Ugur Dogrusoz

According to our database, Ugur Dogrusoz authored at least 40 papers between 1996 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.

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

Frontiers Bioinform., May, 2023

2022

SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more.

Hasan Balci, Ugur Dogrusoz, Yusuf Ziya Ozgul, Perman Atayev

PLoS Comput. Biol., November, 2022

fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support.

Hasan Balci, Ugur Dogrusoz

IEEE Trans. Vis. Comput. Graph., 2022

2021

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.

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

Patterns, 2021

CoSEP: A compound spring embedder layout algorithm with support for ports.

Alihan Okka, Ugur Dogrusoz, Hasan Balci

Inf. Vis., 2021

RSTrace+: Reviewer suggestion using software artifact traceability graphs.

Emre Sülün, Eray Tüzün, Ugur Dogrusöz

Inf. Softw. Technol., 2021

Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps.

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

Bioinform., 2021

2020

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.

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

Nucleic Acids Res., 2020

Systems biology graphical notation markup language (SBGNML) version 0.3.

Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna

J. Integr. Bioinform., 2020

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.

Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev

Bioinform., 2020

2019

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

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

J. Integr. Bioinform., 2019

Community-driven roadmap for integrated disease maps.

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

Briefings Bioinform., 2019

Reviewer Recommendation using Software Artifact Traceability Graphs.

Emre Sülün, Eray Tüzün, Ugur Dogrusöz

Proceedings of the Fifteenth International Conference on Predictive Models and Data Analytics in Software Engineering, 2019

2017

Chisio: A Compound Graph Editing and Layout Framework.

Cihan Küçükkeçeci, Ugur Dogrusoz, Esat Belviranli, Alptug Dilek

CoRR, 2017

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.

Istemi Bahceci, Ugur Dogrusoz, Konnor C. La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz

Bioinform., 2017

2016

An algorithm for automated layout of process description maps drawn in SBGN.

Begüm Genç, Ugur Dogrusoz

Bioinform., 2016

Collaborative Workspaces for Pathway Curation.

Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2013

CiSE: A Circular Spring Embedder Layout Algorithm.

Ugur Dogrusoz, Mehmet E. Belviranli, Alptug Dilek

IEEE Trans. Vis. Comput. Graph., 2013

2012

Software support for SBGN maps: SBGN-ML and LibSBGN.

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

Bioinform., 2012

2010

VISIBIOweb: visualization and layout services for BioPAX pathway models.

Alptug Dilek, Mehmet E. Belviranli, Ugur Dogrusoz

Nucleic Acids Res., 2010

ChiBE: interactive visualization and manipulation of BioPAX pathway models.

Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander

Bioinform., 2010

2009

A layout algorithm for undirected compound graphs.

Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Inf. Sci., 2009

Algorithms for effective querying of compound graph-based pathway databases.

Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur

BMC Bioinform., 2009

2008

Graph Drawing Contest Report.

Ugur Dogrusöz, Christian A. Duncan, Carsten Gutwenger, Georg Sander

Proceedings of the Graph Drawing, 16th International Symposium, 2008

2007

On labeling in graph visualization.

Ugur Dogrusöz, Konstantinos G. Kakoulis, Brendan Madden, Ioannis G. Tollis

Inf. Sci., 2007

2006

Preface.

Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan

Theor. Comput. Sci., 2006

A layout algorithm for signaling pathways.

Burkay Genç, Ugur Dogrusöz

Inf. Sci., 2006

A multi-graph approach to complexity management in interactive graph visualization.

Ugur Dogrusöz, Burkay Genç

Comput. Graph., 2006

Patika<i>web</i>: a Web interface for analyzing biological pathways through advanced querying and visualization.

Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak

Bioinform., 2006

2004

An ontology for collaborative construction and analysis of cellular pathways.

Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay

Bioinform., 2004

A Compound Graph Layout Algorithm for Biological Pathways.

Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Proceedings of the Graph Drawing, 12th International Symposium, 2004

2003

A Constrained, Force-Directed Layout Algorithm for Biological Pathways.

Burkay Genç, Ugur Dogrusöz

Proceedings of the Graph Drawing, 11th International Symposium, 2003

2002

Two-dimensional packing algorithms for layout of disconnected graphs.

Ugur Dogrusöz

Inf. Sci., 2002

Graph Visualization Toolkits.

Ugur Dogrusöz, Qing-Wen Feng, Brendan Madden, Michael Doorley, Arne Frick

IEEE Computer Graphics and Applications, 2002

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk

Bioinform., 2002

A Framework for Complexity Management in Graph Visualization.

Ugur Dogrusöz, Burkay Genç

Proceedings of the Graph Drawing, 10th International Symposium, 2002

2001

Disconnected Graph Layout and the Polyomino Packing Approach.

Karlis Freivalds, Ugur Dogrusöz, Paulis Kikusts

Proceedings of the Graph Drawing, 9th International Symposium, 2001

1998

Edge Labeling in the Graph Layout Toolkit.

Ugur Dogrusöz, Konstantinos G. Kakoulis, Brendan Madden, Ioannis G. Tollis

Proceedings of the Graph Drawing, 6th International Symposium, 1998

1996

Enumerating all Cycles of a Planar Graph.

Ugur Dogrusöz, M. S. Krishnamoorthy

Parallel Algorithms Appl., 1996

Circular Layout in the Graph Layout Toolkit.

Ugur Dogrusöz, Brendan Madden, Patrick Madden

Proceedings of the Graph Drawing, Symposium on Graph Drawing, 1996