@article{BalciRougnyOverallBalaurBlinovBorlinghausDemirDrägerHawMazeinMiMoodieSchreiberSorokinTouréVillégerCzaudernaDogrusozLuna+, url = {https://doi.org/10.1515/jib-2025-0018}, title = {Systems biology graphical notation: process description language level 1 version 2.1}, title = {}, author = {Hasan Balci and Adrien Rougny and Rupert Overall and Irina Balaur and Michael L. Blinov and Hanna Borlinghaus and Emek Demir and Andreas Dräger and Robin Haw and Alexander Mazein and Huaiyu Mi and Stuart Moodie and Falk Schreiber and Anatoly Sorokin and Vasundra Touré and Alice Villéger and Tobias Czauderna and Ugur Dogrusoz and Augustin Luna}, pages = {20250018}, journal = {Journal of Integrative Bioinformatics}, doi = {doi:10.1515/jib-2025-0018}, year = {}, lastchecked = {2026-06-23} }

@article{ozgul2026sybvals, title={SyBValS: a validation and error resolution service for biological pathway maps}, author={Ozgul, Y. Z. and Dogrusoz, U. and Balci, H.}, journal={BMC Genomics}, volume={27}, pages={106}, year={2026}, publisher={Springer Nature} }

@article{merdol2024saa, author = {Merdol, Lara and Tüzün, Eray and Dogrusoz, Ugur}, year = {2024}, month = {01}, volume = {231}, pages = {112589}, title = {{SAA}: A Framework for Improving the Software Development Process Via Visualization-Based Software Analytics}, doi = {10.2139/ssrn.4960058} }

@article{gao2023analysis, title={Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal}, author={Gao, Jianjiong and others}, journal={Cancer Research}, volume={83}, number={23}, pages={3861--3869}, year={2023}, publisher={American Association for Cancer Research} }

@ARTICLE{10.3389/fbinf.2023.1197310, AUTHOR={Mazein, Alexander and Acencio, Marcio Luis and Balaur, Irina and Rougny, Adrien and Welter, Danielle and Niarakis, Anna and Ramirez Ardila, Diana and Dogrusoz, Ugur and Gawron, Piotr and Satagopam, Venkata and Gu, Wei and Kremer, Andreas and Schneider, Reinhard and Ostaszewski, Marek }, TITLE={A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance}, JOURNAL={Frontiers in Bioinformatics}, VOLUME={Volume 3 - 2023}, YEAR={2023}, }

@article{10.1371/journal.pcbi.1010564, doi = {10.1371/journal.pcbi.1010564}, author = {Kucuktunc, Oznur AND Konuk, Mehmet G. AND Cakir, Tamer}, journal = {PLOS Computational Biology}, publisher = {Public Library of Science}, title = {SyBLaRS: A web service for laying out, rendering and mining pathway models}, year = {2022}, month = {11}, volume = {18}, url = {https://doi.org/10.1371/journal.pcbi.1010564}, pages = {1-19}, number = {11} }

@article{balci2021fcose, title={fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support}, author={Balci, Hasan and Dogrusoz, Ugur}, journal={IEEE Transactions on Visualization and Computer Graphics}, volume={28}, number={12}, pages={4582--4593}, year={2022}, publisher={IEEE} }

@article{babur2021causal, title={Causal interactions from proteomic profiles: Molecular data meet pathway knowledge}, author={Babur, {\"O}zg{\"u}n and Luna, Augustin and Korkut, Anil and Wang, Woong-Kyung and Demir, Emek and Sander, Chris}, journal={Patterns}, volume={2}, number={6}, pages={100257}, year={2021}, publisher={Elsevier}, doi={10.1016/j.patter.2021.100257}, pmid={34179843}, pmcid={PMC8212145} }

@article{doi:10.1177/14738716211028136, author = {Alihan Okka and Ugur Dogrusoz and Hasan Balci}, title ={CoSEP: A compound spring embedder layout algorithm with support for ports}, journal = {Information Visualization}, volume = {20}, number = {2-3}, pages = {151-169}, year = {2021}, doi = {10.1177/14738716211028136} }

@article{7554adc5638b456f8534c2771cc445e3, title = "Causal interactions from proteomic profiles: Molecular data meet pathway knowledge", author = "{\"O}zg{\"u}n Babur and Augustin Luna and Anil Korkut and Funda Durupinar and Siper, \{Metin Can\} and Ugur Dogrusoz and \{Vaca Jacome\}, \{Alvaro Sebastian\} and Ryan Peckner and Christianson, \{Karen E.\} and Jaffe, \{Jacob D.\} and Spellman, \{Paul T.\} and Aslan, \{Joseph E.\} and Chris Sander and Emek Demir", note = "Publisher Copyright: {\textcopyright} 2021 The Authors", year = "2021", month = jun, day = "11", doi = "10.1016/j.patter.2021.100257", language = "English (US)", volume = "2", journal = "Patterns", issn = "2666-3899", publisher = "Cell Press", number = "6", }

@article{balci2021newt, title={Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps}, author={Balci, H. and others}, journal={Bioinformatics}, volume={37}, number={10}, pages={1475--1477}, year={2021}, publisher={Oxford University Press} }

@article{Balaur2020, author = {Balaur, Irina and Roy, Ludovic and Mazein, Alexander and Karaca, Sevgi G. and Dogrusoz, Ugur and Barillot, Emmanuel and Auffray, Charles and Zinovyev, Andrei}, title = {{cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats}}, journal = {Bioinformatics}, volume = {36}, number = {8}, pages = {2620--2622}, year = {2020}, month = {05}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btaa528}, url = {https://doi.org/10.1093/bioinformatics/btaa528} }

@article{bergmann2020sbgnml, title={Systems biology graphical notation markup language (SBGNML) version 0.3}, author={Bergmann, Frank T and Czauderna, Tobias and Dogrusoz, Ugur and Rougny, Adrien and Dr{\"a}ger, Andreas and Tour{\'e}, Venue and Mazein, Alexander and Blinov, Michael L and Luna, Augustin}, journal={Journal of Integrative Bioinformatics}, volume={17}, number={2-3}, pages={20200016}, year={2020}, publisher={De Gruyter}, doi={10.1515/jib-2020-0016} }

@incollection{Toure2020, title = {The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine}, author = {Tour\'{e}, Vasundra and Dr\"{a}ger, Andreas and Luna, Augustin and Dogrusoz, Ugur and Rougny, Adrien}, booktitle = {Reference Module in Biomedical Sciences}, publisher = {Elsevier}, year = {2020}, doi = {10.1016/b978-0-12-801238-3.11623-0}, url = {https://sciencedirect.com} }

@article{10.1093/nar/gkz946, author = {Rodchenkov, Igor and Babur, Ozgun and Luna, Augustin and Aksoy, Bulent Arman and Wong, Jeffrey V and Fong, Dylan and Franz, Max and Siper, Metin Can and Cheung, Manfred and Wrana, Michael and Mistry, Harsh and Mosier, Logan and Dlin, Jonah and Wen, Qizhi and O’Callaghan, Caitlin and Li, Wanxin and Elder, Geoffrey and Smith, Peter T and Dallago, Christian and Cerami, Ethan and Gross, Benjamin and Dogrusoz, Ugur and Demir, Emek and Bader, Gary D and Sander, Chris}, title = {Pathway Commons 2019 Update: integration, analysis and exploration of pathway data}, journal = {Nucleic Acids Research}, volume = {48}, number = {D1}, pages = {D489-D497}, year = {2020}, month = {01}, abstract = {Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.}, issn = {0305-1048}, doi = {10.1093/nar/gkz946}, url = {https://doi.org/10.1093/nar/gkz946}, eprint = {https://academic.oup.com/nar/article-pdf/48/D1/D489/31697764/gkz946.pdf}, }

@article{RougnyTouréMoodieBalaurCzaudernaBorlinghausDogrusozMazeinDrägerBlinovVillégerHawDemirMiSorokinSchreiberLuna+2019, url = {https://doi.org/10.1515/jib-2019-0022}, title = {Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0}, title = {}, author = {Adrien Rougny and Vasundra Touré and Stuart Moodie and Irina Balaur and Tobias Czauderna and Hanna Borlinghaus and Ugur Dogrusoz and Alexander Mazein and Andreas Dräger and Michael L. Blinov and Alice Villéger and Robin Haw and Emek Demir and Huaiyu Mi and Anatoly Sorokin and Falk Schreiber and Augustin Luna}, pages = {20190022}, volume = {16}, number = {2}, journal = {Journal of Integrative Bioinformatics}, doi = {doi:10.1515/jib-2019-0022}, year = {2019}, lastchecked = {2026-06-23} }

@article{10.1093/bib/bby024, author = {Ostaszewski, Marek and Gebel, Stephan and Kuperstein, Inna and Mazein, Alexander and Zinovyev, Andrei and Dogrusoz, Ugur and Hasenauer, Jan and Fleming, Ronan M T and Le Novère, Nicolas and Gawron, Piotr and Ligon, Thomas and Niarakis, Anna and Nickerson, David and Weindl, Daniel and Balling, Rudi and Barillot, Emmanuel and Auffray, Charles and Schneider, Reinhard}, title = {Community-driven roadmap for integrated disease maps}, journal = {Briefings in Bioinformatics}, volume = {20}, number = {2}, pages = {659-670}, year = {2019}, month = {03}, issn = {1477-4054}, doi = {10.1093/bib/bby024} }

@article{ORBi-a4715ab5-17ed-4869-8f3b-dbf651c7ff69, AUTHOR = {Mazein, Alexander and OSTASZEWSKI, Marek and Kuperstein, Inna and Watterson, Steven and Le Novere, Nicolas and Lefaudeux, Diane and De Meulder, Bertrand and Pellet, Johann and Balaur, Irina and Saqi, Mansoor and Nogueira, Maria Manuela and He, Feng and Parton, Andrew and Lemonnier, Nathanael and GAWRON, Piotr and GEBEL, Stephan and Hainaut, Pierre and Ollert, Markus and Dogrusoz, Ugur and Barillot, Emmanuel and Zinovyev, Andrei and SCHNEIDER, Reinhard and BALLING, Rudi and Auffray, Charles}, EPRINT = {https://orbilu.uni.lu/handle/10993/36329}, EPRINTTYPE = {hdl}, TITLE = {Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.}, LANGUAGE = {English}, YEAR = {2018}, DOI = {10.1038/s41540-018-0059-y}, PUBLISHER = {Springer Nature}, JOURNAL = {NPJ Systems Biology and Applications}, VOLUME = {4} }

@article{article, author = {Dogrusoz, Ugur and Karacelik, Alper and Safarli, Ilkin and Balcı, Hasan and Dervishi, Leonard and Siper, Metin}, year = {2018}, month = {05}, pages = {e0197238}, title = {Efficient methods and readily customizable libraries for managing complexity of large networks}, volume = {13}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0197238} }

@article{article, author = {Sánchez-Vega, Francisco and Mina, Marco and Armenia, Joshua and Chatila, Walid and Luna, Augustin and La, Konnor and Dimitriadoy, Sofia and Liu, David and Kantheti, Srinivas and Saghafinia, M. Sadegh and Chakravarty, Debyani and Daian, Foysal and Gao, Qingsong and Bailey, Matthew and Liang, Wen-Wei and Foltz, Steven and Shmulevich, Ilya and Ding, Li and Heins, Zachary and Mariamidze, Armaz}, year = {2018}, month = {04}, pages = {321-337.e10}, title = {Oncogenic Signaling Pathways in The Cancer Genome Atlas}, volume = {173}, journal = {Cell}, doi = {10.1016/j.cell.2018.03.035} }

@article{10.1093/bioinformatics/btx149, author = {Bahceci, Istemi and Dogrusoz, Ugur and La, Konnor C and Babur, Özgün and Gao, Jianjiong and Schultz, Nikolaus}, title = {PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data}, journal = {Bioinformatics}, volume = {33}, number = {14}, pages = {2238-2240}, year = {2017}, month = {07}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btx149} }

@article{genc2016algorithm, author = {Gen\c{c}, Beg\"{u}m and Dogrusoz, Ugur}, title = {An algorithm for automated layout of process description maps drawn in {SBGN}}, journal = {Bioinformatics}, volume = {32}, number = {1}, pages = {77--84}, year = {2016}, month = {01}, doi = {10.1093/bioinformatics/btv528}, url = {https://doi.org} }

@article{sari2015sbgnviz, title = {{SBGNViz}: A Tool for Visualization and Complexity Management of {SBGN} Process Description Maps}, author = {Sari, M. and Bahceci, I. and Dogrusoz, U. and Sumer, S. O. and Aksoy, B. A. and Babur, {\"O}. and Demir, E.}, journal = {PLOS ONE}, volume = {10}, number = {6}, pages = {e0128985}, year = {2015}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0128985} }

@article{babur2014chibe, title = {Integrating biological pathways and genomic profiles with {ChiBE} 2}, author = {Babur, {\"O}zg{\"u}r and Dogrusoz, Ugur and Cakir, Merve and Aksoy, Bulent Arman and Schultz, Nikolaus and Sander, Chris and Demir, Emek}, journal = {BMC Genomics}, volume = {15}, number = {1}, pages = {642}, year = {2014}, publisher = {Springer Nature}, doi = {10.1186/1471-2164-15-642}, url = {https://doi.org} }

@article{Gao2013, author = {Gao, J. and Aksoy, B. A. and Dogrusoz, U. and Dresdner, G. and Gross, B. and Sumer, S. O. and Sun, Y. and Jacobsen, A. and Sinha, R. and Larsson, E. and Cerami, E. and Sander, C. and Schultz, N.}, title = {Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal}, journal = {Science Signaling}, volume = {6}, number = {269}, pages = {pl1}, year = {2013}, doi = {10.1126/scisignal.2004088}, url = {https://sciencemag.org} }

@article{belviranli2013cise, author = {Belviranli, M. and Dilek, A. and Dogrusoz, U.}, journal = {IEEE Transactions on Visualization and Computer Graphics}, title = {CiSE: A Circular Spring Embedder Layout Algorithm}, year = {2013}, volume = {19}, number = {6}, pages = {953-966}, doi = {10.1109/TVCG.2012.178} }

@article{vanIersel2012, author = {van Iersel, Martijn P. and Vill{\'e}ger, Alice C. and Czauderna, Tobias and Boyd, Boyd S. E. and Bergmann, Frank T. and Luna, Agustin and Demir, Emek and Sorokin, Anatoly and Dogrusoz, Ugur and Matsuoka, Yukiko and Funahashi, Akira and Kitano, Hiroaki and Allen, Benjamin B. and Blinov, Michael L. and Gomez, Manuel and Hermann, Katja and Ludwig, Carsten and Schreiber, Falk and Nov{\`e}re, Nicolas Le}, title = {Software support for SBGN maps: SBGN-ML and LibSBGN}, journal = {Bioinformatics}, volume = {28}, number = {15}, pages = {2016--2021}, year = {2012}, month = {08}, doi = {10.1093/bioinformatics/bts270}, url = {https://doi.org}, publisher = {Oxford University Press} }

@article{dilek2010visibioweb, title={VISIBIOweb: visualization and layout services for BioPAX pathway models}, author={Dilek, Alptug and Belviranli, Mehmet E. and Dogrusoz, Ugur}, journal={Nucleic Acids Research}, volume={38}, number={Web Server issue}, pages={W150--W154}, year={2010}, publisher={Oxford University Press} }

@article{babur2010chibe, title={ChiBE: interactive visualization and manipulation of BioPAX pathway models}, author={Babur, O. and Dogrusoz, U. and Demir, E. and Sander, C.}, journal={Bioinformatics}, volume={26}, number={3}, pages={429--431}, year={2010}, publisher={Oxford University Press} }

@article{le2009systems, title={The systems biology graphical notation}, author={Le Nov{\`e}re, Nicolas and others}, journal={Nature biotechnology}, volume={27}, number={8}, pages={735--741}, year={2009}, doi={10.1038/nbt.1558} }

@article{DOGRUSOZ2009980, title = {A layout algorithm for undirected compound graphs}, journal = {Information Sciences}, volume = {179}, number = {7}, pages = {980-994}, year = {2009}, issn = {0020-0255}, author = {Ugur Dogrusoz and Erhan Giral and Ahmet Cetintas and Ali Civril and Emek Demir}, keywords = {Information visualization, Graph drawing, Force-directed graph layout, Compound graphs, Bioinformatics} }

@article{dogrusoz2009algorithms, author = {Dogrusoz, Ugur and Cetintas, Ahmet and Demir, Emek and Babur, Ozgun}, title = {Algorithms for effective querying of compound graph-based pathway databases}, journal = {BMC Bioinformatics}, volume = {10}, number = {1}, pages = {376}, year = {2009}, month = {Nov}, day = {16}, issn = {1471-2105} }

@article{https://doi.org/10.1002/pmic.200700769, author = {Babur, Ozgun and Colak, Recep and Demir, Emek and Dogrusoz, Ugur}, title = {PATIKAmad: Putting microarray data into pathway context}, journal = {PROTEOMICS}, volume = {8}, number = {11}, pages = {2196-2198} year = {2008} }

@article{Dogrusoz2007OnLabeling, title = {On labeling in graph visualization}, author = {Dogrus{\"o}z, U{\u g}ur and Kakoulis, Konstantinos G. and Madden, Brendan and Tollis, Ioannis G.}, journal = {Information Sciences}, volume = {177}, number = {12}, pages = {2459--2472}, year = {2007}, issn = {0020-0255}, doi = {https://doi.org}, url = {https://sciencedirect.com} }

@article{10.1093/bioinformatics/bti776, author = {Dogrusoz, U. and Erson, E. Z. and Giral, E. and Demir, E. and Babur, O. and Cetintas, A. and Colak, R.}, title = {Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization}, journal = {Bioinformatics}, volume = {22}, number = {3}, pages = {374-375}, year = {2006}, month = {02}, issn = {1367-4803} }

@article{dogrusoz2006multigraph, title={A multi-graph approach to complexity management in interactive graph visualization}, author={Dogrusoz, Ugur and Genc Burkay}, journal={Computers \& Graphics}, volume={30}, number={1}, pages={86--97}, year={2006} }

@article{GENC2006135, title = {A layout algorithm for signaling pathways}, journal = {Information Sciences}, volume = {176}, number = {2}, pages = {135-149}, year = {2006}, issn = {0020-0255}, doi = {https://doi.org/10.1016/j.ins.2004.11.006}, url = {https://www.sciencedirect.com/science/article/pii/S0020025504003305}, author = {B. Genc and U. Dogrusoz}, keywords = {Bioinformatics, Signaling pathways, Cellular pathway analysis, Information visualization, Pathway visualization, Graph layout} }

@article{dogrusoz2009compound, title={A layout algorithm for undirected compound graphs}, author={Dogrusoz, Ugur and Giral, Erhan and Cetintas, Ahmet and Civril, Ali and Demir, Emek}, journal={Information Sciences}, volume={179}, number={7}, pages={980--994}, year={2009}, publisher={Elsevier}, doi={10.1016/j.ins.2008.11.017} }

@InProceedings{10.1007/978-3-540-24595-7_29, author="Genc, Burkay and Dogrusoz, Ugur", editor="Liotta, Giuseppe", title="A Constrained, Force-Directed Layout Algorithm for Biological Pathways", booktitle="Graph Drawing", year="2004", publisher="Springer Berlin Heidelberg", address="Berlin, Heidelberg", pages="314--319", abstract="We present a new elegant algorithm for layout of biological signaling pathways. It uses a force-directed layout scheme, taking into account directional and regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA and results with respect to computational complexity and quality of the layout have been found satisfactory.", isbn="978-3-540-24595-7" }

@article{dogrusoz2002graph, title={Graph visualization toolkits}, author={Dogrusoz, Ugur and Feng, Qingwen and Madden, Brendan and Doorley, Michael and Frick, Arne}, journal={IEEE Computer Graphics and Applications}, volume={22}, number={1}, pages={30--37}, year={2002}, publisher={IEEE Computer Society} }

@article{10.1093/bioinformatics/18.7.996, author = {Demir, E. and Babur, O. and Dogrusoz, U. and Gursoy, A. and Nisanci, G. and Cetin-Atalay, R. and Ozturk, M.}, title = {Patika: an integrated visual environment for collaborative construction and analysis of cellular pathways}, journal = {Bioinformatics}, volume = {18}, number = {7}, pages = {996-1003}, year = {2002}, month = {07}, issn = {1367-4803}, doi = {10.1093/bioinformatics/18.7.996}, url = {https://doi.org/10.1093/bioinformatics/18.7.996}, eprint = {https://academic.oup.com/bioinformatics/article-pdf/18/7/996/48859820/bioinformatics_18_7_996.pdf}, }

@article{GencDogrusoz2006, title = {A multi-graph approach to complexity management in interactive graph visualization}, author = {Burkay Genc and Ugur Dogrusoz}, journal = {Computers \& Graphics}, volume = {30}, number = {1}, pages = {86--97}, year = {2006}, issn = {0097-8493}, doi = {10.1016/j.cag.2005.10.003}, publisher = {Elsevier} }

@inproceedings{freivalds2002disconnected, title={Disconnected graph layout and the polyomino packing approach}, author={Freivalds, K{\=a}rlis and Do{\u{g}}rus{\"o}z, U{\u{g}}ur and Kikusts, Paulis}, booktitle={Graph Drawing: 9th International Symposium, GD 2001 Vienna, Austria, September 23--26, 2001 Revised Papers}, pages={378--391}, year={2002}, publisher={Springer Berlin Heidelberg}, doi={10.1007/3-540-45848-4_30} }

@article{dogrusoz2002twodimensional, author = {Dogrusoz, Ugur}, title = {Two-dimensional packing algorithms for layout of disconnected graphs}, journal = {Information Sciences}, volume = {143}, number = {1-4}, pages = {147--158}, year = {2002}, publisher = {Elsevier}, doi = {10.1016/S0020-0255(02)00183-4}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0020025502001834} }

@article{dogrusoz1998edge, title={Edge labeling in the graph layout toolkit}, author={Dogrusoz, U and Kakoulis, KG and others}, journal={ACM Digital Library}, year={1998} }

@inproceedings{dorusz1996circular, title={Circular Layout in the Graph Layout Toolkit}, author={Doru{\c{s}}uz, U{\u{g}}ur and Madden, Brendan and Madden, Patrick}, booktitle={Symposium on Graph Drawing}, pages={92--100}, year={1996}, organization={Springer} }