Publications

Found 31 results
Filters: Author is J. SAEZ-RODRIGUEZ  [Clear All Filters]
2013
COKELAER T., Pultz D., Harder L.M, Serra-Musach J., SAEZ-RODRIGUEZ J. "BioServices: a Common Python Package to Access Biological Web Services Programmatically." Bioinformatics (Oxford, England). 2013;Article in press.
GONCALVES E., Bucher J., Ryll A., et al. "Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models." Molecular bioSystems. 2013;Article in press.
Morris M.K, MELAS I., SAEZ-RODRIGUEZ J. "Construction of cell type-specific logic models of signaling networks using CellNOpt." Methods in molecular biology (Clifton, N.J.). 2013;930:179-214.
Aghaeepour N., Finak G., Consortium FCAP, et al. "Critical assessment of automated flow cytometry data analysis techniques." Nature methods. 2013;10:228-238.
GONCALVES E., IERSEL MV, SAEZ-RODRIGUEZ J. "CySBGN: A Cytoscape plug-in to integrate SBGN maps." BMC bioinformatics. 2013;14:17-2105-14-17.
PACINI C., IORIO F., GONCALVES E., et al. "DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data." Bioinformatics (Oxford, England). 2013;29:132-134.
Weirauch MT, Cote A., Norel R., et al. "Evaluation of methods for modeling transcription factor sequence specificity." Nature biotechnology. 2013;31:126-134.
Guziolowski C., Videla S., EDUATI F, et al. "Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming." Bioinformatics (Oxford, England). 2013;29:2320-2326.
GONCALVES E., SAEZ-RODRIGUEZ J. "An interface from Cytoscape to R that provides a user interface to R packages." F1000 Research. 2013;2:192.
MENDEN M.P, IORIO F., Garnett M., et al. "Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties." PloS one. 2013;8:e61318.
MACNAMARA A., HENRIQUES D., SAEZ-RODRIGUEZ J. "Modeling signaling networks with different formalisms: a preview." Methods in molecular biology (Clifton, N.J.). 2013;1021:89-105.
BUCHEL F, RODRIGUEZ N., Swainston N., et al. "Path2Models: large-scale generation of computational models from biochemical pathway maps." BMC systems biology. 2013;7:116.
Casado P., Alcolea M.P, IORIO F., et al. "Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors." Genome biology. 2013;14:R37.
Chaouiya C., Berenguier D., KEATING S.M, et al. "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools." BMC systems biology. 2013;7:135-0509-7-135.
IORIO F., Rittman T., Ge H., MENDEN M, SAEZ-RODRIGUEZ J. "Transcriptional data: a new gateway to drug repositioning?" Drug discovery today. 2013;18:350-357.
2012
Serra-Musach J., Aguilar H., IORIO F., et al. "Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network." Integrative biology : quantitative biosciences from nano to macro. 2012;4:1038-1048.
TERFVE C., COKELAER T., HENRIQUES D., et al. "CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms." BMC systems biology. 2012;6:133-0509-6-133.
Melas I.N, Mitsos A., Messinis D.E, Weiss T.S, SAEZ-RODRIGUEZ J, Alexopoulos L.G. "Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data." Molecular bioSystems. 2012;8:1571-1584.
Kirouac D.C, SAEZ-RODRIGUEZ J, Swantek J., Burke J.M, Lauffenburger D.A, Sorger P.K. "Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks." BMC systems biology. 2012;6:29.
EDUATI F, Rivas D LJ, Camillo DB, Toffolo G, SAEZ-RODRIGUEZ J. "Integrating literature-constrained and data-driven inference of signalling networks." Bioinformatics (Oxford, England). 2012;28:2311-2317.
Sacco F., Gherardini P.F, Paoluzi S., et al. "Mapping the human phosphatome on growth pathways." Molecular systems biology. 2012;8:603.
TERFVE C., SAEZ-RODRIGUEZ J. "Modeling Signaling Networks Using High-throughput Phospho-proteomics." Advances in Experimental Medicine and Biology. 2012;736:19-57.
Mitsos A., Melas I.N, Morris M.K, SAEZ-RODRIGUEZ J, Lauffenburger D.A, Alexopoulos L.G. "Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways." PloS one. 2012;7:e50085.
Videla S., Guziolowski C., EDUATI F, et al. "Revisiting the training of logic models of protein signaling networks with ASP.". In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7605 LNBI. CNRS, UMR 6074 IRISA, Campus de Beaulieu, 35042 Rennes Cedex, France; INRIA, Centre Rennes-Bretagne-Atlantique, Campus de Beaulieu, 35042 Rennes Cedex, France; University Heidelberg, National Center for Tumor Diseases, TIGA Center, Germany; École Central; 2012:3.

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