2013

Modeling signaling networks with different formalisms: a preview
MACNAMARA, A., HENRIQUES D., and SAEZ-RODRIGUEZ J.
Methods in molecular biology (Clifton, N.J.). Volume 1021, (2013), p.89-105 doi:
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
MENDEN, M. P., IORIO F., Garnett M., Mcdermott U., Benes C. H., BALLESTER P. J., and SAEZ-RODRIGUEZ J.
PloS one. Apr 30, Volume 8, Number 4, (2013), p.e61318
Construction of cell type-specific logic models of signaling networks using CellNOpt
Morris, M. K., MELAS I., and SAEZ-RODRIGUEZ J.
Methods in molecular biology (Clifton, N.J.). Volume 930, (2013), p.179-214
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
PACINI, C., IORIO F., GONCALVES E., Iskar M., Klabunde T., Bork P., and SAEZ-RODRIGUEZ J.
Bioinformatics (Oxford, England). Nov 4, Volume 29, Number 1, (2013), p.132-134
Evaluation of methods for modeling transcription factor sequence specificity
Weirauch, M. T., Cote A., Norel R., Annala M., Zhao Y., Riley T. R., SAEZ-RODRIGUEZ J., COKELAER T., Vedenko A., Talukder S., et al.
Nature biotechnology. Jan 27, Volume 31, Number 2, (2013), p.126-134
Critical assessment of automated flow cytometry data analysis techniques
Aghaeepour, N., Finak G., Consortium FlowCAP, Dougall D., Khodabakhshi A. H., Mah P., Obermoser G., Spidlen J., Taylor I., Wuensch S. A., et al.
Nature methods. Mar, Volume 10, Number 3, (2013), p.228-238
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
GONCALVES, E., Bucher J., Ryll A., Niklas J., Mauch K., Klamt S., Rocha M., and SAEZ-RODRIGUEZ J.
Molecular bioSystems. Mar 25, Volume Article in press, (2013),
Transcriptional data: a new gateway to drug repositioning?
IORIO, F., Rittman T., Ge H., MENDEN M., and SAEZ-RODRIGUEZ J.
Drug discovery today. Aug 7, Volume 18, Number 7-8, (2013), p.350-357
CySBGN: A Cytoscape plug-in to integrate SBGN maps
GONCALVES, E., IERSEL MV, and SAEZ-RODRIGUEZ J.
BMC bioinformatics. Jan 16, Volume 14, (2013), p.17-2105-14-17

2012

State-time spectrum of signal transduction logic models
MACNAMARA, A., TERFVE C., HENRIQUES D., BERNABE B. P., and SAEZ-RODRIGUEZ J.
Physical biology. Aug, Volume 9, Number 4, (2012), p.045003
Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways
Mitsos, A., Melas I. N., Morris M. K., SAEZ-RODRIGUEZ J., Lauffenburger D. A., and Alexopoulos L. G.
PloS one. Volume 7, Number 11, (2012), p.e50085
Mapping the human phosphatome on growth pathways
Sacco, F., Gherardini P. F., Paoluzi S., SAEZ-RODRIGUEZ J., Helmer-Citterich M., Ragnini-Wilson A., Castagnoli L., and Cesareni G.
Molecular systems biology. Aug 14, Volume 8, (2012), p.603
Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network
Serra-Musach, J., Aguilar H., IORIO F., Comellas F., Berenguer A., Brunet J., SAEZ-RODRIGUEZ J., and Pujana M. A.
Integrative biology : quantitative biosciences from nano to macro. Sep, Volume 4, Number 9, (2012), p.1038-1048
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 M. K., IERSEL MV, Lauffenburger D. A., and SAEZ-RODRIGUEZ J.
BMC systems biology. Oct 18, Volume 6, (2012), p.133-0509-6-133
Modeling Signaling Networks Using High-throughput Phospho-proteomics
TERFVE, C., and SAEZ-RODRIGUEZ J.
Advances in Experimental Medicine and Biology. Volume 736, (2012), p.19-57
Integrating literature-constrained and data-driven inference of signalling networks
EDUATI, F., Rivas De Las J., Camillo Di B., Toffolo G., and SAEZ-RODRIGUEZ J.
Bioinformatics (Oxford, England). Sep 15, Volume 28, Number 18, (2012), p.2311-2317
Revisiting the training of logic models of protein signaling networks with ASP
Videla, S., Guziolowski C., EDUATI F., Thiele S., Grabe N., SAEZ-RODRIGUEZ J., and Siegel A.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Volume 7605 LNBI, (2012), p.342-361
Systematic identification of genomic markers of drug sensitivity in cancer cells
Garnett, M. J., Edelman E. J., Heidorn S. J., Greenman C. D., Dastur A., Lau King W., Greninger P., Thompson I. R., Luo X., Soares J., et al.
Nature. 03/29, Volume 483, Number 7391, (2012), p.570-575
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
Kirouac, D. C., SAEZ-RODRIGUEZ J., Swantek J., Burke J. M., Lauffenburger D. A., and Sorger P. K.
BMC systems biology. May 1, Volume 6, (2012), p.29
Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data
Melas, I. N., Mitsos A., Messinis D. E., Weiss T. S., SAEZ-RODRIGUEZ J., and Alexopoulos L. G.
Molecular bioSystems. Apr 3, Volume 8, Number 5, (2012), p.1571-1584 doi:

2011

Training signaling pathway maps to biochemical data with constrained fuzzy logic: Quantitative analysis of liver cell responses to inflammatory stimuli
Morris, M. K., SAEZ-RODRIGUEZ J., Clarke D. C., Sorger P. K., and Lauffenburger D. A.
PLoS Computational Biology. Volume 7, Number 3, (2011), p.Art. No.: e1001099
Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge
PRILL, R. J., SAEZ-RODRIGUEZ J., Alexopoulos L. G., Sorger P. K., and Stolovitzky G.
Science signaling. Sep 6, Volume 4, Number 189, (2011), p.mr7
Retroactivity as a Criterion to Define Modules in Signaling Networks
SAEZ-RODRIGUEZ, J., Conzelmann H., Ederer M., and Gilles E. D.
Design and Analysis of Biomolecular Circuits. (2011), p.139-159
Setting the standards for signal transduction research
SAEZ-RODRIGUEZ, J., Alexopoulos L. G., and Stolovitzky G.
Science signaling. Feb 15, Volume 4, Number 160, (2011), p.pe10