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Publications of "Julio Saez-Rodriguez" ( http://dblp.L3S.de/Authors/Julio_Saez-Rodriguez )

URL (Homepage):  https://orcid.org/0000-0002-8552-8976  Author page on DBLP  Author page in RDF  Community of Julio Saez-Rodriguez in ASPL-2

Publication years (Num. hits)
2001-2012 (20) 2013-2014 (16) 2015-2019 (17)
Publication types (Num. hits)
article(49) inproceedings(3) proceedings(1)
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Found 54 publication records. Showing 53 according to the selection in the facets
Hits ? Authors Title Venue Year Link Author keywords
1Patricia González, Pablo Argüeso-Alejandro, David R. Penas, Xoán C. Pardo, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. Search on Bibsonomy The Journal of Supercomputing The full citation details ... 2019 DBLP  DOI  BibTeX  RDF
1Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbury, Pierre Jannin, Henning Müller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken, Annette Kopp-Schneider, Bennett A. Landman BIAS: Transparent reporting of biomedical image analysis challenges. Search on Bibsonomy CoRR The full citation details ... 2019 DBLP  BibTeX  RDF
1Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders. Search on Bibsonomy CoRR The full citation details ... 2019 DBLP  BibTeX  RDF
1Thomas Cokelaer, Elisabeth Chen, Francesco Iorio, Michael P. Menden, Howard Lightfoot, Julio Saez-Rodriguez, Mathew Garnett GDSCTools for mining pharmacogenomic interactions in cancer. Search on Bibsonomy Bioinformatics The full citation details ... 2018 DBLP  DOI  BibTeX  RDF
1Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks. Search on Bibsonomy CoRR The full citation details ... 2018 DBLP  BibTeX  RDF
1Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas Schuppert, Marc Brehme A systematic atlas of chaperome deregulation topologies across the human cancer landscape. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2018 DBLP  DOI  BibTeX  RDF
1Claudia Hernandez-Armenta, David Ochoa, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, Pedro Beltrão Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Search on Bibsonomy Bioinformatics The full citation details ... 2017 DBLP  DOI  BibTeX  RDF
1Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel caspo: a toolbox for automated reasoning on the response of logical signaling networks families. Search on Bibsonomy Bioinformatics The full citation details ... 2017 DBLP  DOI  BibTeX  RDF
1Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2017 DBLP  DOI  BibTeX  RDF
1David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2017 DBLP  DOI  BibTeX  RDF
1Robert Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Lustrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2016 DBLP  DOI  BibTeX  RDF
1Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez Efficient randomization of biological networks while preserving functional characterization of individual nodes. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2016 DBLP  DOI  BibTeX  RDF
1Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2015 DBLP  DOI  BibTeX  RDF
1Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Saez-Rodriguez, Torsten Schaub, Anne Siegel Learning Boolean logic models of signaling networks with ASP. Search on Bibsonomy Theor. Comput. Sci. The full citation details ... 2015 DBLP  DOI  BibTeX  RDF
1Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya Cooperative development of logical modelling standards and tools with CoLoMoTo. Search on Bibsonomy Bioinformatics The full citation details ... 2015 DBLP  DOI  BibTeX  RDF
1David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Search on Bibsonomy Bioinformatics The full citation details ... 2015 DBLP  DOI  BibTeX  RDF
1Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid 0004, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes 0001, Johannes Jaeger, Julio R. Banga BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. Search on Bibsonomy BMC Systems Biology The full citation details ... 2015 DBLP  DOI  BibTeX  RDF
1A. Ryll, J. Bucher, A. Bonin, Sophia Bongard, Emanuel J. V. Gonçalves, Julio Saez-Rodriguez, J. Niklas, Steffen Klamt A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. Search on Bibsonomy Biosystems The full citation details ... 2014 DBLP  DOI  BibTeX  RDF
1Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2014 DBLP  DOI  BibTeX  RDF
1Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Núria López-Bigas, Mathew Garnett, Giuseppe Jurman, Julio Saez-Rodriguez Fast randomization of large genomic datasets while preserving alteration counts. Search on Bibsonomy Bioinformatics The full citation details ... 2014 DBLP  DOI  BibTeX  RDF
1Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Search on Bibsonomy Bioinformatics The full citation details ... 2014 DBLP  DOI  BibTeX  RDF
1Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid 0004, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes 0001, Johannes Jaeger, Julio R. Banga BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. Search on Bibsonomy CoRR The full citation details ... 2014 DBLP  BibTeX  RDF
1Thomas Cokelaer, Julio Saez-Rodriguez Using Python to Dive into Signalling Data with CellNOpt and BioServices. Search on Bibsonomy CoRR The full citation details ... 2014 DBLP  BibTeX  RDF
1Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. Search on Bibsonomy BMC Systems Biology The full citation details ... 2014 DBLP  DOI  BibTeX  RDF
1Julio Saez-Rodriguez, Miguel P. Rocha, Florentino Fdez-Riverola, Juan F. De Paz Santana (eds.) 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2014, 4-6 June, 2014, Salamanca, Spain Search on Bibsonomy PACBB The full citation details ... 2014 DBLP  DOI  BibTeX  RDF
1Emanuel J. V. Gonçalves, Martijn P. van Iersel, Julio Saez-Rodriguez CySBGN: A Cytoscape plug-in to integrate SBGN maps. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Search on Bibsonomy Bioinformatics The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach, Julio Saez-Rodriguez BioServices: a common Python package to access biological Web Services programmatically. Search on Bibsonomy Bioinformatics The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Clare Pacini, Francesco Iorio, Emanuel J. V. Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Search on Bibsonomy Bioinformatics The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. Search on Bibsonomy CoRR The full citation details ... 2013 DBLP  BibTeX  RDF
1Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller 0001, Pedro Mendes 0001, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère Path2Models: large-scale generation of computational models from biochemical pathway maps. Search on Bibsonomy BMC Systems Biology The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Francesco Iorio, Julio Saez-Rodriguez, Diego di Bernardo Network based elucidation of drug response: from modulators to targets. Search on Bibsonomy BMC Systems Biology The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. Search on Bibsonomy BMC Systems Biology The full citation details ... 2013 DBLP  DOI  BibTeX  RDF
1Federica Eduati, Javier De Las Rivas, Barbara Di Camillo, Gianna Toffolo, Julio Saez-Rodriguez Integrating literature-constrained and data-driven inference of signalling networks. Search on Bibsonomy Bioinformatics The full citation details ... 2012 DBLP  DOI  BibTeX  RDF
1Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming Search on Bibsonomy CoRR The full citation details ... 2012 DBLP  BibTeX  RDF
1Michael P. Menden, Francesco Iorio, Mathew Garnett, Ultan McDermott, Cyril Benes, Pedro J. Ballester, Julio Saez-Rodriguez Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties Search on Bibsonomy CoRR The full citation details ... 2012 DBLP  BibTeX  RDF
1Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel J. V. Gonçalves, Melody K. Morris, Martijn P. van Iersel, Douglas A. Lauffenburger, Julio Saez-Rodriguez CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. Search on Bibsonomy BMC Systems Biology The full citation details ... 2012 DBLP  DOI  BibTeX  RDF
1Daniel C. Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M. Burke, Douglas A. Lauffenburger, Peter K. Sorger Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. Search on Bibsonomy BMC Systems Biology The full citation details ... 2012 DBLP  DOI  BibTeX  RDF
1Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. Search on Bibsonomy CMSB The full citation details ... 2012 DBLP  DOI  BibTeX  RDF
1Melody K. Morris, Julio Saez-Rodriguez, David C. Clarke, Peter K. Sorger, Douglas A. Lauffenburger Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2011 DBLP  DOI  BibTeX  RDF
1Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy Muhlich, Peter K. Sorger, Douglas A. Lauffenburger Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2009 DBLP  DOI  BibTeX  RDF
1Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2009 DBLP  DOI  BibTeX  RDF
1Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2009 DBLP  DOI  BibTeX  RDF
1Dominik M. Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A. Lauffenburger, Steffen Klamt, Fabian J. Theis Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. Search on Bibsonomy BMC Systems Biology The full citation details ... 2009 DBLP  DOI  BibTeX  RDF
1Julio Saez-Rodriguez, Arthur Goldsipe, Jeremy Muhlich, Leonidas G. Alexopoulos, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger Flexible informatics for linking experimental data to mathematical models via DataRail. Search on Bibsonomy Bioinformatics The full citation details ... 2008 DBLP  DOI  BibTeX  RDF
1Julio Saez-Rodriguez, Stefan Gayer, Martin Ginkel, Ernst Dieter Gilles Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. Search on Bibsonomy ECCB The full citation details ... 2008 DBLP  DOI  BibTeX  RDF
1Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, Utz-Uwe Haus, Robert Weismantel, Ernst Dieter Gilles, Steffen Klamt, Burkhart Schraven A Logical Model Provides Insights into T Cell Receptor Signaling. Search on Bibsonomy PLoS Computational Biology The full citation details ... 2007 DBLP  DOI  BibTeX  RDF
1Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles Structural and functional analysis of cellular networks with CellNetAnalyzer. Search on Bibsonomy BMC Systems Biology The full citation details ... 2007 DBLP  DOI  BibTeX  RDF
1Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris N. Kholodenko, Ernst Dieter Gilles A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2006 DBLP  DOI  BibTeX  RDF
1Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles, Martin Ginkel Visual setup of logical models of signaling and regulatory networks with ProMoT. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2006 DBLP  DOI  BibTeX  RDF
1Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. Lindquist, Luca Simeoni, Ernst Dieter Gilles A methodology for the structural and functional analysis of signaling and regulatory networks. Search on Bibsonomy BMC Bioinformatics The full citation details ... 2006 DBLP  DOI  BibTeX  RDF
1Julio Saez-Rodriguez, Andreas Kremling, Ernst Dieter Gilles Dissecting the puzzle of life: modularization of signal transduction networks. Search on Bibsonomy Computers & Chemical Engineering The full citation details ... 2005 DBLP  DOI  BibTeX  RDF
1Knut Behrendt, Andreas Politzer, Julio Saez-Rodriguez, Matthias Reuss, Klaus Mauch Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems. Search on Bibsonomy German Conference on Bioinformatics The full citation details ... 2001 DBLP  BibTeX  RDF
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