Saez-Rodriguez J - Search Results

1

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

Henriques D, Rocha M, Saez-Rodriguez J, Banga JR. Henriques D, et al. Bioinformatics. 2015 Sep 15;31(18):2999-3007. doi: 10.1093/bioinformatics/btv314. Epub 2015 May 21. Bioinformatics. 2015. PMID: 26002881 Free PMC article.

2

Flexible informatics for linking experimental data to mathematical models via DataRail.

Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK. Saez-Rodriguez J, et al. Bioinformatics. 2008 Mar 15;24(6):840-7. doi: 10.1093/bioinformatics/btn018. Epub 2008 Jan 24. Bioinformatics. 2008. PMID: 18218655 Free PMC article.

3

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

Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA. Morris MK, et al. Biochemistry. 2010 Apr 20;49(15):3216-24. doi: 10.1021/bi902202q. Biochemistry. 2010. PMID: 20225868 Free PMC article. Review.

4

Modeling signaling networks using high-throughput phospho-proteomics.

Terfve C, Saez-Rodriguez J. Terfve C, et al. Adv Exp Med Biol. 2012;736:19-57. doi: 10.1007/978-1-4419-7210-1_2. Adv Exp Med Biol. 2012. PMID: 22161321 Review.

5

Integrating literature-constrained and data-driven inference of signalling networks.

Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J. Eduati F, et al. Bioinformatics. 2012 Sep 15;28(18):2311-7. doi: 10.1093/bioinformatics/bts363. Epub 2012 Jun 25. Bioinformatics. 2012. PMID: 22734019 Free PMC article.

6

State-time spectrum of signal transduction logic models.

MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J. MacNamara A, et al. Phys Biol. 2012 Aug;9(4):045003. doi: 10.1088/1478-3975/9/4/045003. Epub 2012 Aug 7. Phys Biol. 2012. PMID: 22871648 Review.

7

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. Terfve C, et al. BMC Syst Biol. 2012 Oct 18;6:133. doi: 10.1186/1752-0509-6-133. BMC Syst Biol. 2012. PMID: 23079107 Free PMC article.

8

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J. Pacini C, et al. Bioinformatics. 2013 Jan 1;29(1):132-4. doi: 10.1093/bioinformatics/bts656. Epub 2012 Nov 4. Bioinformatics. 2013. PMID: 23129297 Free PMC article.

9

CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Gonçalves E, van Iersel M, Saez-Rodriguez J. Gonçalves E, et al. BMC Bioinformatics. 2013 Jan 16;14:17. doi: 10.1186/1471-2105-14-17. BMC Bioinformatics. 2013. PMID: 23324051 Free PMC article.

10

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J. Gonçalves E, et al. Mol Biosyst. 2013 Jul;9(7):1576-83. doi: 10.1039/c3mb25489e. Epub 2013 Mar 25. Mol Biosyst. 2013. PMID: 23525368 Review.

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