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Toward Community Standards and Software for Whole-Cell Modeling.
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. Waltemath D, et al. Among authors: czauderna t. IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10. IEEE Trans Biomed Eng. 2016. PMID: 27305665 Free PMC article.
Information Visualization for Biological Data.
Czauderna T, Schreiber F. Czauderna T, et al. Methods Mol Biol. 2017;1526:403-415. doi: 10.1007/978-1-4939-6613-4_21. Methods Mol Biol. 2017. PMID: 27896753
Editing, validating and translating of SBGN maps.
Czauderna T, Klukas C, Schreiber F. Czauderna T, et al. Bioinformatics. 2010 Sep 15;26(18):2340-1. doi: 10.1093/bioinformatics/btq407. Epub 2010 Jul 13. Bioinformatics. 2010. PMID: 20628075 Free PMC article.
Systems biology graphical notation markup language (SBGNML) version 0.3.
Bergmann FT, Czauderna T, Dogrusoz U, Rougny A, Dräger A, Touré V, Mazein A, Blinov ML, Luna A. Bergmann FT, et al. Among authors: czauderna t. J Integr Bioinform. 2020 Jun 22;17(2-3):20200016. doi: 10.1515/jib-2020-0016. J Integr Bioinform. 2020. PMID: 32568733 Free PMC article.
Software support for SBGN maps: SBGN-ML and LibSBGN.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. van Iersel MP, et al. Among authors: czauderna t. Bioinformatics. 2012 Aug 1;28(15):2016-21. doi: 10.1093/bioinformatics/bts270. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581176 Free PMC article.
32 results