• 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, 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.
• B. Genc and U. Dogrusoz, "A Layout Algorithm for Signaling Pathways", Information Sciences, 176, pp. 135-149, 2006.
• C. Aksay, F. Arik, E. Ataer, A. Ayaz, O. Babur, E. Belviranli, A. Cetintas, R. Colak, G. Cozen, E. Demir, A. Dilek, U. Dogrusoz, E. Z. Erson, E. Giral, E. Kaya, H. Kucuk, A. S. Tekin, H. Yildirim, "PATIKAweb: A Web Service for Querying, Visualizing, and Analyzing a Graph Based Pathway Database", Poster Presentation in ISMB 2005, Detroit, USA, June 26-29, 2005.
• O. Babur, E. Demir, A. Ayaz, U. Dogrusoz, O. Sakarya, "Pathway Activity Inference Using Microarray Data", Technical report, Bilkent Center for Bioinformatics (BCBI), 2004.
• C. Aksay, A. Ayaz, O. Babur, C. Bilgin, A. Cetintas, A. Civril, R. Colak, G. Cozen, E. Demir, U. Dogrusoz, Z. Erson, O. Gerdaneri, E. Giral, G. Gulesir, G. Nisanci, O. Sakarya, and H. Yildirim, "PATIKA: An informatics infrastructure for cellular networks", Poster Presentation in ISMB 2004, Glasgow, Scotland, July 31 - August 4, 2004.
• O. Babur, E. Demir, A. Ayaz, U. Dogrusoz, O. Sakarya, "Microarray Data Analysis and Pathway Activity Inference in PATIKA", Poster Presentation in ISMB 2004, Glasgow, Scotland, July 31 - August 4, 2004.
• U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "A Compound Graph Layout Algorithm for Biological Pathways", LNCS, 3383, pp. 442-447, 2004.
• E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci and R. Cetin-Atalay, "An Ontology for Collaborative Construction and Analysis of Cellular Pathways", Bioinformatics, 20(3), pp. 349-356, 2004.
• B. Genc and U. Dogrusoz, "A Constrained, Force-Directed Layout Algorithm for Biological Pathways", LNCS, 2912, pp. 314-319, 2004.
• E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, and M. Ozturk, "PATIKA: An Integrated Visual Environment for Collaborative Construction and Analysis of Cellular Pathways", Bioinformatics, 18(7), pp. 996-1003, 2002.
• 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", Proc. of the First HUPO World Congress, Human Proteome Organisation, HUPO 2002, Versailles, France, pp. 716, Nov 22-24, 2002.