• I. de Bruijn, R. Kundra, B. Mastrogiacomo, T.N. Tran, L. Sikina, T. Mazor, X. Li, A. Ochoa, G. Zhao, B. Lai, A. Abeshouse, D. Baiceanu, E. Ciftci, U. Dogrusoz, A. Dufilie, Z. Erkoc, E. G. Lara, Z. Fu, B. Gross, C. Haynes, A. Heath, D. Higgins, P. Jagannathan, K. Kalletla, P. Kumari, J. Lindsay, A. Lisman, B. Leenknegt, P. Lukasse, D. Madela, R. Madupuri, P. van Nierop, O. Plantalech, J. Quach, A.C. Resnick, S.Y.A. Rodenburg, B.A. Satravada, F. Schaeffer, R. Sheridan, J. Singh, R. Sirohi, S.O. Sumer, S. van Hagen, A. Wang, M. Wilson, H. Zhang, K. Zhu, N. Rusk, S. Brown, J.A. Lavery, K.S. Panageas, J.E. Rudolph, M.L. LeNoue-Newton, J.L. Warner, X. Guo, H. Hunter-Zinck, T.V. Yu, S. Pilai, C. Nichols, S.M. Gardos, J. Philip, AACR Project GENIE BPC Core Team, AACR Project GENIE Consortium, K.L. Kehl, G.J. Riely, D. Schrag, J. Lee, M.V. Fiandalo, S.M. Sweeney, T.J. Pugh, C. Sander, E. Cerami, J. Gao, N. Schultz, "Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal", Cancer Research, 83(23), pp. 3861-3867, 2023.
• A. Mazein, M.L. Acencio, I. Balaur, A. Rougny, D. Welter, A. Niarakis, D.R. Ardila, U. Dogrusoz, P. Gawron, V. Satagopam, W. Gu, A. Kremer, R. Schneider, M. Ostaszewski, "A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance", Frontiers in Bioinformatics, 3, 2023.
• H. Balci, U. Dogrusoz, Y.Z. Ozgul, P. Atayev, "SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more", PLoS Computational Biology, 18(11), pp. e1010635, 2022.
• H. Balci and U. Dogrusoz, "fCoSE: a fast compound graph layout algorithm with constraint support", IEEE Transactions on Visualization and Computer Graphics, 28(12), pp. 4582-4593, 2022.
• O. Babur, A. Luna, A. Korkut, F. Durupinar, M.C. Siper, U. Dogrusoz, J.E. Aslan, C. Sander, E. Demir, "Causal Relationships in Proteomic Profiles using CausalPath", Star Protocols, 2(4), pp. 100955, 2021.
• A. Okka, U. Dogrusoz, and H. Balci, "CoSEP: a compound spring embedder layout algorithm with support for ports", Information Visualization, 20(2-3), pp. 151-169, 2021.
• O. Babur, A. Luna, A. Korkut, F. Durupinar, M.C. Siper, U. Dogrusoz, J.E. Aslan, C. Sander, E. Demir, "Causal interactions from proteomic profiles: molecular data meets pathway knowledge", Patterns, 2(6), pp. 100257, 2021.
• H. Balci, M.C. Siper, N. Saleh, I. Safarli, L. Roy, M. Kilicarslan, R. Ozaydin, A. Mazein, C. Auffray, O. Babur, E. Demir and U. Dogrusoz, "Newt: a comprehensive web-based tool for viewing,constructing, and analyzing biological maps", Bioinformatics, 37(10), pp.1475-1477, 2021.
• I. Balaur, L. Roy, A. Mazein, S.G. Karaca, U. Dogrusoz, E. Barillot, A. Zinovyev, "cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats", Bioinformatics, btz969, 2020.
• F.T. Bergmann, T. Czauderna, U. Dogrusoz, A. Rougny, A. Drager, V. Toure, A. Mazein, M.L. Blinov, A. Luna, "Systems biology graphical notation markup language (SBGNML) version 0.3", Journal of Integrative Bioinformatics, 17(2-3), pp. 20200016, 2020.
• V. Toure, A. Drager, A. Luna, U. Dogrusoz, A. Rougny, "The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine", in Systems Medicine: Integrative, Qualitative and Computational Approaches, 2020.
• I. Rodchenkov, O. Babur, A. Luna, B.A. Aksoy, J. V Wong, D. Fong, M. Franz, M.C. Siper, M. Cheung, M. Wrana, H. Mistry, L. Mosier, J. Dlin, Q. Wen, C. O'Callaghan, W. Li, G. Elder, P.T. Smith, C. Dallago, E. Cerami, B. Gross, U. Dogrusoz, E. Demir, G.D. Bader, C. Sander, "Pathway Commons 2019 Update: integration, analysis and exploration of pathway data", Nucleic Acids Research, gkz946, 2019.
• A. Rougny, V. Toure, S. Moodie, I. Balaur, T. Czauderna, H. Borlinghaus, U. Dogrusoz, A. Mazein, A. Drager, M.L. Blinov, A. Villeger, R. Haw, E. Demir, H. Mi, A. Sorokin, F. Schreiber, A. Luna, "Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0", Journal of Integrative Bioinformatics, 16, 2019.
• J. Gao, T. Mazor, A. Abeshouse, E. Ciftci, I. de Bruijn, B. Gross, K. Kalletla, P. Kumari, R. Kundra, J. Lindsay, A. Lisman, P. Lukasse, R. Madupuri, A. Ochoa, O. Plantalech, P. Raman, F. Schaeffer, R. Sheridan, J. Su, S.O. Sumer, Y. Sun, S. Tan, S. van Hagen, A. Wang, M. Wilson, H. Zhang, G. Zhao, K. Zhu, K. van Bochove, U. Dogrusoz, T.J. Pugh, A. Resnick, C. Sander, E. Cerami, N. Schultz, "The cBioPortal for cancer genomics", Cancer Research, 79(13 suppl), Abstract 910, July 2019.
• M. Ostaszewski, S. Gebel, I. Kuperstein, A. Mazein, A. Zinovyev, U. Dogrusoz, J. Hasenauer, R. Fleming, N. Le Novere, P. Gawron, T. Ligon, A. Niarakis, D. Nickerson, D. Weindl, R. Balling, E. Barillot, C. Auffray, R. Schneider, "Community-driven roadmap for integrated disease maps", Briefings in Bioinformatics, bby024, March 2019.
• A. Mazein, M. Ostaszewski, I. Kuperstein, S. Watterson, M. Saqi, B. De Meulder, I. Balaur, F. He, A. Parton, N. Lemonnier, D. Lefaudeux, J. Pellet, P. Gawron, S. Gebel, P. Hainaut, M. Ollert, U. Dogrusoz, N. Le Novere, E. Barillot, A. Zinovyev, R. Schneider, R. Balling and C. Auffray, "Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms", npj Systems Biology and Applications, 2018.
• U. Dogrusoz, A. Karacelik, I. Safarli, H. Balci, L. Dervishi, M.C. Siper, "Efficient methods and readily customizable libraries for managing complexity of large networks", PLOS ONE, 13(5): e0197238, 2018.
• F. Sanchez-Vega, M. Mina, J. Armenia, W.K. Chatila, A. Luna, K.C. La, S. Dimitriadoy, D.L. Liu, H.S. Kantheti, S. Saghafinia, D. Chakravarty, F. Daian, Q. Gao, M.H. Bailey, W. Liang, S.M. Foltz, I. Shmulevich, L. Ding, Z. Heins, A. Ochoa, B. Gross, J. Gao, H. Zhang, R. Kundra, C. Kandoth, I. Bahceci, L. Dervishi, U. Dogrusoz, W. Zhou, H. Shen, P.W. Laird, G.P. Way, C.S. Greene, H. Liang, Y. Xiao, C. Wang, A. Iavarone, A.H. Berger, T.G. Bivona, A.J. Lazar, G.D. Hammer, T. Giordano, L.N. Kwong, G. McArthur, C. Huang, A.D. Tward, M.J. Frederick, F. McCormick, M. Meyerson, The Cancer Genome Atlas Research Network, E.M. Van Allen, A.D. Cherniack, G. Ciriello, C. Sander, N. Schultz, "Oncogenic Signaling Pathways in The Cancer Genome Atlas", Cell, 173(2), pp. 321-337.e10, 2018.
• F. Sanchez-Vega, M. Mina, J. Armenia, W.K. Chatila, A. Luna, K.C. La, S. Dimitriadoy, D.L. Liu, H.S. Kantheti, Z. Heins, A. Ochoa, B. Gross, J. Gao, H. Zhang, R. Kundra, C. Kandoth, I. Bahceci, L. Dervishi, U. Dogrusoz, W. Zhou, H. Shen, P.W. Laird, A.H. Berger, T.G. Bivona, A.J. Lazar, G. Hammer, T. Giordano, L. Kwong, G. McArthur, C. Huang, M.J. Frederick, F. McCormick, M. Meyerson, The Cancer Genome Atlas Research Network, E. Van Allen, A.D. Cherniack, G. Ciriello, C. Sander and N. Schultz, "The molecular landscape of oncogenic signaling pathways in The Cancer Genome Atlas", Cancer Research, 78(13 Suppl), Abstract 3302, 2018.
• J. Gao, T. Mazor, E. Ciftci, P. Raman, P. Lukasse, I. Bahceci, A. Sigaras, A. Abeshouse, I. de Bruijn, B. Gross, R. Kundra, A. Lisman, A. Ochoa, R. Sheridan, J. Su, S.O. Sumer, Y. Sun, A. Wang, J. Wang, M. Wilson, H. Zhang, P. Kumari, J. Lindsay, K. Kalletla, K. Zhu, O. Plantalech, F. Schaeffer, S. Tan, D. Zaal, S. van Hagen, K. van Bochove, U. Dogrusoz, T.J. Pugh, A. Resnick, C. Sander, N. Schultz, E. Cerami, "The cBioPortal for Cancer Genomics: An intuitive open-source platform for exploration, analysis and visualization of cancer genomics data", Cancer Research, 78(13 Suppl), Abstract 923, 2018.
• J. Gao, E. Ciftci, P. Raman, P. Lukasse, I. Bahceci, A. Abeshouse, H.W. Chen, I. de Bruijn, B. Gross, Z. Heins, R. Kundra, A. Lisman, A. Ochoa, R. Sheridan, O. Sumer, Y. Sun, J. Wang, M. Wilson, H. Zhang, J. Xu, A. Dufilie, P. Kumari, J. Lindsay, A. Cros, K. Kalletla, F. Schaeffer, S. Tan, S. van Hagen, J. Reis-Filho, K. van Bochove, U. Dogrusoz, T. Pugh, A. Resnick, C. Sander, E. Cerami, N. Schultz, "The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine", Cancer Research, 77(13 Suppl), Abstract 2607, 2017.
• I. Bahceci, U. Dogrusoz, K.C. La, O. Babur, J. Gao, N. Schultz, "PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data", Bioinformatics, 33(14), pp. 2238-2240, 2017.
• B. Genc, U. Dogrusoz, "An Algorithm for Automated Layout of Process Description Maps Drawn in SBGN", Bioinformatics, 32(1), pp. 77-84, 2016.
• J. Gao, J. Lindsay, S. Watt, I. Bahceci, P. Lukasse, A. Abeshouse, H.W. Chen, I. de Bruijn, B. Gross, D. Li, R. Kundra, Z. Heins, J. Reis-Filho, O. Sumer, Y. Sun, J. Wang, Q. Wang, H. Zhang, P. Kumari, M.F. Sahin, S. de Ridder, F. Schaeffer, K. van Bochove, U. Dogrusoz, T. Pugh, C. Sander, E. Cerami, N. Schultz, "The cBioPortal for cancer genomics and its application in precision oncology", Cancer Research, 76(14 Suppl), Abstract 5277, 2016.
• M. Sari, I. Bahceci, U. Dogrusoz, S.O. Sumer, B.A. Aksoy, O. Babur, E. Demir, "SBGNViz: a tool for visualization and complexity management of SBGN process description maps", PLOS ONE, 10(6), e0128985, 2015.
• O.Babur, U. Dogrusoz, M. Cakir, B.A. Aksoy, N. Schultz, C. Sander, E. Demir, "Integrating biological pathways and genomic profiles with ChiBE 2", BMC Genomics, 15(642), 2014.
• J. Gao, B. A. Aksoy, U. Dogrusoz, G. Dresdner, B. Gross, S.O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson, E. Cerami, C. Sander, N. Schultz, "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal", Science Signaling, 6(269), pl1, 2013.
• U. Dogrusoz, M.E. Belviranli, and A. Dilek, "CiSE: A Circular Spring Embedder Layout Algorithm", IEEE Transactions on Visualization and Computer Graphics, 19(6), pp. 953-66, 2013.
• A.C. Villeger, 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 Novere, and F. Schreiber, "Software support for SBGN maps: SBGN-ML and LibSBGN", Bioinformatics, 28(15), pp. 2016-2021, 2012.
• 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, 2012.
• 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 Novere, 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. Villeger, 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, C.A. Duncan, C. Gutwenger, and G. Sander, "Graph Drawing Contest Report", LNCS, 5417, pp. 453-458, 2009.
• U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "(CoSE:) A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 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.
• 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.
• 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.
• B. Genc and U. Dogrusoz, "A Constrained, Force-Directed Layout Algorithm for Biological Pathways", LNCS, 2912, pp. 314-319, 2004.
• U. Dogrusoz, Q. Feng, B. Madden, M. Doorley, and A. Frick, "Graph Visualization Toolkits", IEEE Computer Graphics and Applications, 22(1), pp. 30-37, January/February 2002.
• 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.
• U. Dogrusoz and B. Genc, "A Framework for Complexity Management in Graph Visualization", LNCS, 2528, pp. 368-369, 2002.
• K. Freivalds, U. Dogrusoz, and P. Kikusts, "Disconnected Graph Layout and the Polyomino Packing Approach", LNCS, 2265, pp. 378-391, 2002.
• U. Dogrusoz, "Two-dimensional packing algorithms for layout of disconnected graphs", Information Sciences, 143(1-4), pp. 147-158, 2002.
• U. Dogrusoz, K.G. Kakoulis, B. Madden, and I.G. Tollis, "Edge Labeling in the Graph Layout Toolkit", LNCS, 1547, pp. 356-363, 1998.
• U. Dogrusoz, B. Madden, and P. Madden, "Circular Layout in the Graph Layout Toolkit", LNCS, 1190, pp. 92-100, 1997.