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How to cite:

The rxncon language: Romers JC and Krantz M (2017)
rxncon 2.0: a language for executable molecular systems biology , bioRxiv, doi:10.1101/107136

Parameter-free simulation of rxncon networks: Thieme S*, Romers JC*, Münzner U and Krantz M (2017)
Bipartite Boolean modelling-a method for mechanistic simulation and validation of large-scale signal transduction networks, bioRxiv, doi: 10.1101/107235

The rxncon workbench and graph formats: Wajnberg M, Thieme S, Romers J and Krantz M
The rxncon workbench. In preparation.

Further rxncon 2.0 publications

Mütnzner U, Klipp E and Krantz M
A comprehensive, mechanistically detailed, and executable model of the Cell Division Cycle. In preparation.

Romers J, Thieme S, Münzner, U and Krantz, M
Using rxncon to develop rule based models, to appear in Modeling Biomolecular Site Dynamics (Springer Methods in Molecular Biology).

Münzner U, Lubitz T, Klipp E and Krantz M (2017)
Toward Genome-Scale Models of Signal Transduction Networks, in Systems Biology (eds J. Nielsen and S. Hohmann) DOI: 10.1002/9783527696130.ch8

rxncon 1.0 publications

Tiger CF, Krause F, Cedersund G, Palmér R, Klipp E, Hohmann S, Kitano H & Krantz M (2012)
A framework for mapping, visualisation and automatic model creation of signal transduction networks. Mol Syst Biol, 2012. 8: 578. DOI: 10.1038/msb.2012.12

Lubitz T, Welkenhuysen N, Shashkova S, Bendrioua L, Hohmann S, Klipp E, Krantz M (2015)
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review, npj Systems Biology and Applications 1. doi:10.1038/npjsba.2015.7

Max Flöttmann, Falko Krause, Edda Klipp and Marcus Krantz (2013)
Reaction-contingency based bipartite Boolean modelling. BMC Syst Biol. 7, 58. DOI: 10.1186/1752-0509-7-58

Mori T, Flöttmann M, Krantz M, Akutsu T, Klipp E (2015)
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks, BMC systems biology 9 (1), 1. DOI: 10.1186/s12918-015-0193-8

Magdalena Rother, Ulrike Münzner, Sebastian Thieme and Marcus Krantz (2013)
Information content and scalability in signal transduction network reconstruction formats. Molecular BioSystems 9 (8), 1993-2004. DOI: 10.1039/C3MB00005B

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