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Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.

PLoS Comput Biol. 2011 Mar;7(3):e1001099. doi: 10.1371/journal.pcbi.1001099. Epub 2011 Mar 3.


Construction of cell type-specific logic models of signaling networks using CellNOpt.

Morris MK, Melas I, Saez-Rodriguez J.

Methods Mol Biol. 2013;930:179-214. doi: 10.1007/978-1-62703-059-5_8.


CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.

Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J.

BMC Syst Biol. 2012 Oct 18;6:133. doi: 10.1186/1752-0509-6-133.


Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions.

Morris MK, Shriver Z, Sasisekharan R, Lauffenburger DA.

Biotechnol J. 2012 Mar;7(3):374-86. doi: 10.1002/biot.201100222. Epub 2012 Jan 10.


Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.

BMC Syst Biol. 2012 May 1;6:29. doi: 10.1186/1752-0509-6-29.


State-time spectrum of signal transduction logic models.

MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.

Phys Biol. 2012 Aug;9(4):045003. doi: 10.1088/1478-3975/9/4/045003. Epub 2012 Aug 7. Review.


Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG.

PLoS One. 2012;7(11):e50085. doi: 10.1371/journal.pone.0050085. Epub 2012 Nov 30.


Multi-pathway network analysis of mammalian epithelial cell responses in inflammatory environments.

Clarke DC, Lauffenburger DA.

Biochem Soc Trans. 2012 Feb;40(1):133-8. doi: 10.1042/BST20110633. Review.


A dynamic analysis of IRS-PKR signaling in liver cells: a discrete modeling approach.

Wu M, Yang X, Chan C.

PLoS One. 2009 Dec 1;4(12):e8040. doi: 10.1371/journal.pone.0008040.


Logic-based models for the analysis of cell signaling networks.

Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA.

Biochemistry. 2010 Apr 20;49(15):3216-24. doi: 10.1021/bi902202q. Review.


Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling.

Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA.

PLoS Comput Biol. 2009 Apr;5(4):e1000340. doi: 10.1371/journal.pcbi.1000340. Epub 2009 Apr 3.


Fuzzy ARTMAP prediction of biological activities for potential HIV-1 protease inhibitors using a small molecular data set.

Andonie R, Fabry-Asztalos L, Abdul-Wahid CB, Abdul-Wahid S, Barker GI, Magill LC.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):80-93. doi: 10.1109/TCBB.2009.50.


The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data.

Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S.

PLoS Comput Biol. 2009 Aug;5(8):e1000438. doi: 10.1371/journal.pcbi.1000438. Epub 2009 Aug 7.


Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction.

Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK.

Mol Syst Biol. 2009;5:331. doi: 10.1038/msb.2009.87. Epub 2009 Dec 1.


Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation.

Peng SC, Wong DS, Tung KC, Chen YY, Chao CC, Peng CH, Chuang YJ, Tang CY.

BMC Bioinformatics. 2010 Jun 8;11:308. doi: 10.1186/1471-2105-11-308.


Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles.

Jack J, Wambaugh JF, Shah I.

BMC Syst Biol. 2011 Jul 11;5:109. doi: 10.1186/1752-0509-5-109.


A Boolean approach to linear prediction for signaling network modeling.

Eduati F, Corradin A, Di Camillo B, Toffolo G.

PLoS One. 2010 Sep 16;5(9). pii: e12789. doi: 10.1371/journal.pone.0012789.


Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network.

Qin T, Tsoi LC, Sims KJ, Lu X, Zheng WJ.

BMC Syst Biol. 2012;6 Suppl 3:S3. doi: 10.1186/1752-0509-6-S3-S3. Epub 2012 Dec 17.

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