Publications

Ilankaikone Senthooran, Matthias Klapperstueck, Gleb Belov, Tobias Czauderna, Kevin Leo, Mark Wallace, Michael Wybrow, Maria Garcia de la Banda (2021). Human-Centred Feasibility Restoration. 27th International Conference on Principles and Practice of Constraint Programming (CP 2021).

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community (2021). COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms. Molecular Systems Biology.

Michael Aichem, Tobias Czauderna, Yan Zhu, Jinxin Zhao, Matthias Klapperstück, Karsten Klein, Jian Li, Falk Schreiber (2021). Visual Exploration of Large Metabolic Models. Bioinformatics.

Kadek Ananta Satriadi, Barrett Ens, Tobias Czauderna, Maxime Cordeil, Bernhard Jenny (2021). Quantitative Data Visualisation on Virtual Globes. Proceedings of the 2021 CHI Conference on Human Factors in Computing Systems.

Tim Dwyer, Maxime Cordeil, Tobias Czauderna, Pari Delir Haghighi, Barrett Ens, Sarah Goodwin, Bernhard Jenny, Kim Marriott, Michael Wybrow (2020). The Data Visualisation and Immersive Analytics Research Lab at Monash University. Visual Informatics.

Kadek Ananta Satriadi, Barrett Ens, Maxime Cordeil, Tobias Czauderna, Bernhard Jenny (2020). Maps Around Me: 3D Multiview Layouts in Immersive Spaces. Proceedings of the ACM on Human-Computer Interaction.

Shoko Sawada, Takayuki Itoh, Takashi Misaka, Shigeru Obayashi, Tobias Czauderna, Kingsley Stephens (2020). Streamline pair selection for comparative flow field visualization. Visual Computing for Industry, Biomedicine, and Art.

Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna (2020). Systems biology graphical notation markup language (SBGNML) version 0.3. Journal of Integrative Bioinformatics.

Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath (2020). Specifications of standards in systems and synthetic biology: status and developments in 2020. Journal of Integrative Bioinformatics.

Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He (2020). OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. IEEE Transactions on Visualization and Computer Graphics.

Kaya Okada, Mitsuo Yoshida, Takayuki Itoh, Tobias Czauderna, Kingsley Stephens (2019). VR system for spatio-temporal visualization of tweet data and support of map exploration. Multimedia Tools and Applications.

Midori Yano, Takayuki Itoh, Yuusuke Tanaka, Daisuke Matsuoka, Fumiaki Araki, Tobias Czauderna, Kingsley Stephens (2019). Viewpoint Selection for Shape Comparison of Mode Water Regions in a VR Space. Proceedings 23rd International Conference Information Visualisation (IV).

Kadek Ananta Satriadi, Barrett Ens, Maxime Cordeil, Bernhard Jenny, Tobias Czauderna, Wesley Willett (2019). Augmented Reality Map Navigation with Freehand Gestures. Proceedings IEEE Conference on Virtual Reality and 3D User Interfaces (VR).

Adrien Rougny, Vasundra Touré, Stuart 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 Sorokin, Falk Schreiber, Augustin Luna (2019). Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. Journal of Integrative Bioinformatics.

Kaya Okada, Mitsuo Yoshida, Takayuki Itoh, Tobias Czauderna, Kingsley Stephens (2018). VR System for Spatio-Temporal Visualization of Tweet Data. Proceedings 22nd International Conference Information Visualisation (IV).

Tobias Czauderna, Jason Haga, Jinman Kim, Matthias Klapperstück, Karsten Klein, Torsten Kuhlen, Steffen Oeltze-Jafra, Björn Sommer, Falk Schreiber (2018). Immersive Analytics Applications in Life and Health Sciences. Immersive Analytics.

Gleb Belov, Tobias Czauderna, Maria Garcia de la Banda, Matthias Klapperstueck, Ilankaikone Senthooran, Mitch Smith, Michael Wybrow, Mark Wallace (2018). Process Plant Layout Optimization: Equipment Allocation. Principles and Practice of Constraint Programming (CP 2018).

Matthias Klapperstueck, Tobias Czauderna, Cagatay Goncu, Jaroslaw Glowacki, Tim Dwyer, Falk Schreiber, Kim Marriott (2018). ContextuWall: Multi-site collaboration using display walls. Journal of Visual Languages & Computing.

Yan Zhu, Tobias Czauderna, Jinxin Zhao, Matthias Klapperstueck, Mohd Hafidz Mahamad Maifiah, Mei-Ling Han, Jing Lu, Björn Sommer, Tony Velkov, Trevor Lithgow, Jiangning Song, Falk Schreiber, Jian Li (2018). Genome-scale metabolic modelling of responses to polymyxins in emphPseudomonas aeruginosa. GigaScience.

Kaya Okada, Mitsuo Yoshida, Takayuki Itoh, Tobias Czauderna, Kingsley Stephens (2018). Spatio-Temporal Visualization of Tweet Data around Tokyo Disneyland Using VR. Proceedings 23rd International Conference on Intelligent User Interfaces Companion.

Shoko Sawada, Takayuki Itoh, Takashi Misaka, Shigeru Obayashi, Tobias Czauderna, Kingsley Stephens (2017). Streamline Selection for Comparative Visualization of 3D Fluid Simulation Result. Proceedings 21st International Conference Information Visualisation (IV).

Kadek Ananta Satriadi, Kingsley Stephens, Callum Atkinson, Maxime Cordeil, Tobias Czauderna (2017). Immersive Isosurface Visualisation for Engineering Datasets. 2017 International Symposium on Big Data Visual Analytics (BDVA).

Gleb Belov, Tobias Czauderna, Amel Dzaferovic, Maria Garcia de la Banda, Michael Wybrow, Mark Wallace (2017). An Optimization Model for 3D Pipe Routing with Flexibility Constraints. Principles and Practice of Constraint Programming (CP 2017).

Tobias Czauderna, Falk Schreiber (2017). Information Visualization for Biological Data. Bioinformatics – Volume II: Structure, Function, and Applications.

Björn Sommer, David G. Barnes, Sarah Boyd, Tom Chandler, Maxime Cordeil, Tobias Czauderna, Matthias Klapperstück, Karsten Klein, Toan D. Nguyen, Hieu Nim, Kingsley Stephens, Dany Vohl, Stephen Wang, Elliott Wilson, Yan Zhu, Jian Li, Jon McCormack, Kim Mariott, Falk Schreiber (2017). 3D-Stereoscopic Immersive Analytics Projects at Monash University and University of Konstanz. Electronic Imaging.

Matthias Klapperstück, Tobias Czauderna, Cagatay Goncu, Jaroslaw Glowacki, Tim Dwyer, Falk Schreiber, Kim Marriott (2016). ContextuWall: Peer Collaboration Using (Large) Displays. 2016 Big Data Visual Analytics (BDVA).

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber (2016). Toward Community Standards and Software for Whole-Cell Modeling. IEEE Transactions on Biomedical Engineering.

Björn Sommer, Andreas Hamacher, Owen Kaluza, Tobias Czauderna, Matthias Klapperstück, Niklas Biere, Marco Civico, Bruce H. Thomas, David G. Barnes, Falk Schreiber (2016). Stereoscopic Space Map Semi-immersive Configuration of 3D-stereoscopic Tours in Multi-display Environments. Electronic Imaging.

Tom Chandler, Maxime Cordeil, Tobias Czauderna, Tim Dwyer, Jaroslaw Glowacki, Cagatay Goncu, Matthias Klapperstueck, Karsten Klein, Kim Marriott, Falk Schreiber, Elliot Wilson (2015). Immersive Analytics. 2015 Big Data Visual Analytics (BDVA).

Anatoly Sorokin, Nicolas Le Novère, Augustin Luna, Tobias Czauderna, Emek Demir, Robin Haw, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Alice Villéger (2015). Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. Journal of Integrative Bioinformatics.

Huaiyu Mi, Falk Schreiber, Stuart Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly Sorokin, Alice Villéger (2015). Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. Journal of Integrative Bioinformatics.

Camilla Beate Hill, Tobias Czauderna, Matthias Klapperstück, Ute Roessner, Falk Schreiber (2015). Metabolomics, standards and metabolic modeling for synthetic biology in plants. Frontiers in Bioengineering and Biotechnology.

Tobias Czauderna (2015). Methoden und Algorithmen für die Systems Biology Graphical Notation.

Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet (2014). Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences.

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology.

Torsten Vogt, Tobias Czauderna, Falk Schreiber (2013). Translation of SBGN maps: Process Description to Activity Flow. BMC Systems Biology.

Tobias Czauderna, Michael Wybrow, Kim Marriott, Falk Schreiber (2013). Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. BMC Bioinformatics.

Falk Schreiber, Ralf Hofestädt, Matthias Lange, Uwe Scholz, Tobias Czauderna, Roland Schnee, Stephan Weise (2013). Proceedings 9th International Symposium on Integrative Bioinformatics. Informationsmanagement in der Biotechnologie e.V..

Christian Colmsee, Tobias Czauderna, Eva Grafahrend-Belau, Anja Hartmann, Matthias Lange, Martin Mascher, Stephan Weise, Uwe Scholz, Falk Schreiber (2013). OPTIMAS-DW, MetaCrop and VANTED: A case study for data integration, curation and visualisation in life sciences. INFORMATIK 2013 – Informatik angepasst an Mensch, Organisation und Umwelt.

Christian Colmsee, Martin Mascher, Tobias Czauderna, Anja Hartmann, Urte Schlüter, Nina Zellerhoff, Jessica Schmitz, Andrea Bräutigam, Thea R. Pick, Philipp Alter, Manfred Gahrtz, Sandra Witt, Alisdair R. Fernie, Frederik Börnke, Holger Fahnenstich, Marcel Bucher, Thomas Dresselhaus, Andreas P. M. Weber, Falk Schreiber, Uwe Scholz, Uwe Sonnewald (2012). OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biology.

Hendrik Rohn, Astrid Junker, Anja Hartmann, Eva Grafahrend-Belau, Hendrik Treutler, Matthias Klapperstück, Tobias Czauderna, Christian Klukas, Falk Schreiber (2012). VANTED v2: a framework for systems biology applications. BMC Systems Biology.

Astrid Junker, Anatoly Sorokin, Tobias Czauderna, Falk Schreiber, Alexander Mazein (2012). Wiring diagrams in biology: towards the standardized representation of biological information. Trends in Biotechnology.

Martijn P. van Iersel, Alice C. Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly Sorokin, Ugur Dogrusoz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber (2012). Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics.

Astrid Junker, Hendrik Rohn, Tobias Czauderna, Christian Klukas, Anja Hartmann, Falk Schreiber (2012). Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nature Protocols.

Falk Schreiber, Christian Colmsee, Tobias Czauderna, Eva Grafahrend-Belau, Anja Hartmann, Astrid Junker, Björn H. Junker, Matthias Klapperstück, Uwe Scholz, Stephan Weise (2012). MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Research.

Anja Hartmann, Tobias Czauderna, Roberto Hoffmann, Nils Stein, Falk Schreiber (2011). HTPheno: An image analysis pipeline for high-throughput plant phenotyping. BMC Bioinformatics.

Klaus Hippe, Christian Colmsee, Tobias Czauderna, Eva Grafahrend-Belau, Björn H. Junker, Christian Klukas, Uwe Scholz, Falk Schreiber, Stephan Weise (2010). Novel Developments of the MetaCrop Information System for Facilitating Systems Biological Approaches. Journal of Integrative Bioinformatics.

Tobias Czauderna, Christian Klukas, Falk Schreiber (2010). Editing, validating and translating of SBGN maps. Bioinformatics.

Ali Mohammad Banaei Moghaddam, Jörg Fuchs, Tobias Czauderna, Andreas Houben, Michael Florian Mette (2010). Intraspecific hybrids of emphArabidopsis thaliana revealed no gross alterations in endopolyploidy, DNA methylation, histone modifications and transcript levels. TAG Theoretical and Applied Genetics.

Johannes Thiel, Diana Weier, Nese Sreenivasulu, Marc Strickert, Nicola Weichert, Michael Melzer, Tobias Czauderna, Ulrich Wobus, Hans Weber, Winfriede Weschke (2008). Different Hormonal Regulation of Cellular Differentiation and Function in Nucellar Projection and Endosperm Transfer Cells: A Microdissection-Based Transcriptome Study of Young Barley Grains. Plant Physiology.

Marc Strickert, Tobias Czauderna, Silke Peterek, Andrea Matros, Hans-Peter Mock, Udo Seiffert (2006). Full-Length HPLC Signal Clustering and Biomarker Identification in Tomato Plants. Applied Artificial Intelligence – Proceedings 7th International FLINS Conference.

Tobias Czauderna, Udo Seiffert (2004). Implementation of MLP Networks Running Backpropagation on Various Parallel Computer Hardware Using MPI. Proceedings 5th International Conference on Recent Advances in Soft Computing (RASC2004).

Tobias Czauderna (2003). Implementation künstlicher neuronaler Netze auf Parallelcomputern unter Berücksichtigung spezifischer Hardwareeigenschaften.

Jan Machotka, Zorica Nedic, Tobias Czauderna, Thanh H. Vo (2002). Postgraduate students' involvement in the development of a remote laboratory for undergraduate teaching. Proceedings 6th Baltic Region Seminar on Engineering Education.