20102018
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Research Output 2010 2018

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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 journalArticle

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 journalArticle

Open Access
File
2016

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 others Goldberg, 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 journalArticle

2015

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 journalArticle

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 journalArticle

Open Access
File

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 journalArticle

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 others Bonnet, E. 2014 In : Standards in Genomic Sciences. 9, 3, p. 1285 - 1301 17 p.

Research output: Contribution to journalArticle

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 journalArticle

Open Access
File

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 others Chaouiya, 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 journalArticle

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 journalArticle

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 journalArticle

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 journalArticle

Open Access
File

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 others Sonnewald, U. 2012 In : BMC Plant Biology. 12, 29, p. 1 - 10 10 p.

Research output: Contribution to journalArticle

Open Access
File

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 journalArticle

Open Access
File

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 journalArticle

Open Access
File

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 journalArticle

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 journalArticle

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 journalArticle

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 journalArticle

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 journalArticle