Julio Saez-Rodriguez

发表

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

David Henriques, Miguel Rocha, Julio Saez-Rodriguez, 2015, Bioinform..

Footprint-based functional analysis of multiomic data

Julio Saez-Rodriguez, Aurelien Dugourd, J. Sáez-Rodríguez, 2019, Current opinion in systems biology.

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

Pedro Beltrão, Julio Saez-Rodriguez, Claudia Hernandez-Armenta, 2016, bioRxiv.

Network based elucidation of drug response: from modulators to targets

Julio Saez-Rodriguez, Diego di Bernardo, Francesco Iorio, 2013, BMC Systems Biology.

Retroactivity as a Criterion to Define Modules in Signaling Networks

Julio Saez-Rodriguez, Ernst Dieter Gilles, Holger Conzelmann, 2011 .

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling

Julio Saez-Rodriguez, Peter K. Sorger, Douglas A. Lauffenburger, 2007, PLoS Comput. Biol..

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

Julio Saez-Rodriguez, Martijn P. van Iersel, Emanuel J. V. Gonçalves, 2012, BMC Systems Biology.

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models

Steffen Klamt, Julio Saez-Rodriguez, Emanuel J. V. Gonçalves, 2014, Biosyst..

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

Julio Saez-Rodriguez, Peer Bork, Emanuel J. V. Gonçalves, 2012, Bioinform..

Interactive visualization of complex and structured biological networks

Julio Saez-Rodriguez, Martin Ginkel, E. D. Gilles, 2006 .

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

Julio Saez-Rodriguez, Peter K. Sorger, Douglas A. Lauffenburger, 2011, PLoS Comput. Biol..

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast

Pedro Beltrão, Julio Saez-Rodriguez, David Ochoa, 2016, bioRxiv.

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

Eva Balsa-Canto, David Henriques, Julio Saez-Rodriguez, 2015, BMC Systems Biology.

Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology

Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo, 2019, The Journal of Supercomputing.

Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways

Julio Saez-Rodriguez, Alexander Mitsos, Douglas A. Lauffenburger, 2012, PloS one.

Adaptive visualization of complex hierarchical signaling networks

Julio Saez-Rodriguez, Martin Ginkel, E. D. Gilles, 2005 .

Fast randomization of large genomic datasets while preserving alteration counts

Julio Saez-Rodriguez, David Tamborero, Francesco Iorio, 2014, Bioinform..

Biomedical Image Analysis Challenges (BIAS) Reporting Guideline

Lena Maier-Hein, Annika Reinke, Matthias Eisenmann, 2020 .

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming pdf

Julio Saez-Rodriguez, Carito Guziolowski, Niels Grabe, 2012, ArXiv.

Modular Analysis of Signal

Julio Saez-Rodriguez, Andreas Kremling, Ernst Dieter Gilles, 2004 .

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

Julio Saez-Rodriguez, Jens Timmer, Erhan Bilal, 2014, BMC Systems Biology.

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Julio Saez-Rodriguez, Carito Guziolowski, Thomas Cokelaer, 2013, Bioinform..

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies

Steffen Klamt, Julio Saez-Rodriguez, Carito Guziolowski, 2015, BMC Bioinformatics.

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin

Julio Saez-Rodriguez, Mitja Lustrek, Robert Patro, 2016, BMC Bioinformatics.

Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data

Ke Xu, Thomas Yu, Julio Saez-Rodriguez, 2019, bioRxiv.

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology pdf

Eva Balsa-Canto, David Henriques, Julio Saez-Rodriguez, 2014, ArXiv.

Designing Experiments to Discriminate Families of Logic Models

Torsten Schaub, Julio Saez-Rodriguez, Carito Guziolowski, 2015, Front. Bioeng. Biotechnol..

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

Visual Support for the Structural Analysis of Complex Signaling Networks in ProMoT

Julio Saez-Rodriguez, Martin Ginkel, E. D. Gilles, 2008 .

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models

Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga, 2017, PLoS Comput. Biol..

Visual setup of logical models of signaling and regulatory networks with ProMoT

Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles, 2006, BMC Bioinformatics.

GDSCTools for mining pharmacogenomic interactions in cancer

Julio Saez-Rodriguez, Howard Lightfoot, Francesco Iorio, 2017, bioRxiv.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

David Henriques, Julio Saez-Rodriguez, Thomas Cokelaer, 2013, BMC Bioinformatics.

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

Steffen Klamt, Fabian J. Theis, Julio Saez-Rodriguez, 2009, BMC Systems Biology.

Dissecting the puzzle of life: modularization of signal transduction networks

Julio Saez-Rodriguez, Andreas Kremling, Ernst Dieter Gilles, 2005, Comput. Chem. Eng..

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

Steffen Klamt, Julio Saez-Rodriguez, Peter K. Sorger, 2009, PLoS Comput. Biol..

Logical Modeling and Dynamical Analysis of Cellular Networks

Denis Thieffry, Claudine Chaouiya, Julio Saez-Rodriguez, 2016, Front. Genet..

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks

Julio Saez-Rodriguez, Boris N. Kholodenko, Ernst Dieter Gilles, 2006, BMC Bioinformatics.

Robustness and applicability of functional genomics tools on scRNA-seq data

Douglas A. Lauffenburger, Julio Saez-Rodriguez, Oliver Stegle, 2019, bioRxiv.

Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems

Julio Saez-Rodriguez, Matthias Reuss, Klaus Mauch, 2001, German Conference on Bioinformatics.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Steffen Klamt, Aurélien Naldi, Denis Thieffry, 2013, BMC Systems Biology.

GDSCTools for Mining Pharmacogenomic Interactions in Cancer

Julio Saez-Rodriguez, Howard Lightfoot, Francesco Iorio, 2017 .

Visual support for structural and functional analysis of complex signaling networks in ProMoT

Julio Saez-Rodriguez, Martin Ginkel, E. D. Gilles, 2008, ICONS 2008.

A Logical Model Provides Insights into T Cell Receptor Signaling

Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles, 2007, PLoS Comput. Biol..

caspo: a toolbox for automated reasoning on the response of logical signaling networks families

Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel, 2017, Bioinform..

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

Julio Saez-Rodriguez, Panuwat Trairatphisan, Jonathan Barratt, 2019, NPJ systems biology and applications.

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

Julio Saez-Rodriguez, Alexander Mitsos, Leonidas G. Alexopoulos, 2009, PLoS Comput. Biol..

Modeling signaling networks using high-throughput phospho-proteomics.

Julio Saez-Rodriguez, Camille Terfve, J. Sáez-Rodríguez, 2012, Advances in experimental medicine and biology.

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP

Julio Saez-Rodriguez, Carito Guziolowski, Niels Grabe, 2012, CMSB.

Literature and data-driven based inference of signalling interactions using time-course data

Julio Saez-Rodriguez, Julio Saez-Rodriguez, Attila Gábor, 2019 .

Structural and functional analysis of cellular networks with CellNetAnalyzer

Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles, 2007, BMC Systems Biology.

Path2Models: large-scale generation of computational models from biochemical pathway maps

Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, 2013, BMC Systems Biology.

Flexible informatics for linking experimental data to mathematical models via DataRail

Julio Saez-Rodriguez, Peter K. Sorger, Douglas A. Lauffenburger, 2008, Bioinform..

Efficient randomization of biological networks while preserving functional characterization of individual nodes

Julio Saez-Rodriguez, Francesco Iorio, Giuseppe Jurman, 2016, BMC Bioinformatics.

Learning Boolean logic models of signaling networks with ASP

Martin Gebser, Torsten Schaub, Julio Saez-Rodriguez, 2015, Theor. Comput. Sci..

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules

Julio Saez-Rodriguez, Ernst Dieter Gilles, Martin Ginkel, 2008, ECCB.

CySBGN: A Cytoscape plug-in to integrate SBGN maps

Julio Saez-Rodriguez, Martijn P. van Iersel, Emanuel J. V. Gonçalves, 2012, BMC Bioinformatics.

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

Julio Saez-Rodriguez, Javier De Las Rivas, Gianna Toffolo, 2012, Bioinform..

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

Using Python to Dive into Signalling Data with CellNOpt and BioServices pdf

Julio Saez-Rodriguez, Thomas Cokelaer, 2014, ArXiv.

BioServices: a common Python package to access biological Web Services programmatically

Julio Saez-Rodriguez, Thomas Cokelaer, Jordi Serra-Musach, 2013, Bioinform..

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

Julio Saez-Rodriguez, Peter K. Sorger, Douglas A. Lauffenburger, 2012, BMC Systems Biology.

A methodology for the structural and functional analysis of signaling and regulatory networks

Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles, 2006, BMC Bioinformatics.

Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

Julio Saez-Rodriguez, Francesco Iorio, Pedro J. Ballester, 2012, PloS one.

A systematic atlas of chaperome deregulation topologies across the human cancer landscape

Julio Saez-Rodriguez, Andreas Schuppert, Ali Hadizadeh Esfahani, 2017, bioRxiv.

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

Julio Saez-Rodriguez, Wenyu Wang, Justin Guinney, 2021 .

FUNKI: interactive functional footprint-based analysis of omics data pdf

Rosa D. Hernansaiz-Ballesteros, Julio Saez-Rodriguez, Aurelien Dugourd, 2021, Bioinform..

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2020, Briefings Bioinform..

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Claudine Chaouiya, Julio Saez-Rodriguez, Anna Niarakis, 2021, Bioinform..

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions

Julio Saez-Rodriguez, Francesco Iorio, Viji M. Draviam, 2015, PloS one.

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

Steffen Klamt, Miguel Rocha, Julio Saez-Rodriguez, 2013, Molecular bioSystems.

Cellular Regulatory Networks

Julio Saez-Rodriguez, Douglas A. Lauffenburger, R. Krishna Murthy Karuturi, 2010 .

High Throughput Protein-based Technologies and Computational Models for Drug Development, Efficacy and Toxicity

Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Christopher W. Espelin, 2022 .

A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes

Linda G. Griffith, Julio Saez-Rodriguez, Douglas A. Lauffenburger, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics

Julio Saez-Rodriguez, Federica Eduati, Ramesh Utharala, 2016, bioRxiv.

Whither systems medicine?

Ingo Roeder, Olaf Wolkenhauer, Nils Blüthgen, 2018, Experimental & Molecular Medicine.

Signatures of cell death and proliferation in perturbation transcriptomics data—from confounding factor to effective prediction

Julio Saez-Rodriguez, Bence Szalai, J. Sáez-Rodríguez, 2018, bioRxiv.

Mapping the human phosphatome on growth pathways

Julio Saez-Rodriguez, Manuela Helmer-Citterich, Pier Federico Gherardini, 2012, Molecular systems biology.

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.

Julio Saez-Rodriguez, Theodore Sakellaropoulos, Leonidas G Alexopoulos, 2015, Integrative biology : quantitative biosciences from nano to macro.

Abstract A44: A landscape of pharmacogenomic interactions in cancer

Julio Saez-Rodriguez, Lodewyk F. A. Wessels, Francesco Iorio, 2017 .

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.

Tero Aittokallio, Julio Saez-Rodriguez, Francesco Iorio, 2016, Drug discovery today.

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Julio Saez-Rodriguez, Francesco Iorio, Kosuke Yusa, 2017 .

Perturbation-response genes reveal signaling footprints in cancer gene expression

Bertram Klinger, Nils Blüthgen, Julio Saez-Rodriguez, 2016 .