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Ugur Dogrusoz
Person information
- 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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