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EBIGroupsSaez-Rodriguez GroupPublications

Saez-Rodriguez Group Publications


Saez-Rodriguez Group Publications

(including selected previous publications from Julio Saez-Rodriguez)

2012

Daniel C Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M Burke, Douglas A Lauffenburger and Peter K Sorger.
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
BMC Systems Biology 2012, 6:29.
Abstract

IN Melas, A Mitsos, DE Messinis, TS Weiss, J. Saez-Rodriguez, LG Alexopoulos.
Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.
Mol Biosyst. 2012 Apr 3;8(5):1571-84.
citation details

M.J. Garnett, E.J. Edelman, S.J. Heidorn, C.D. Greenman, A. Dastur, K. Wai Lau, P. Greninger, I.R. Thompson, X. Luo, J. Soares, Q. Liu, F. Iorio, D. Surdez, L. Chen, R.J. Milano, G.R. Bignell, A.T. Tam, H. Davies, J.A. Stevenson, S. Barthorpe, S.R. Lutz, F. Kogera, K. Lawrence, A. McLaren-Douglas, X. Mitropoulos, T. Mironenko, H. Thi, L. Richardson, W. Zhou, F. Jewitt, T. Zhang, P. O'Brien, J.L. Boisvert, S/ Price, W. Hur, W. Yang, X. Deng, A. Butler, H. Geun Choi, J. Won Chang, J. Baselga, I. Stamenkovic, J.A. Engelman, S.V. Sharma, O. Delattre, J. Saez-Rodriguez, N.S. Gray, J. Settleman, P.A. Futreal, D.A. Haber, M.R. Stratton, S. Ramaswamy, U. McDermott & C.H. Benes.
Systematic identification of genomic markers of drug sensitivity in cancer cells.
Nature 483, 570–575
citation details

C. Terfve, J. Saez-Rodriguez.
Modeling signaling networks using high-throughput phospho- proteomics.
Advances in Systems Biology, Adv Exp Med Biol. 736:19-57, 2012.
preprint


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2011

R. J. Prill*, J. Saez-Rodriguez*, L. G. Alexopoulos, P. K. Sorger, G. Stolovitzky.
Crowdsourcing network inference: the DREAM predictive signaling network challenge.
Science Signaling, 4, mr7, 2011.
citation details

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); 1-12, 2011.
citation details

J. Saez-Rodriguez*,L. G. Alexopoulos*, G. Stolovitzky. (2011)
Setting the standards in signal transduction research.
Science Signaling, 4, pe10, 2011.
citation detail

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

M. K. Morris, J. Saez-Rodriguez, D. Clarke, P. K. Sorger, D. A. Lauffenburger. (2011)
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.
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2010

L. G. Alexopoulos*, J. Saez-Rodriguez*, B. Cosgrove, D. A. Lauffenburger, P. K. Sorger. (2010)
Networks inferred from biochemical data reveal profound differences in TLR and inflammatory signaling between normal and transformed hepatocytes.
Mol. Cell. Proteomics, 9(9):1849, 2010.
citation detail

M. K. Morris, J. Saez-Rodriguez, P. K. Sorger, D. A. Lauffenburger. (2010)
Logic-based models for the analysis of cell signaling networks.
Biochemistry, 49(15):3216-24, 2010.
citation detail

R. J. Prill, D. Marbach, J. Saez-Rodriguez, P. K. Sorger, L. G. Alexopoulos, X. Xue, N. D. Clarke, G. Altan-Bonnet, G. Stolovitzky. (2010)
Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges.
PLoS One, 5(2): 9202, 2010.
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2009

J. Saez-Rodriguez*, L. G. Alexopoulos*, J. Epperlein R. Samaga, D. A. Lauffenburger, S. Klamt, P. K. Sorger. (2009)
Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction.
Molecular Systems Biology, 5:331, 2009.
citation detail

R. Samaga, J. Saez-Rodriguez, L. Alexopoulos, P. K. Sorger, S. Klamt. (2009)
The logic of EGR/ErbB signaling: theoretical properties and analysis of high-throughput data.
PLoS Comp. Biol., 5(8): e1000438, 2009.
citation detail

B. Aldridge, J. Saez-Rodriguez, J. Muhlich, P. K. Sorger, D. A. Lauffenburger. (2009)
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/Insulin-induced signaling.
PLoS Comp. Biol. 5(4): e1000340, 2009.
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2008

J. Saez-Rodriguez*, A. Goldsipe*, J. Muhlich, L. G. Alexopoulos, B. Millard, D. A. Lauffenburger, P. K. Sorger. (2008)
Flexible informatics for linking experimental data to mathematical models via DataRail.
Bioinformatics 24(6):840-7 2008.
citation detail

J. Saez-Rodriguez*, S. Gayer*, M. Ginkel, E. D. Gilles. (2008)
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.
Bioinformatics, 24: i213-i219, 2008.
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[* denotes equal contribution]





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