Publications

CellNOpt Publications

Articles describing CellNOpt and list of publications where CellNOpt was used.

Please contact us at cellnopt-developers@googlegroups.com if you have used CellNOpt in a paper. Thanks!

References

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

• E Gjerga, P Trairatphisan, A Gabor, H Koch, C Chevalier, F Ceccarelli, A Dugourd, A Mitsos, J Saez-Rodriguez, Converting networks to predictive logic models from perturbation signalling data with CellNOpt. Bioinformatics, Volume 36, Issue 16, 15 August 2020, Pages 4523–4524,PDF, (open access version on BioRXiv)

• C Terfve, T Cokelaer, A MacNamara, D Henriques, E Goncalves, MK Morris, M van Iersel, DA Lauffenburger, J Saez-Rodriguez. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Systems Biology, 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

Publications where CellNOpt was used

• M. Tognetti, A. Gabor, M. Yang, V. Cappelletti, J. Windhager, O. M. Rueda, K. Charmpi, E. Esmaeilishirazifard, A. Bruna, N. de Souza, C. Caldas, A. Beyer, P. Picotti, J. Saez-Rodriguez, B. Bodenmiller, Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Systems, 12(5), 2021, DOI:10.1016/j.cels.2021.04.002.

• F. Eduati, V. Doldan-Martelli, B. Klinger, T. Cokelaer, A. Sieber, F. Kogera, M. Dorel, M. J. Garnett, N. Bluthgen, J. Saez-Rodriguez. Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type–Specific Dynamic Logic Models Cancer Research, DOI: 10.1158/0008-5472.CAN-17-0078 Published June 2017

• P. Traynard, L. Tobalina, F. Eduati, L. Calzone, J. Saez-Rodriguez. Logic Modeling in Quantitative Systems Pharmacology . CPTPharmacometrics Syst. Pharmacol. (2017) 00, 00; doi:10.1002/psp4.12225

• R. Schlatter, D. Knies, M. Ederer O. Sawodny. Analysis of Boolean Models using Quality Assurance Methods from Software Engineering. Control Applications (CCA), IEEE International Conference on Analysis of Boolean Models Using Quality Assurance Methods from Software Engineering, 2010

• A.MacNamara, D.Henriques, J.Saez-Rodriguez. Modeling Signaling Networks with Different Formalisms: A Preview. In Silico Systems Biology Methods in Molecular Biology Volume 1021, 2013, pp 89-105

• J. Saez-Rodriguez, L. G. Alexopoulos, M. Zhang, M. K Morris, D. A Lauffenburger, P. K Sorger. Comparing Signaling Networks Between Normal and Transformed Hepatocytes Using Discrete Logical Models. Cancer research 71 (16), 5400, 2011

• F. Sacco, P. F. Gherardini, S. Paoluzi, Serena, J. Saez-Rodriguez, M. Helmer-Citterich, A. Ragnini-Wilson, L. Castagnoli, G. Cesareni. Mapping the human phosphatome on growth pathways. Molecular Systems Biology, 8,1,2012

• 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

• I. N. Melas, A. Mitsos, D. E. Messinis, T. S. Weiss, J. Saez-Rodriguez, L. G Alexopoulos. Construction of Large Signaling Pathways Using an Adaptive Perturbation Approach With Phosphoproteomic Data. Molecular BioSystems 8 (5), 1571-1584, 2012

• Carito Guziolowski, Santiago Videla, Federica Eduati Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics (2013) 29 (18) 2320-2326

• S. Vaga, M. Bernardo-Faura, T. Cokelaer, A. Maiolica, C.A. Barnes, L.C. Gillet1, B. Hegemann, F. van Drogen, H. Sharifian, E. Klipp, M. Peter, J Saez-Rodriguez, R Aebersold. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Mol Syst Biol 10:76, 2014