Ugur Dogrusoz

Publication Activity (10 Years)

Years Active: 2010-2023
Publications (10 Years): 16

Top Topics

Description Language

Systems Biology

Bidirectional Search

Community Driven

Top Venues

J. Integr. Bioinform.

IEEE Trans. Vis. Comput. Graph.

Publications

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)
Hasan Balci, Ugur Dogrusoz
fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support. IEEE Trans. Vis. Comput. Graph. 28 (12) (2022)
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) (2022)
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) (2021)
Alihan Okka, Ugur Dogrusoz, Hasan Balci
CoSEP: A compound spring embedder layout algorithm with support for ports. Inf. Vis. 20 (2-3) (2021)
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) (2021)
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) (2020)
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) (2020)
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)
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) (2020)
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) (2019)
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)
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) (2017)
Cihan Küçükkeçeci, Ugur Dogrusoz, Esat Belviranli, Alptug Dilek
Chisio: A Compound Graph Editing and Layout Framework. CoRR (2017)
Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir
Collaborative Workspaces for Pathway Curation. ICBO/BioCreative (2016)
Begüm Genç, Ugur Dogrusoz
An algorithm for automated layout of process description maps drawn in SBGN. Bioinform. 32 (1) (2016)
Ugur Dogrusoz, Mehmet E. Belviranli, Alptug Dilek
CiSE: A Circular Spring Embedder Layout Algorithm. IEEE Trans. Vis. Comput. Graph. 19 (6) (2013)
Alptug Dilek, Mehmet E. Belviranli, Ugur Dogrusoz
VISIBIOweb: visualization and layout services for BioPAX pathway models. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)