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Research Output 2006 2020

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Article
2008
78 Citations (Scopus)

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

2010
46 Citations (Scopus)

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

34 Citations (Scopus)

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

2 Citations (Scopus)

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

2011
144 Citations (Scopus)

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
2012
15 Citations (Scopus)

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

36 Citations (Scopus)

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
File
31 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
File
43 Citations (Scopus)

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
File
92 Citations (Scopus)

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
File
6 Citations (Scopus)

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

2013
5 Citations (Scopus)

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
File
78 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
3 Citations (Scopus)

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
2014
12 Citations (Scopus)

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 journalArticleOther

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 journalArticleResearchpeer-review

Open Access
File
5 Citations (Scopus)

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
10 Citations (Scopus)

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
File
2016
21 Citations (Scopus)

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 journalArticleResearchpeer-review

2018
4 Citations (Scopus)

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

8 Citations (Scopus)

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

Zhu, Y., Czauderna, T., Zhao, J., Klapperstueck, M., Mahamad Maifiah, M. H. B., Han, M-L., Lu, J., Sommer, B., Velkov, T., Lithgow, T., Song, J., Schreiber, F. & Li, J., 1 Apr 2018, In : GigaScience. 7, 4, 18 p., giy021.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2019

Systems Biology Graphical Notation: process description language Level 1 Version 2.0

Rougny, A., Touré, V., Moodie, S., Balaur, I., Czauderna, T., Borlinghaus, H., Dogrusoz, U., Mazein, A., Dräger, A., Blinov, M. L., Villéger, A., Haw, R., Demir, E., Mi, H., Sorokin, A., Schreiber, F. & Luna, A., 13 Jun 2019, In : Journal of integrative bioinformatics. 16, 2, 87 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

VR system for spatio-temporal visualization of tweet data and support of map exploration

Okada, K., Yoshida, M., Itoh, T., Czauderna, T. & Stephens, K., Dec 2019, In : Multimedia Tools and Applications. 78, 23, p. 32849-32868 20 p.

Research output: Contribution to journalArticleResearchpeer-review

2020

OntoPlot: a novel visualisation for non-hierarchical associations in large ontologies

Yang, Y., Wybrow, M., Li, Y. F., Czauderna, T. & He, Y., Jan 2020, In : IEEE Transactions on Visualization and Computer Graphics. 26, 1, p. 1140-1150 11 p., 8809833.

Research output: Contribution to journalArticleResearchpeer-review