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CellNOpt CellNOpt publications

Articles describing CellNOpt and list of publications where CellNOpt was used

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The following articles describe the methodology behind CellNOpt

- Main reference describing CellNOpt, which can be used to cite it:

C. Terfve, T. Cokelaer, A. MacNamara, D. Henriques, E. Goncalves, M. K. Morris, M. van Iersel, D. A. Lauffenburger, J. Saez-Rodriguez. CellNOptR: a flexible toolkit to train protein signaling net- works to data using multiple logic formalisms.
BMC Systems Biol, 2012, 6:133 . PDF.

- An overview of the different model formalisms available in CellNOpt:

A. MacNamara, C. Terfve, D. Henriques, B. Peñalver Bernabé, J. Saez-Rodriguez. State-time spectrum of signal transduction logic models.
Physical Biology, 9 045003, 2012. Reprint.

- For the core workflow implemented for Boolean modeling:

J. Saez-Rodriguez*, L. G. Alexopoulos*, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology, 5:331, 2009. [* these authors contributed equally to this work].

- For the constrained Fuzzy Logic implementation:

M. K. Morris, J. Saez-Rodriguez, D. Clarke, P. K. Sorger, D. A. Lauffenburger. Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. PLoS Comp. Biol., 7(3): e1001099, 2011.

- For the CNORFeeder package

F. Eduati, J. De Las Rivas, B. Di Camillo, G. Toffolo, J. Saez-Rodriguez. Integrating literature-constrained and data-driven inference of signalling networks Bioinformatics, 2012 , 28 (18)

- For the MATLAB toolbox:

M. K. Morris, I. Melas, J. Saez-Rodriguez. Construction of cell type-specific logic models of signaling networks using CellNetOptimizer. to appear in Methods in Molecular Biology:Computational Toxicology, Ed. B. Reisfeld and A. Mayeno, Humana Press. Preprint