ChiBE: interactive visualization and manipulation of BioPAX pathway models", Bioinformatics, 26(3), pp. 429-431, 2010. N. Le Novère, M. Hucka, H. Mi, S. Moodie, F. Schreiber, A. Sorokin, E. Demir, K. Wegner, M.I. Aladjem, S.M. Wimalaratne, F.T. Bergman, R. Gauges, P. Ghaza, H. Kawaji, L. Li, Y. Matsuoka, A. Villéger, S.E. Boyd, L. Calzone, M. Courtot, U. Dogrusoz, T. Freeman, A. Funahashi, S. Ghosh, A. Jouraku, S. Kim, F. Kolpakov, A. Luna, S. Sahle, E. Schmidt, S. Watterson, G. Wu, I. Goryanin, D.B. Kell, C. Sander, H. Sauro, J.L. Snoep, K. Kohn, H. Kitano, "The Systems Biology Graphical Notation", Nature Biotechnology, 27, pp. 735-741, 2009. U. Dogrusoz, A. Cetintas, E. Demir, and O. Babur, "Algorithms for Effective Querying of Compound Graph-Based Pathway Databases", BMC Bioinformatics, 10:376, 2009. U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 2009. O. Babur, R. Colak, E. Demir, and U. Dogrusoz, "PATIKAmad: putting microarray data into pathway context", Proteomics, 8(11), pp. 2196-2198, 2008. U. Dogrusoz, K.G. Kakoulis, B. Madden, and I.G. Tollis, "On Labeling in Graph Visualization", Special Issue on Graph Theory and Applications, Information Sciences, 177(12), pp. 2459-2472, 2007. U. Dogrusoz, E.Z. Erson, E. Giral, E. Demir, O. Babur, A. Cetintas, and R. Colak, "PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization", Bioinformatics, 22(3), pp. 374-375, 2006. U. Dogrusoz and B. Genc, "A Multi-Graph Approach to Complexity Management in Interactive Graph Visualization", Computers & Graphics, 30(1), pp. 86-97, 2006. B. Genc and U. Dogrusoz, "A Layout Algorithm for Signaling Pathways", Information Sciences, 176, pp. 135-149, 2006. complete list >> In Progress U. Dogrusoz, M.E. Belviranli, and A. Dilek, "CiSE: A Circular Spring Embedder Layout Algorithm", under review.
Projects	[2011-] cBio Cancer Genomics Portal [Collaboration with MSKCC, USA] [2011-] Cytoscape Web [Collaboration with Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Canada] [2007-] ChiBE (Chisio BioPAX Editor) [Collaboration with MSKCC, USA] [2006-] PVS - VISIBIOweb (Pathway Visualization Services) [2006-] Chisio (Compound or Clustered Graph Visualization Tools) [sponsored by TUBITAK] [2000-2011] PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition) [sponsored by TUBITAK] [2000-2001] Complexity Management Techniques in Graph Visualization Cntd. [sponsored by Tom Sawyer Software, USA] [2000] Complexity Management Techniques in Graph Visualization [sponsored by Tom Sawyer Software, USA]
Theses Supervised	In Progress Alper Karacelik, MS candidate Merve Cakir, MS candidate Can Cagdas Cengiz, MS candidate Completed Selcuk Onur Sumer, MS, March 2012, Chisio Web: Customizable Web-Based Visualization of Relational Information, currently a Software Engineer in Memorial Sloan-Kettering Cancer Center, New York. Ozgun Babur, PhD, Jan 2010, Causality Analysis in Biological Networks, currently a [Computational Biology] Post-doc in Memorial Sloan-Kettering Cancer Center, New York. Alptug Dilek, MS, Aug 2009, VISIBIOweb: a web-based visualization and layout service for biological pathways Mehmet Esat Belviranli, MS, Aug 2009, A Circular Layout Algorithm for Clustered Graphs, currently a [CSE] PhD candidate in UC Riverside. Ahmet Cetintas, MS, Jul 2007, Algorithms for Effective Querying of Graph-Based Pathway Databases. Cihan Kucukkececi, MS, Jun 2007, Chisio: A Visual Framework for Compound Graph Editing and Layout. Emek Demir, PhD, Oct 2005, An Ontology for Computer-Aided Modeling of Cellular Processes, currently a [Computational Biology] Research Associate in Memorial Sloan-Kettering Cancer Center, New York. Erhan Giral, MS, Aug 2005, A Layout Algorithm for Undirected Compound Graphs, currently with Computer Associates, San Francisco, CA. E.Zeynep Erson, MS, Jul 2005, PATIKAweb: A Web Service for Accessing and Visualizing Pathway Data in PATIKA Database, currently a [Bioinformatics] Post-doc at Yale University, School of Medicine, New Haven, CT. Asli Ayaz, MS, Aug 2004, Clustering Protein-Protein Interactions Based on Conserved Domain Similarities, currently a [Visual Neuroscience] Research Associate at University College London. Ozgun Babur, MS, Sep 2003, Methods for Signaling Pathway Analysis using Microarray Data. Gurcan Gulesir, MS, Sep 2003, A Framework for Management of Multiple Views of Cellular Pathway Graphs, currently a [CS] post-doc in U Twente, Netherlands. Cihad Baskoy, MS, Jan 2003, Polygon Packing Approach to Disconnected Graph Layout. Burkay Genc, MS, Sep 2002, Complexity Management Techniques in Graph Visualization, currently a [CS] faculty in Izmir University of Economics. Alpay Erdem [co-advised with A. Gursoy], MS, Apr 2002, Time Domain Based Web Usage Mining for Web Site Improvement. H.Mehmet Yuksel, MS, Jan 2002, Extending Hierarchical Graph Layout for Drawing UML Activity Diagrams.