UGUR DOGRUSOZ

Bilkent University, Computer Eng. Dept., Ankara 06800, Turkey

+90 (312) 290 1612, http://www.cs.bilkent.edu.tr/~ugur

PERSONAL INformation

 

·     Born in Corum, Turkey on Aug 28, 1968

Education

 

PhD, Computer Science

Rensselaer Polytechnic Institute

1995

“Cyclic structure and coloring of graphs and their parallel implementations” supervised by Mukkai S. Krishnamoorthy

MS, Computer Science

Rensselaer Polytechnic Institute

1991

“Simulators for abstract formal machines as an educational tool” supervised by Sam M. Kim

BS, Computer Engineering

Middle East Technical University

 

1989

EMPLOYMENT

 

Professor

July 2015 – present

Associate Professor

Jun 2007 – July 2015

Assistant Professor

Aug 1998 – Jun 2007

Computer Engineering Dept., Bilkent University, Ankara, Turkey

Have been teaching (courses on Algorithms, Data Structures, Graph Theory, and Object-Oriented Software Engineering) and actively doing research (on topics including Information Visualization, Bioinformatics and Graph Algorithms).

Visiting Investigator
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York

Worked on Pathway Informatics projects within Pathway Commons project.

2015

Director

2002 – 2010

Bilkent Center for Bioinformatics, Bilkent University, Ankara, Turkey

Co-founded the Center to encourage and coordinate research on bioinformatics at Bilkent.

Senior Research Staff Member
Tom Sawyer Software, Oakland, CA

Aug 2007 – Jul 2008

Vice President of Engineering

Feb – Aug 1998

Tom Sawyer Software, Berkeley, CA

·     Coordinated various on-going software products within the company,

·     Supervised research on graph layout,

·     Communicated with sales, marketing, and human resources divisions to keep them synched with the engineering effort,

·     Actively involved in recruiting to maintain the company's growth.

Product Manager

Aug 1996 – Feb 1998

Tom Sawyer Software, Berkeley, CA

·     Directed and supervised several researchers on graph drawing as part of a research grant on Graph Visualization Technology by National Institute of Standards and Technology - Advanced Technology Program,

·     Organized and oversaw the release of the Graph Layout Toolkit which is a suite of portable libraries designed to bring sophisticated graph visualization technology to application developers.

Research Staff Member

Aug 1995 – Aug 1996

Tom Sawyer Software, Berkeley, CA

·     Worked as a researcher and algorithm developer for the Graph Layout Toolkit which is a suite of portable libraries designed to bring sophisticated graph visualization technology to application developers.

Instructor

Fall 1994 – Spring 1995

Rensselaer Polytechnic Institute, Troy, New York

·     Taught Computing Languages; a course on fundamental programming language concepts through exposure to three languages (namely, C, C++, and Lisp) of various programming paradigms and improving programming skills to the junior level.

Research Assistant

Summer 1992 & 1994

Rensselaer Polytechnic Institute, Troy, New York

·     Participated in an NSF supported project to improve (designed an algorithm for automatic layout of the DFA obtained during the creation of a parse table) the educational tool named LRparse created to help students learn LR parsing with the aid of a graphical interface in C++,

·     Implemented a user interface in C using X Window System for software developed in Mechanical Engineering Department of RPI to simulate flow behavior in injection mold cavity.

Teaching Assistant

Spring 1990 – 1994

Rensselaer Polytechnic Institute, Troy, New York

·     Assisted in teaching of a variety of courses including Computer Algorithms, Formal Languages and Automata, Computer Structures, Discrete Mathematics, and Numerical Computing.

Software Engineer

Summer 1991

Çağıl Makina A.Ş., Çorum, Turkey

·     Implemented in AutoLISP drawings of widely used machine parts as menu items of AutoCAD v.11 used in the company for constructing technical drawings.

Software Engineer

Spring 1987 – 1989

Aselsan Electronics Inc., Ankara, Turkey

·     Developed software in FORTRAN and COBOL dealing with accounting of the company (such as generating paychecks),

·     Designed a relational database system for the library of the company to keep track of the books, journals, and other documents in the library.

Scholarly & PROFESSIONAL DUTIES, ACTIVITIES, AWARDS

 

Awards & Achievements

·     National Young Scientist Career Development Award (Ulusal Genç Araştırmacı Kariyer Geliştirme Programı), TÜBİTAK (The Scientific and Technical Research Council of Turkey), 2005 – 2011.

·     First place (with VISIBIOweb), in the contest for best support for SGBN layout and rendering, 2010.

·     Publication awards by TÜBİTAK, 1998 – present.

·     Received the rank of Associate Professor from the Turkish Inter-University Council (ÜAK), March 2003.

·     Graduate scholarship award by Türk Petrol Vakfı (Turkish Oil Foundation), 1989 – 1990.

·     TÜBİTAK (The Scientific and Technical Research Council of Turkey) scholar during 1987 – 1989.

·     Dean's List of Distinguished Students, throughout entire higher education;

·     Third highest GPA as of graduation in Computer Eng. Dept., Middle East Technical University, Ankara, Turkey, 1989.

Duties

·     Editor (2016 – present), SBGN (Systems Biology Graphical Notation).

·     Co-founder (2002) and Director (2002 – 2010), BCBI (Bilkent Center for Bioinformatics).

·     Have been involved in initiatives and communities such as BioPAX (www.biopax.org) and SBGN (sbgn.org) to help develop standards for biological pathway exchange languages and notations.

·     Mentor, Academy Summer Session, National Resource for Network Biology, 1 project during Summer 2015.

·     Mentor, Google Summer of Code, National Resource for Network Biology, 2 projects during Summer 2016, 1 project during Summer 2013, and 2 projects during Summer 2012.

·     Co-editor, Special Issue on Combinatorial Pattern Matching, Theoretical Computer Science, volume 368, issue 3, pp. 195-248, December 10, 2006.

·     Conference Chair and Program Committee Member, CPM 2004, Fifteenth Annual Combinatorial Pattern Matching Symposium, Istanbul, Turkey, July 5-7, 2004.

·     Scientific Committee Member, The International Congress of Bioinformatics and Biomics, 2011.

·     Scientific Committee Member, Workshop on Recent Advances in Applications of Bioinformatics and Biomics, 2010.

·     Program Committee Member, First International Conference on Bioinformatics, Valencia, Spain, January 20-23, 2010.

·     Program Committee Member, National Conference on Software Architecture (UYMK), Ankara, Turkey, November 4-5, 2010.

·     Academic Committee Member, National Programming Training and Contest Program (UPEM), September 13-19, 2010.

·     Graph Drawing Contest Committee Member, 16th International Symposium on Graph Drawing, Creete, Greece, September 21-24, 2008.

·     Program Committee Member, Biotechnology and Bioinformatics Symposium (BIOT), 2008 – present.

·     Program Committee Member, International Symposium on Health Informatics and Bioinformatics (HIBIT), 2008 – present.

·     Program Committee Member, International Symposium on Computer and Information Sciences (ISCIS), 2004, 2008, and 2009.

·     Program Committee Member, IMPROQ 2003, Workshop on Impact of Software Process on Quality, Ankara, Turkey, June 6, 2003.

·     Have been serving as a reviewer for journals – including Bioinformatics, NAR (Nucleic Acids Research), AMS (Applied Mathematics Letters), JGAA (Journal of Graph Algorithms and Applications), Algorithmica, IJFCS (International Journal of Foundations of Computer Science), IEEE Transactions on Visualization and Computer Graphics – symposiums and conferences, and organizations such as AMS (American Mathematical Society).

·     Have been serving as a referee for TÜBİTAK (The Scientific and Technical Research Council of Turkey) TIDEB (Technology Monitoring and Evaluation Board) and TTGV (Turkish Technology Advancement Foundation) projects and as a panel member for evaluation of academic project proposals.

·     Product Manager of Graph Layout Toolkit 2.4 of Tom Sawyer Software, Berkeley, CA, 1997.

·     Chief Architect of Graph Layout Toolkit version 4 of Tom Sawyer Software, Berkeley, CA, 1997-1998.

Membership

·     ACM SIGACT (Special Interest Group on Algorithms and Computation Theory) since 2000.

·     IEEE Computer Society since 2000.

·     ISCB (International Society for Computational Biology) since 2003.

INVITED LECTURES & TALKS

 

·     “Interactive web based analysis and curation of biological pathways with advanced layout and complexity management support”, BioNetVisA: from biological network reconstruction to data visualization and analysis in molecular biology and medicine, Basel, Switzerland, Sept 2017.

·     “Collaborative curation and visual analysis of biological pathways with advanced layout and complexity management”, The Institute Curie, Paris, France, June 2017.

·     “Newt: An open source web-based SBGN (graph) editor”, Disease Maps Meeting, European Institute for Systems Biology and Medicine, Lyon, France, February 2017.

·     “Role of Documentation in OO Software Engineering”, Senior Design Course Seminar Series, Computer Eng. Dept., Bilkent Univ., Ankara, Fall 2014, 2016, and 2017.

·     “ChiBE 2: Integrating biological pathways and genomic profiles”, 9th International Workshop on Systems Biology Graphical Notation, Edinburgh University, Edinburgh, Scotland, May 2013.

·     “Pathway Visualization Methods and Tools”, Workshop on Recent Advances in Applications of Bioinformatics and Biomics, Cesme, Izmir, Turkey, July 2010.

·     “Pathway Visualization Methods and Tools”, Department of Computer Science and Engineering, Sabanci University, Istanbul, Turkey, May 2010.

·     “VISIBIOweb: a web-based SBGN-compliant layout and visualization service for BioPAX pathway models”, 5th International Workshop on Systems Biology Graphical Notation, SRI International, Menlo Park, CA, USA, October 2009.

·     “Pathway Visualization Methods and Tools”, PharmGKB, Department of Genetics, Stanford University Medical Center, Palo Alto, CA, USA, January 2009.

·     “Pathway Visualization Methods and Tools”, Gladstone Institute of Cardiovascular Disease, UCSF, San Francisco, CA, USA, January 2009.

·     “Pathway Visualization Methods and Tools”, SRI International, Menlo Park, CA, USA, January 2009.

·     “PATIKAweb: A Web-based tool for querying and visualizing PATIKA database”, Gladstone Institute of Cardiovascular Disease, UCSF, San Francisco, CA, USA, November 2006.

·     “PATIKAweb: A Web-based tool for querying and visualizing PATIKA database”, SRI International, Menlo Park, CA, USA, November 2006.

·     “Pathway Ontology, Visualization Notation & Methods in PATIKA”, 1st International SBGN Workshop, Tokyo, Japan, February 2006.

·     “PATIKA Ontology, A comparison with BioPAX”, BioPAX F2F Meeting / Technical Workshop, Tokyo, Japan, November 2005.

·     “PATIKA Ontology, Tools, Modeling Language and Exchange Facilities”, 1st International BioPAX Symposium, Tokyo, Japan, November 2005.

·     “The PATIKA Project”, Stein Lab, Cold Spring Harbor Lab, New York, USA, September 2004.

·     “The PATIKA Project”, Special Interest Group on BioPathways, ISMB 2004, Glasgow, Scotland, July 2004.

·     “The PATIKA Project”, Computational Biology and Medicine (IAM), METU, Ankara, Turkey, June 2004.

·     “Biological Pathway Visualization with PATIKA”, Tom Sawyer Software, Oakland, California, USA, August 2003.

·     “PATIKA: Pathway Analysis Tool for Integration and Knowledge Acquisition”, Special Interest Group on BioPathways, ISMB 2003, Brisbane, Australia, June 2003.

·     “Graph Visualization, Challenges, and Applications”, Computer Eng. Dept., METU, Ankara, Turkey, March 2002.

·     “Disconnected Graph Layout”, Tom Sawyer Software, Oakland, California, USA, August 2001.

educational development activities

 

·     Attended workshop on Critical Thinking, Bilkent University, Ankara, Turkey, March 2000.

·     Attended workshop on Leadership Development, Rensselaer Polytechnic Institute, Troy, NY, April 1994.

TEACHING

 

Graduate Courses

Fall 1998 – present

Computer Eng. Dept., Bilkent University, Ankara, Turkey

·     CS 571 Topics in Graph Theory and Algorithms

·     CS 570 Graph Theory

·     CS 502 Algorithms II

·     CS 573 Algorithms I

Undergraduate Courses

Fall 1994 – present

Computer Eng. Dept., Bilkent University, Ankara, Turkey

·     CS 476 Automata Theory & Formal Languages

·     CS 473 Algorithms I

·     CS 319 Object-Oriented Software Engineering

·     CS 280 Combinatorics & Graph Theory

·     CS 202 Fundamental Structures of Computer Science II

·     CS 101 Algorithms and Programming I

Rensselaer Polytechnic Institute, Troy, New York

·     Computing Languages

Graduate student supervision

 

In Progress

Computer Eng. Dept., Bilkent University, Ankara, Turkey

·     Istemi Bahceci (Ph.D. candidate), 09/2016 – present

·     Hasan Balci (Ph.D. candidate), 09/2016 – present

·     Enes Karaca (M.S. candidate), 01/2016 – present

·     Ilkin Safarli (M.S. candidate), 09/2016 – present

·     Leonard Dervishi (M.S. candidate), 09/2016 – present

·     Umut Utku Calis (M.S. candidate), 09/2016 – present

Completed

Computer Eng. Dept., Bilkent University, Ankara, Turkey

·     Metin Can Siper, (M.S.), July 2017, “Libraries and Tools for Viewing and Editing Biological Maps in SBGN”,

·     currently a Software Engineer at the Demir Lab at OHSU, Portland.

·     Istemi Rahman Bahceci, (M.S.), August 2016, “Software Tools for Visual Analysis of Cancer Genomics Data in the Context of Pathways”.

·     Can Cagdas Cengiz (M.S.), "A Layout Algorithm for Graphs with Overlapping Clusters", 07/2014

·     Begum Genc (M.S.), "Automated Layout of Process Description Maps Drawn in SBGN", 07/2014

·     Mecit Sari (M.S.), "Methods & Tools for Visualization and Management of SBGN PD Maps", 07/2014

·     Merve Cakir (M.S.), "Integrating Biological Pathways and Genomic Profiles with ChiBE 2", 07/2013

·     Alper Karacelik (M.S.), "An Improved Spring Embedder Layout Algorithm for Compound Graphs", 08/2012

·     Selcuk Onur Sumer (M.S.), "Chisio Web: Customizable Web-Based Visualization of Relational Information", 03/2012

·     Ozgun Babur (Ph.D.), “Causality Analysis in Biological Networks”, 01/2010

·     Alptug Dilek (M.S.), “VISIBIOweb: a web-based visualization and layout service for biological pathways”, 08/2009

·     Esat Belviranli (M.S.), “A Circular Layout Algorithm for Clustered Graphs”, 08/2009

·     Ahmet Cetintas (M.S.), “Algorithms for Effective Querying of Graph-Based Pathway Databases”, 07/2007

·     Cihan Kucukkececi (M.S.), “Chisio: A Visual Framework for Compound Graph Editing and Layout”, 06/2007

·     Emek Demir (Ph.D.), “An Ontology for Computer-Aided Modeling of Cellular Processes”, 09/2005

·     Erhan Giral (M.S.), “A Layout Algorithm for Undirected Compound Graphs”, 08/2005

·     Zeynep Erson (M.S.), “PATIKAweb: A Web Service for Accessing and Visualizing Pathway Data in PATIKA Database”, 07/2005

·     Asli Ayaz (M.S.). “Clustering Protein-Protein Interactions Based on Conserved Domain Similarities”, 08/2004

·     Ozgun Babur (M.S.), “Methods for Signaling Pathway Analysis using Microarray Data”, 09/2003

·     Gurcan Gulesir (M.S.), “A Framework for Management of Multiple Views of Cellular Pathway Graphs”, 09/2003

·     Cihad Baskoy (M.S.), “Polygon Packing Approach to Disconnected Graph Layout”, 01/2003

·     Burkay Genc (M.S.), “Complexity Management Techniques in Graph Visualization”, 09/2002

·     Alpay Erdem [co-advised with A. Gursoy] (M.S.), “Time Domain Based Web Usage Mining for Web Site Improvement”, 04/2002

·     H.Mehmet Yuksel (M.S.), “Extending Hierarchical Graph Layout for Drawing UML Activity Diagrams”, 01/2002

Publications

 

PhD Dissertation

·     “Cyclic structure and coloring of graphs and their parallel implementations”, August 1995, Mukkai S. Krishnamoorthy, Rensselaer Polytechnic Institute, Troy, NY.

Edited Books

·     S.C. Sahinalp, S. Muthukrishnan, and U. Dogrusoz (Eds.), Proceedings of Fifteenth Annual Symposium on Combinatorial Pattern Matching (CPM ’04), LNCS, vol. 3109, ISBN 3-540-22341-X, Springer, 2004.

Journal Special Issues

·     S.C. Sahinalp, U. Dogrusoz, and S. Muthukrishnan (Eds.), Special Issue on Combinatorial Pattern Matching, Theoretical Computer Science, volume 368, issue 3, pp. 195-248, 10 December 2006.

Chapters in Books

·     M.S. Krishnamoorthy, F. Oxaal, U. Dogrusoz, D. Pape, A. Robayo, R. Koyanagi, Y. Hsu, D. Hollinger, and A. Hashimi, “GraphPack: Design and Features'', Chapter in Software Visualisation: Series on Software Engineering and Knowledge Engineering, Vol. 7, pp. 83-99, 1996.

Articles in Refereed Journals

·     I. Bahceci, U. Dogrusoz, K.C. La, Ö. Babur, J. Gao, and B. Schultz, "PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data", Bioinformatics, to appear, 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, pp. 5277-5277, 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, to appear in IEEE Transactions on Visualization and Computer Graphics, 19(6), pp. 953-66, 2013.

·     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", Bioinformatics, 28(15), pp. 2016-21, 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, 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.

·     U. Dogrusoz, A. Cetintas, E. Demir, and O. Babur, "Algorithms for Effective Querying of Compound Graph-Based Pathway Databases", BMC Bioinformatics, 10:376, 2009.

·     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, vol. 27, pp. 735-741, 2009.

·     U. Dogrusoz, C.A. Duncan, C. Gutwenger, and G. Sander, Graph Drawing Contest Report, LNCS, vol. 5417, pp. 453–458, 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.

·     S.C. Sahinalp, U. Dogrusoz, and S. Muthukrishnan, Preface, Special Issue on Combinatorial Pattern Matching, Theoretical Computer Science, 368(3), pp. 195, 2006.

·     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, vol. 30/1, pp. 86-97, 2006.

·     B. Genc and U. Dogrusoz, "A Layout Algorithm for Signaling Pathways", Information Sciences, vol. 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, vol. 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, vol. 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.

·     U. Dogrusoz and B. Genc, "A Framework for Complexity Management in Graph Visualization", LNCS, vol. 2528, pp. 368-369, 2002.

·     K. Freivalds, U. Dogrusoz, and P. Kikusts, "Disconnected Graph Layout and the Polyomino Packing Approach", LNCS, vol. 2265, pp. 378-391, 2002.

·     U. Dogrusoz, "Two-dimensional packing algorithms for layout of disconnected graphs", Information Sciences, vol. 143/1-4, pp. 147-158, 2002.

·     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.

·     U. Dogrusoz, K.G. Kakoulis, B. Madden, and I.G. Tollis, "Edge Labeling in the Graph Layout Toolkit", LNCS, vol. 1547, pp. 356-363, 1998.

·     U. Dogrusoz, B. Madden, and P. Madden, "Circular Layout in the Graph Layout Toolkit", Lecture Notes in Computer Science (LNCS), vol. 1190, pp. 92-100, 1997.

·     U. Dogrusoz and M.S. Krishnamoorthy, "Enumerating all cycles of a planar graph", Parallel Algorithms and Applications, vol. 10, pp. 21-36, 1996.

·     M. Benantar, U. Dogrusoz, J.E. Flaherty, and M.S. Krishnamoorthy, "Triangle graphs", Applied Numerical Mathematics, vol. 17, pp. 85-96, 1995.

·     U. Dogrusoz and M.S. Krishnamoorthy, "VLSI algorithms for finding a fundamental set of cycles and a fundamental set of cutsets of a graph", Journal of Computing and Information, 1(1), pp. 46-65, 1994.

Conference Publications

·     F. Durupinar-Babur, M.C. Siper, U. Dogrusoz, I. Bahceci, O. Babur, E. Demir, "Collaborative Workspaces for Pathway Curation", in the Proceedings of the International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016), Corvallis, Oregon, USA, 1-2 August 2016.

·     U. Dogrusoz, S.O. Sumer, S. Sonlu, J. Gao, B.A. Aksoy, B.E. Gross, N. Schultz, E. Cerami, C. Sander, "Network Visualization and Analysis in the cBio Cancer Genomics Portal", Network Biology SIG Meeting at ISMB, Long Beach, CA, USA, July 13, 2012.

·     O. Babur, E. Demir, and U. Dogrusoz, "PATIKAweb Components for Microarray Data Analysis & Advanced Graph-Theoretic Querying", The 8th BioPathways SIG Meeting at ISMB, Vienna, Austria, July 19-20, 2007.

·     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, and H. Yildirim, "PATIKAweb: A Web-based tool for querying and visualizing PATIKA database, integrating pathway data from various popular databases", The 7th BioPathways SIG Meeting at ISMB, Detroit, Michigan, USA, June 23-24, 2005.

·     E. Demir, U. Dogrusoz, O. Babur, A. Ayaz, E. Giral, Z. Erson, G. Nisanci and G. Gulesir, "The PATIKA Project", The 6th BioPathways SIG Meeting at ISMB, Glasgow, Scotland, July 29-30, 2004.

·     U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, “A Compound Graph Layout Algorithm for Biological Pathways”, Proc. of the 12th International Symposium on Graph Drawing, GD 2004, NYC, NY, Sept. 29 – Oct. 2, 2004.

·     B. Genc and U. Dogrusoz, "A Constrained, Force-Directed Layout Algorithm for Biological Pathways", Proc. of the 11th International Symposium on Graph Drawing, GD 2003, Perugia, Italy, September 21 – 24.

·     U. Dogrusoz and B. Genc, "A Framework for Complexity Management in Graph Visualization", Proc. of the 10th International Symposium on Graph Drawing, GD 2002, Irvine, California, pp. 368-369, August 26 – 28, 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", Proc. of the First HUPO World Congress, Human Proteome Organisation, HUPO 2002, Versailles, France, pp. 716, Nov 22 – 24, 2002.

·     K. Freivalds, U. Dogrusoz, and P. Kikusts, "Disconnected Graph Layout and the Polyomino Packing Approach", Proc. of the 9th International Symposium on Graph Drawing, GD 2001, Vienna, Austria, pp. 378-391, September 23 – 26, 2001.

·     U. Dogrusoz, "Algorithms for Layout of Disconnected Graphs", Proc. of the Fifth International Conference on Computer Science and Informatics, CS&I 2000, Atlantic City, NJ, USA, vol. 1, pp. 539-542, February 27 – March 3, 2000.

·     U. Dogrusoz, K.G. Kakoulis, B. Madden, and I.G. Tollis, "Edge Labeling in the Graph Layout Toolkit", Proc. of the 6th International Symposium on Graph Drawing, GD 1998, Montreal, Canada, pp. 356-363, August 13 – 15, 1998.

·     U. Dogrusoz, M. Doorley, Q. Feng, A. Frick, B. Madden, and G. Sander, "Toolkits for Development of Software Diagramming Applications", Tenth International Conference on Software Engineering and Knowledge Engineering, SEKE 1998, San Francisco Bay, USA, pp. 442-449, June 18 – 20, 1998.

·     U. Dogrusoz, B. Madden, and P. Madden, "Circular Layout in the Graph Layout Toolkit", Proc. of the 5th International Symposium on Graph Drawing, GD 1997, Berkeley, CA, USA, pp. 92 - 100, September 18 – 20, 1997.

·     U. Dogrusoz and M.S. Krishnamoorthy, "VLSI algorithms for finding a fundamental set of cycles and a fundamental set of cutsets of a graph", Proc. of the 6th International Conference on Computing and Information, ICCI 1994, Peterborough, Ontario, Canada, pp. 46-65, May 26 – 28, 1994.

Miscellaneous Other Work

·     M. van Iersel, S. Boyd, F. Bergmann, S. Moodie, F. Schreiber, T. Czauderna, E. Demir, N. Le Novère, A. Sorokin, H. Mi, A. Luna, U. Dogrusoz, Y. Matsuoka, A. Funahashi, H. Kitano, M. Aladjem, M. Blinov, and A. Villéger, " LibSBGN: Electronic Processing of SBGN maps", Poster Presentation in ICSB 2010, Edinburgh, UK, October 10 – 16, 2010.

·     U. Dogrusoz, “On Compound Graphs in Modeling, Querying and Visualizing Biological Networks”, Contributed talk in NCB 2006, Ankara, Turkey, Sept. 10 – 12, 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, and H. Yildirim, "PATIKAweb: A Web service for querying, visualizing and analyzing a graph-based pathway database", Poster Presentation in ISMB 2005, Detroit, MI, USA, June 25 – 29, 2005.

·     O. Babur, E. Demir, A. Ayaz, U. Dogrusoz, and O. Sakarya, "Microarray Data Analysis and Pathway Activity Inference in PATIKA", Poster Presentation in ISMB 2004, Glasgow, Scotland, July 31 – August 4, 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.

·     E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, R. Cetin-Atalay, and M. Ozturk, "PATIKA: Pathway Analysis Tool for Integration and Knowledge Acquisition", Poster Presentation in ISMB 2003, Brisbane, Australia, June 29 – July 4, 2003.

·     U. Dogrusoz and G. Sander, "Graph Visualization", Unpublished manuscript, 1998.

·     U. Dogrusoz and M.S. Krishnamoorthy, "Hamiltonian Cycles in Triangle Graphs", Unpublished manuscript, 1998.

·     M. Benantar, U. Dogrusoz, J.E. Flaherty, and M.S. Krishnamoorthy, "Coloring Quadtrees", Unpublished manuscript, 1996.

·     M.S. Krishnamoorthy, F. Oxaal, U. Dogrusoz, D. Pape, A. Robayo, R. Koyanagi, Y. Hsu, D. Hollinger, and A. Hashimi, "Further improvements to GraphPack", Poster Presentation in GD 1994, DIMACS Workshop on Graph Drawing, Princeton, New Jersey, USA, October 10-12, 1994.

GRANTS

 

Methods and Tools for Effective Analysis of Biological Processes with SBGN Diagrams

2014 – 2016

Assignment: Principle Investigator

Sponsor: TÜBİTAK (The Scientific and Technical Research Council of Turkey)

Budget: ~$65,000

CHISIO (Querying, layout, and visualization of clustered or hierarchical relational information)

2011 – 2014

Assignment: Principle Investigator

Sponsor: TÜBİTAK (The Scientific and Technical Research Council of Turkey)

Budget: ~$120,000

IST-TURKEY (New Information Society Technologies for Turkey)

Assignment: Investigator

Principle Investigator: Bulent Ozguler, EE Dept, Bilkent Univ.

Sponsor: TÜBİTAK (The Scientific and Technical Research Council of Turkey)

Budget: ~$425,000

2005 – 2008

PATIKA (Pathway Analysis Tools for Integration & Knowledge Acquisition - www.patika.org)

2005 – 2011

Assignment: Principle Investigator

Sponsor: TÜBİTAK (The Scientific and Technical Research Council of Turkey)

Budget: ~$130,000

Complexity Management Techniques in Graph Visualization Cntd.

May – Oct 2001

Assignment: Principle Investigator

Researchers: Burkay Genc, Erhan Meric, Erdinc Basci

Sponsor: Tom Sawyer Software, Oakland, CA, USA

Budget: ~$36,000

Modeling Cellular Processes

Dec 2001

Assignment: Principle Investigator (jointly with A. Gürsoy and R.Çetin-Atalay)

Sponsor: Bilkent University

Budget: $2,100

Complexity Management Techniques in Graph Visualization

Nov – Apr 2001

Assignment: Principle Investigator

Researchers: Burkay Genc, Yusuf Atas

Sponsor: Tom Sawyer Software, Berkeley, CA, USA

Budget: ~$42,000

Graph Visualization Technology

1995 – 1998

Assignment: Investigator / Academic Coordinator

Principle Investigator: Tom Sawyer Software, Berkeley, CA, USA

Subcontractors: The Univ. of Texas at Dallas and Arizona State University

Sponsor: Advanced Technology Program, NIST, USA

Budget: ~$2,000,000

NON-Scholarly activities

 

·     Served on several committees in Bilkent University, including Traffic Committee (2000 – 2012), Department Curriculum Committee (2000 – 2007), Department ABET Accreditation Committee (2003 – 2007), Faculty Executive Committee (2000 – 2003), and Student Council Election Committee (2003 – 2015);

·     Served as a consultant for various institutions and companies such as Memorial Sloan Kettering Cancer Center (New York), Microwave Electronic Systems, Inc. – MiKES, (Ankara), Ereğli Steel Company (Kdz. Ereğli), and Tom Sawyer Software (Berkeley, CA).

·     President of Turkish Students Association at Rensselaer Polytechnic Institute, Troy, NY (1991 – 1994).