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Research Output 2006 2018

2018

ContextuWall: multi-site collaboration using display walls

Klapperstueck, M., Czauderna, T., Goncu, C., Glowacki, J., Dwyer, T., Schreiber, F. & Marriott, K., Jun 2018, In : Journal of Visual Languages and Computing. 46, p. 35-42 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Genome-scale metabolic modelling of responses to polymyxins in Pseudomonas aeruginosa

Zhu, Y., Czauderna, T., Zhao, J., Klapperstueck, M., Mahamad Maifiah, M. H., Han, M-L., Lu, J., Sommer, B., Velkov, T., Lithgow, T., Song, J., Schreiber, F. & Li, J., Apr 2018, In : GigaScience. 7, 4, 18 p., giy021.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2017

3D-stereoscopic immersive analytics projects at Monash University and University of Konstanz

Sommer, B., Barnes, D. G., Boyd, S., Chandler, T., Cordeil, M., Czauderna, T., Klapperstueck, M., Klein, K., Nguyen, T. D., Nim, H., Stephens, K., Vohl, D., Wang, S., Wilson, E., Zhu, Y., Li, J., McCormack, J., Marriott, K. & Schreiber, F., 2017, Stereoscopic Displays and Applications XXVIII (SD&A 2017): 30 January - 1 February 2017, Burlingame, California, USA, part of IS&T's International Symposium on Electronic Imaging: Science and Technology [Proceedings]. Springfield VA USA: Society for Imaging Science and Technology, p. 1-9 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperOtherpeer-review

An optimization model for 3D pipe routing with flexibility constraints

Belov, G., Czauderna, T., Dzaferovic, A., de la Banda, M. G., Wybrow, M. & Wallace, M., 2017, Principles and Practice of Constraint Programming : 23rd International Conference CP 2017, Proceedings. Beck, C. (ed.). Cham Switzerland: Springer, Vol. 10416 . p. 321-337 17 p. (1Lecture Notes in Computer Science; vol. 10416 ).

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Immersive isosurface visualisation for engineering datasets

Satriadi, K. A., Stephens, K., Atkinson, C., Cordeil, M. & Czauderna, T., 17 Nov 2017, 2017 International Symposium on Big Data Visual Analytics (BDVA). Mayer, W. & Wybrow, M. (eds.). Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, p. 1-8 8 p. 8114624

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Information visualization for biological data

Czauderna, T. & Schreiber, F., 2017, Bioinformatics: Volume II: Structure, Function, and Applications. Keith, J. M. (ed.). 2nd ed. New York, NY: Humana Press, p. 403-415 13 p. (Methods in Molecular Biology; vol. 1526).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

Streamline selection for comparative visualization of 3D fluid simulation result

Sawada, S., Itoh, T., Misaka, T., Obayashi, S., Czauderna, T. & Stephens, K., 14 Nov 2017, Proceedings - 2017 21st International Conference Information Visualisation: iV 2017. Zhang, J. J. & Counsell, J. (eds.). Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, p. 268-273 6 p. 8107981

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2016

ContextuWall: Peer collaboration using (large) displays

Klapperstuck, M., Czauderna, T., Goncu, C., Glowacki, J., Dwyer, T., Schreiber, F. & Marriott, K., 16 Dec 2016, 2016 Big Data Visual Analytics (BDVA 2016): Sydney, Australia, 22 – 25 November 2016 [Proceedings]. Klein, K. & Heinrich, J. (eds.). Piscataway, NJ: IEEE, Institute of Electrical and Electronics Engineers, 8 p. 7787047

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Stereoscopic space map – semi-immersive configuration of 3D-stereoscopic tours in multi-display environments

Sommer, B., Hamacher, A., Kaluza, O., Czauderna, T., Klapperstueck, M., Biere, N., Civico, M., Thomas, B., Barnes, D. G. & Schreiber, F., 14 Feb 2016, Stereoscopic Displays and Applications XXVII (SD&A 2016): 15–17 February 2016, San Francisco, CA, USA, part of IS&T's International Symposium on Electronic Imaging: Science and Technology [Proceedings]. Springfield, VA: Society for Imaging Science and Technology, 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearch

Open Access
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Toward community standards and software for whole-cell modeling

Waltemath, D., Karr, J. R., Bergmann, F. T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C. J., Pir, P., Alaybeyoglu, B., Aranganathan, N. K., Baghalian, K., Bittig, A. T., Burke, P. E. P., Cantarelli, M., Chew, Y. H., Costa, R. S., Cursons, J., Czauderna, T. & 37 othersGoldberg, A. P., Gomez, H. F., Hahn, J., Hameri, T., Gardiol, D. F. H., Kazakiewicz, D., Kiselev, I., Knight-Schrijver, V., Knupfer, C., Konig, M., Lee, D., Lloret-Villas, A., Mandrik, N., Medley, J. K., Moreau, B., Naderi-Meshkin, H., Palaniappan, S. K., Priego-Espinosa, D., Scharm, M., Sharma, M., Smallbone, K., Stanford, N. J., Song, J-H., Theile, T., Tokic, M., Tomar, N., Toure, V., Uhlendorf, J., Varusai, T. M., Watanabe, L. H., Wendland, F., Wolfien, M., Yurkovich, J. T., Zhu, Y., Zardilis, A., Zhukova, A. & Schreiber, F., 1 Oct 2016, In : IEEE Transactions on Biomedical Engineering. 63, 10, p. 2007-2014 8 p., 7489010.

Research output: Contribution to journalArticleResearchpeer-review

2015

Immersive analytics

Chandler, T., Cordeil, M., Czauderna, T., Dwyer, T., Glowacki, J., Goncu, C., Klapperstueck, M., Klein, K., Marriott, K., Schreiber, F. & Wilson, E., 2015, 2015 Big Data Visual Analytics (BDVA): Hobart, Australia, 22 - 25 September 2015. Engelke, U., Heinrich, J., Bednarz, T., Klein, K. & Nguyen, Q. V. (eds.). Piscataway, NJ: IEEE, Institute of Electrical and Electronics Engineers, 8 p. 7314296

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Metabolomics, standards, and metabolic modeling for synthetic biology in plants

Hill, C. B., Czauderna, T., Klapperstueck, M., Roessner, U. & Schreiber, F., 21 Oct 2015, In : Frontiers in Bioengineering and Biotechnology. 3, 12 p., 167.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Mi, H., Schreiber, F., Moodie, S., Czauderna, T., Demir, E., Haw, R., Luna, A., Le Novère, N., Sorokin, A. & Villéger, A., 2015, In : Journal of integrative bioinformatics. 12, 2, p. 340-381 42 p., 265.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Sorokin, A., Le Novère, N., Luna, A., Czauderna, T., Demir, E., Haw, R., Mi, H., Moodie, S., Schreiber, F. & Villéger, A., 2015, In : Journal of integrative bioinformatics. 12, 2, p. 281-340 59 p., 264.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2014

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Waltemath, D., Bergmann, F. T., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C., Golebiewski, M., Hucka, M., Juty, N., Krebs, O., Le Novere, N., Mi, H., Moraru, I. I., Myers, C. J., Nickerson, D., Olivier, B. G., Rodriguez, N., Schreiber, F., Smith, L., Zhang, F. & 1 othersBonnet, E., 2014, In : Standards in Genomic Sciences. 9, 3, p. 1285 - 1301 17 p.

Research output: Contribution to journalArticleOther

2013

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

Czauderna, T., Wybrow, M. J., Marriott, K. G. & Schreiber, F., 2013, In : BMC Bioinformatics. 14, p. 1 - 17 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Optimas-DW, MetaCrop and Vanted: A case study for data integration, curation and visualisation in life sciences

Colmsee, C., Horbach, M. (ed.), Czauderna, T., Grafahrend-Belau, E., Hartmann, A., Lange, M., Mascher, M., Weise, S., Scholz, U. & Schreiber, F., 2013, p. 1834 - 1840. 7 p.

Research output: Contribution to conferenceOtherOther

Path2Models: Large-scale generation of computational models from biochemical pathway maps

Buchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M., van Iersel, M. P., Keating, S., Rall, M., Wybrow, M. J., Hermjakob, H., Hucka, M., Kell, D. B., Muller, W., Mendes, P., Zell, A. & 6 othersChaouiya, C., Saez-Rodriguez, J., Schreiber, F., Laibe, C., Drager, A. & Le Novere, N., 2013, In : BMC Systems Biology. 7, p. 1 - 19 19 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

Translation of SBGN maps: Process description to activity flow

Vogt, T., Czauderna, T. & Schreiber, F., 2013, In : BMC Systems Biology. 7, p. 1 - 19 19 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
2012

Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation

Junker, A., Rohn, H., Czauderna, T., Klukas, C., Hartmann, A. & Schreiber, F., 2012, In : Nature Protocols. 7, 3, p. 579 - 593 15 p.

Research output: Contribution to journalArticleResearchpeer-review

MetaCrop 2.0: Managing and exploring information about crop plant metabolism

Schreiber, F., Colmsee, C., Czauderna, T., Grafahrend-Belau, E., Hartmann, A., Junker, A., Junker, B., Klapperstueck, M., Scholz, U. & Weise, S., 2012, In : Nucleic Acids Research. 40, p. 1173 - 1177 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Optimas-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize

Colmsee, C., Mascher, M., Czauderna, T., Hartmann, A., Schluter, U., Zellerhoff, N., Schmitz, J., Brautigam, A., Pick, T. R., Alter, P., Gahrtz, M., Witt, S., Fernie, A. R., Bornke, F. A. J., Fahnenstich, H., Bucher, M., Dresselhaus, T., Weber, A. P. M., Schreiber, F., Scholz, U. & 1 othersSonnewald, U., 2012, In : BMC Plant Biology. 12, 29, p. 1 - 10 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Software support for SBGN maps: SBGN-ML and LibSBGN

van Iersel, M. P., Villeger, A., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M. I., Mi, H., Moodie, S., Kitano, H., Le Novere, N. & Schreiber, F., 2012, In : Bioinformatics. 28, 15, p. 2016 - 2021 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Vanted v2: A framework for systems biology applications

Rohn, H., Junker, A., Hartmann, A., Grafahrend-Belau, E., Treutler, H., Klapperstueck, M., Czauderna, T., Klukas, C. & Schreiber, F., 2012, In : BMC Systems Biology. 6, p. 1 - 13 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Wiring diagrams in biology: Towards the standardized representation of biological information

Junker, A., Sorokin, A., Czauderna, T., Schreiber, F. & Mazein, A., 2012, In : Trends in Biotechnology. 30, 11, p. 555 - 557 3 p.

Research output: Contribution to journalArticleResearchpeer-review

2011

HTPheno: An image analysis pipeline for high-throughput plant phenotyping

Hartmann, A., Czauderna, T., Hoffmann, R., Stein, N. & Schreiber, F., 2011, In : BMC Bioinformatics. 12, p. 1 - 9 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2010

Editing, validating and translating of SBGN maps

Czauderna, T., Klukas, C. & Schreiber, F., 2010, In : Bioinformatics. 26, 18, p. 2340-2341 2 p.

Research output: Contribution to journalArticleResearchpeer-review

Intraspecific hybrids of Arabidopsis thaliana revealed no gross alterations in endopolyploidy, DNA methylation, histone modifications and transcript levels

Moghaddam, A. M. B., Fuchs, J., Czauderna, T., Houben, A. & Mette, M. F., Jan 2010, In : Theoretical and Applied Genetics. 120, 2, p. 215-226 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Novel developments of the MetaCrop information system for facilitating systems biological approaches

Hippe, K., Colmsee, C., Czauderna, T., Grafahrend-Belau, E., Junker, B., Klukas, C., Scholz, U., Schreiber, F. & Weise, S., 2010, In : Journal of integrative bioinformatics. 7, 3, p. 1 - 9 9 p.

Research output: Contribution to journalArticleResearchpeer-review

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

Thiel, J., Weier, D., Sreenivasulu, N., Strickert, M., Weichert, N., Melzer, M., Czauderna, T., Wobus, U., Weber, H. & Weschke, W., 1 Nov 2008, In : Plant Physiology. 148, 3, p. 1436-1452 17 p.

Research output: Contribution to journalArticleResearchpeer-review

2006

Full-length HPLC signal clustering and biomarker identification in tomato plants

Strickert, M., Czauderna, T., Peterek, S., Matros, A., Mock, H. P. & Seiffert, U., 1 Jan 2006, Applied Artificial Intelligence - Proceedings of the 7th International FLINS Conference, FLINS 2006. World Scientific Publishing, p. 549-556 8 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review