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Ugur Dogrusoz
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- affiliation: Bilkent University, Ankara, Turkey
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2020 – today
- 2023
- [j31]Alexander Mazein, Marcio Luis Acencio, Irina Balaur, Adrien Rougny, Danielle Welter, Anna Niarakis, Diana Ramirez Ardila, Ugur Dogrusoz, Piotr Gawron, Venkata P. Satagopam, Wei Gu, Andreas Kremer, Reinhard Schneider, Marek Ostaszewski:
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. Frontiers Bioinform. 3 (2023) - 2022
- [j30]Hasan Balci, Ugur Dogrusoz, Yusuf Ziya Ozgul, Perman Atayev:
SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more. PLoS Comput. Biol. 18(11): 1010635 (2022) - [j29]Hasan Balci, Ugur Dogrusoz:
fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support. IEEE Trans. Vis. Comput. Graph. 28(12): 4582-4593 (2022) - 2021
- [j28]Hasan Balci, Metin Can Siper, Nasim Saleh, Ilkin Safarli, Ludovic Roy, Merve Kilicarslan, Rumeysa Ozaydin, Alexander Mazein, Charles Auffray, Özgün Babur, Emek Demir, Ugur Dogrusoz:
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinform. 37(10): 1475-1477 (2021) - [j27]Emre Sülün, Eray Tüzün, Ugur Dogrusöz:
RSTrace+: Reviewer suggestion using software artifact traceability graphs. Inf. Softw. Technol. 130: 106455 (2021) - [j26]Alihan Okka, Ugur Dogrusoz, Hasan Balci:
CoSEP: A compound spring embedder layout algorithm with support for ports. Inf. Vis. 20(2-3) (2021) - [j25]Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupinar, Metin Can Siper, Ugur Dogrusoz, Alvaro Sebastian Vaca Jacome, Ryan Peckner, Karen E. Christianson, Jacob D. Jaffe, Paul T. Spellman, Joseph E. Aslan, Chris Sander, Emek Demir:
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns 2(6): 100257 (2021) - 2020
- [j24]Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36(8): 2620-2622 (2020) - [j23]Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36(19): 4975 (2020) - [j22]Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna:
Systems biology graphical notation markup language (SBGNML) version 0.3. J. Integr. Bioinform. 17(2-3) (2020) - [j21]Igor V. Rodchenkov, Ozgun Babur, Augustin Luna, Bülent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander:
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 48(Database-Issue): D489-D497 (2020)
2010 – 2019
- 2019
- [j20]Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider:
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20(2): 659-670 (2019) - [j19]Adrien Rougny, Vasundra Touré, Stuart L. Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Ugur Dogrusoz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly A. Sorokin, Falk Schreiber, Augustin Luna:
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J. Integr. Bioinform. 16(2) (2019) - [c9]Emre Sülün, Eray Tüzün, Ugur Dogrusöz:
Reviewer Recommendation using Software Artifact Traceability Graphs. PROMISE 2019: 66-75 - 2017
- [j18]Istemi Bahceci, Ugur Dogrusoz, Konnor C. La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz:
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. Bioinform. 33(14): 2238-2240 (2017) - [i1]Cihan Küçükkeçeci, Ugur Dogrusoz, Esat Belviranli, Alptug Dilek:
Chisio: A Compound Graph Editing and Layout Framework. CoRR abs/1708.07762 (2017) - 2016
- [j17]Begüm Genç, Ugur Dogrusoz:
An algorithm for automated layout of process description maps drawn in SBGN. Bioinform. 32(1): 77-84 (2016) - [c8]Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir:
Collaborative Workspaces for Pathway Curation. ICBO/BioCreative 2016 - 2013
- [j16]Ugur Dogrusoz, Mehmet E. Belviranli, Alptug Dilek:
CiSE: A Circular Spring Embedder Layout Algorithm. IEEE Trans. Vis. Comput. Graph. 19(6): 953-966 (2013) - 2012
- [j15]Martijn P. van Iersel, Alice Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly A. Sorokin, Ugur Dogrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber:
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinform. 28(15): 2016-2021 (2012) - 2010
- [j14]Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander:
ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinform. 26(3): 429-431 (2010) - [j13]Alptug Dilek, Mehmet E. Belviranli, Ugur Dogrusoz:
VISIBIOweb: visualization and layout services for BioPAX pathway models. Nucleic Acids Res. 38(Web-Server-Issue): 150-154 (2010)
2000 – 2009
- 2009
- [j12]Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur:
Algorithms for effective querying of compound graph-based pathway databases. BMC Bioinform. 10: 376 (2009) - [j11]Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir:
A layout algorithm for undirected compound graphs. Inf. Sci. 179(7): 980-994 (2009) - 2008
- [c7]Ugur Dogrusöz, Christian A. Duncan, Carsten Gutwenger, Georg Sander:
Graph Drawing Contest Report. GD 2008: 453-458 - 2007
- [j10]Ugur Dogrusöz, Konstantinos G. Kakoulis, Brendan Madden, Ioannis G. Tollis:
On labeling in graph visualization. Inf. Sci. 177(12): 2459-2472 (2007) - 2006
- [j9]Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak:
Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinform. 22(3): 374-375 (2006) - [j8]Ugur Dogrusöz, Burkay Genç:
A multi-graph approach to complexity management in interactive graph visualization. Comput. Graph. 30(1): 86-97 (2006) - [j7]Burkay Genç, Ugur Dogrusöz:
A layout algorithm for signaling pathways. Inf. Sci. 176(2): 135-149 (2006) - [j6]Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan:
Preface. Theor. Comput. Sci. 368(3): 195 (2006) - 2004
- [j5]Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay:
An ontology for collaborative construction and analysis of cellular pathways. Bioinform. 20(3): 349-356 (2004) - [c6]Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir:
A Compound Graph Layout Algorithm for Biological Pathways. GD 2004: 442-447 - [e1]Süleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusöz:
Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings. Lecture Notes in Computer Science 3109, Springer 2004, ISBN 3-540-22341-X [contents] - 2003
- [c5]Burkay Genç, Ugur Dogrusöz:
A Constrained, Force-Directed Layout Algorithm for Biological Pathways. GD 2003: 314-319 - 2002
- [j4]Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk:
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinform. 18(7): 996-1003 (2002) - [j3]Ugur Dogrusöz, Qing-Wen Feng, Brendan Madden, Michael Doorley, Arne Frick:
Graph Visualization Toolkits. IEEE Computer Graphics and Applications 22(1): 30-37 (2002) - [j2]Ugur Dogrusöz:
Two-dimensional packing algorithms for layout of disconnected graphs. Inf. Sci. 143(1-4): 147-158 (2002) - [c4]Ugur Dogrusöz, Burkay Genç:
A Framework for Complexity Management in Graph Visualization. GD 2002: 368-369 - 2001
- [c3]Karlis Freivalds, Ugur Dogrusöz, Paulis Kikusts:
Disconnected Graph Layout and the Polyomino Packing Approach. GD 2001: 378-391
1990 – 1999
- 1998
- [c2]Ugur Dogrusöz, Konstantinos G. Kakoulis, Brendan Madden, Ioannis G. Tollis:
Edge Labeling in the Graph Layout Toolkit. GD 1998: 356-363 - 1996
- [j1]Ugur Dogrusöz, M. S. Krishnamoorthy:
Enumerating all Cycles of a Planar Graph. Parallel Algorithms Appl. 10(1-2): 21-36 (1996) - [c1]Ugur Dogrusöz, Brendan Madden, Patrick Madden:
Circular Layout in the Graph Layout Toolkit. GD 1996: 92-100
Coauthor Index
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