Multiscale networks in multiple sclerosis. - Kennedy, Keith E.; Rosbo, Nicole Kerlero de; Uccelli, Antonio; Cellerino, Maria; Ivaldi, Federico; Contini, Paola; Palma, Raffaele De; Harbo, Hanne F.; Berge, Tone; Bos, Steffan D.; Høgestøl, Einar A.; Brune-Ingebretsen, Synne; et al. (PLoS Comput. Biol., 2024)

DOT: Fast Cell Type Decomposition of Spatial Omics by Optimal Transport. - Rahimi, Arezou; Silva, Luís A. Vale; Savitski, Maria Faelth; Tanevski, Jovan; Saez-Rodriguez, Julio (CoRR, 2023)

Understanding metric-related pitfalls in image analysis validation. - Reinke, Annika; Tizabi, Minu; Baumgartner, Michael; Eisenmann, Matthias; Heckmann-Nötzel, Doreen; Kavur, A. Emre; Rädsch, Tim; Sudre, Carole H.; Ación, Laura; Antonelli, Michela; Arbel, Tal; Bakas, Spyridon; et al. (CoRR, 2023)

AI Competitions and Benchmarks: The life cycle of challenges and benchmarks. - Stolovitzky, Gustavo; Saez-Rodriguez, Julio; Bletz, Julie; Albrecht, Jacob; Andreoletti, Gaia; Costello, James C.; Boutros, Paul C. (CoRR, 2023)

FUNKI: interactive functional footprint-based analysis of omics data. - Hernansaiz-Ballesteros, Rosa D.; Holland, Christian H.; Dugourd, Aurélien; Saez-Rodriguez, Julio (Bioinform., 2022)

Parallel ant colony optimization for the training of cell signaling networks. - González, Patricia; Prado-Rodriguez, Roberto; Gábor, Attila; Saez-Rodriguez, Julio; Banga, Julio R.; Doallo, Ramón (Expert Syst. Appl., 2022)

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity. - Barsi, Szilvia; Papp, Henrietta; Valdeolivas, Alberto; Tóth, Dániel J.; Kuczmog, Anett; Madai, Mónika; Hunyady, László; Várnai, Péter; Saez-Rodriguez, Julio; Jakab, Ferenc; Szalai, Bence (PLoS Comput. Biol., 2022)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Maier-Hein, Lena; Reinke, Annika; Christodoulou, Evangelia; Glocker, Ben; Godau, Patrick; Isensee, Fabian; Kleesiek, Jens; Kozubek, Michal; Reyes, Mauricio; Riegler, Michael A.; Wiesenfarth, Manuel; Baumgartner, Michael; et al. (CoRR, 2022)

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. - Niarakis, Anna; Kuiper, Martin; Ostaszewski, Marek; Malik-Sheriff, Rahuman S.; Casals-Casas, Cristina; Thieffry, Denis; Freeman, Tom C.; Thomas, Paul D.; Touré, Vasundra; Noël, Vincent; Stoll, Gautier; Saez-Rodriguez, Julio; et al. (Briefings Bioinform., 2021)

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. - Mazein, Alexander; Rougny, Adrien; Karr, Jonathan R.; Saez-Rodriguez, Julio; Ostaszewski, Marek; Schneider, Reinhard (Briefings Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Touré, Vasundra; Vercruysse, Steven; Acencio, Marcio Luis; Lovering, Ruth C.; Orchard, Sandra E.; Bradley, Glyn; Casals-Casas, Cristina; Chaouiya, Claudine; del-Toro, Noemi; Flobak, Åsmund; Gaudet, Pascale; Hermjakob, Henning; et al. (Bioinform., 2021)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - Dräger, Andreas; Helikar, Tomás; Barberis, Matteo; Birtwistle, Marc R.; Calzone, Laurence; Chaouiya, Claudine; Hasenauer, Jan; Karr, Jonathan R.; Niarakis, Anna; Martínez, María Rodríguez; Saez-Rodriguez, Julio; Thakar, Juilee (Bioinform., 2021)

A comprehensive database for integrated analysis of omics data in autoimmune diseases. - Martorell-Marugan, Jordi; López-Domínguez, Raúl; García-Moreno, Adrián; Toro-Domínguez, Daniel; Villatoro-García, Juan Antonio; Barturen, Guillermo; Martín-Gómez, Adoración; Troulé, Kevin; Gómez-López, Gonzalo; Al-Shahrour, Fátima; González-Rumayor, Víctor; Peña-Chilet, María; et al. (BMC Bioinform., 2021)

FUNKI: Interactive functional footprint-based analysis of omics data. - Hernansaiz-Ballesteros, Rosa D.; Holland, Christian H.; Dugourd, Aurélien; Saez-Rodriguez, Julio (CoRR, 2021)

Bringing data from curated pathway resources to Cytoscape with OmniPath. - Ceccarelli, Francesco; Türei, Dénes; Gábor, Attila; Saez-Rodriguez, Julio (Bioinform., 2020)

Converting networks to predictive logic models from perturbation signalling data with CellNOpt. - Gjerga, Enio; Trairatphisan, Panuwat; Gábor, Attila; Koch, Hermann; Chevalier, Céline; Ceccarelli, Franceco; Dugourd, Aurélien; Mitsos, Alexander; Saez-Rodriguez, Julio; Wren, Jonathan D. (Bioinform., 2020)

BIAS: Transparent reporting of biomedical image analysis challenges. - Maier-Hein, Lena; Reinke, Annika; Kozubek, Michal; Martel, Anne L.; Arbel, Tal; Eisenmann, Matthias; Hanbury, Allan; Jannin, Pierre; Müller, Henning; Onogur, Sinan; Saez-Rodriguez, Julio; Ginneken, Bram van; et al. (Medical Image Anal., 2020)

Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. - González, Patricia; Argüeso-Alejandro, Pablo; Penas, David R.; Pardo, Xoán C.; Saez-Rodriguez, Julio; Banga, Julio R.; Doallo, Ramón (J. Supercomput., 2019)

Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders. - Manica, Matteo; Oskooei, Ali; Born, Jannis; Subramanian, Vigneshwari; Sáez-Rodríguez, Julio; Martínez, María Rodríguez (CoRR, 2019)

BIAS: Transparent reporting of biomedical image analysis challenges. - Maier-Hein, Lena; Reinke, Annika; Kozubek, Michal; Martel, Anne L.; Arbel, Tal; Eisenmann, Matthias; Hanbury, Allan; Jannin, Pierre; Müller, Henning; Onogur, Sinan; Saez-Rodriguez, Julio; Ginneken, Bram van; et al. (CoRR, 2019)

GDSCTools for mining pharmacogenomic interactions in cancer. - Cokelaer, Thomas; Chen, Elisabeth; Iorio, Francesco; Menden, Michael P.; Lightfoot, Howard; Saez-Rodriguez, Julio; Garnett, Mathew (Bioinform., 2018)

A systematic atlas of chaperome deregulation topologies across the human cancer landscape. - Esfahani, Ali Hadizadeh; Sverchkova, Angelina; Saez-Rodriguez, Julio; Schuppert, Andreas; Brehme, Marc (PLoS Comput. Biol., 2018)

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. - Razzaq, Misbah; Paulevé, Loïc; Siegel, Anne; Saez-Rodriguez, Julio; Bourdon, Jérémie; Guziolowski, Carito (PLoS Comput. Biol., 2018)

PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks. - Oskooei, Ali; Born, Jannis; Manica, Matteo; Subramanian, Vigneshwari; Sáez-Rodríguez, Julio; Martínez, María Rodríguez (CoRR, 2018)

caspo: a toolbox for automated reasoning on the response of logical signaling networks families. - Videla, Santiago; Saez-Rodriguez, Julio; Guziolowski, Carito; Siegel, Anne (Bioinform., 2017)

Benchmarking substrate-based kinase activity inference using phosphoproteomic data. - Hernandez-Armenta, Claudia; Ochoa, David; Gonçalves, Emanuel J. V.; Saez-Rodriguez, Julio; Beltrão, Pedro (Bioinform., 2017)

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. - Gonçalves, Emanuel J. V.; Nakic, Zrinka Raguz; Zampieri, Mattia; Wagih, Omar; Ochoa, David; Sauer, Uwe; Beltrão, Pedro; Saez-Rodriguez, Julio (PLoS Comput. Biol., 2017)

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. - Henriques, David; Villaverde, Alejandro Fernández; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R. (PLoS Comput. Biol., 2017)

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. - Patro, Rob; Norel, Raquel; Prill, Robert J.; Saez-Rodriguez, Julio; Lorenz, Peter; Steinbeck, Felix; Ziems, Bjoern; Lustrek, Mitja; Barbarini, Nicola; Tiengo, Alessandra; Bellazzi, Riccardo; Thiesen, Hans-Jürgen; et al. (BMC Bioinform., 2016)

Efficient randomization of biological networks while preserving functional characterization of individual nodes. - Iorio, Francesco; Bernardo-Faura, Marti; Gobbi, Andrea; Cokelaer, Thomas; Jurman, Giuseppe; Saez-Rodriguez, Julio (BMC Bioinform., 2016)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Naldi, Aurélien; Monteiro, Pedro T.; Müssel, Christoph; Kestler, Hans A.; Thieffry, Denis; Xenarios, Ioannis; Saez-Rodriguez, Julio; Helikar, Tomás; Chaouiya, Claudine (Bioinform., 2015)

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. - Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R. (Bioinform., 2015)

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. - Thiele, Sven; Cerone, Luca; Saez-Rodriguez, Julio; Siegel, Anne; Guziolowski, Carito; Klamt, Steffen (BMC Bioinform., 2015)

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. - Villaverde, Alejandro Fernández; Henriques, David; Smallbone, Kieran; Bongard, Sophia; Schmid, Joachim; Cicin-Sain, Damjan; Crombach, Anton; Saez-Rodriguez, Julio; Mauch, Klaus; Balsa-Canto, Eva; Mendes, Pedro; Jaeger, Johannes; et al. (BMC Syst. Biol., 2015)

Learning Boolean logic models of signaling networks with ASP. - Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Gebser, Martin; Nicolas, Jacques; Saez-Rodriguez, Julio; Schaub, Torsten; Siegel, Anne (Theor. Comput. Sci., 2015)

DREAMTools: a Python package for scoring collaborative challenges. - Cokelaer, Thomas; Bansal, Mukesh; Bare, Christopher; Bilal, Erhan; Bot, Brian M.; Neto, Elias Chaibub; Eduati, Federica; Gönen, Mehmet; Hill, Steven M.; Hoff, Bruce R.; Karr, Jonathan R.; Küffner, Robert; et al. (F1000Research, 2015)

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. - Guziolowski, Carito; Videla, Santiago; Eduati, Federica; Thiele, Sven; Cokelaer, Thomas; Siegel, Anne; Saez-Rodriguez, Julio (Bioinform., 2014)

Fast randomization of large genomic datasets while preserving alteration counts. - Gobbi, Andrea; Iorio, Francesco; Dawson, Kevin J.; Wedge, David C.; Tamborero, David; Alexandrov, Ludmil B.; López-Bigas, Núria; Garnett, Mathew; Jurman, Giuseppe; Saez-Rodriguez, Julio (Bioinform., 2014)

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. - Ryll, Anke; Bucher, Joachim; Bonin, Anne; Bongard, Sophia; Gonçalves, Emanuel J. V.; Saez-Rodriguez, Julio; Niklas, Jens; Klamt, Steffen (Biosyst., 2014)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Egea, Jose A.; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro Fernández; MacNamara, Aidan; Danciu, Diana-Patricia; Banga, Julio R.; Saez-Rodriguez, Julio (BMC Bioinform., 2014)

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. - Meyer, Pablo; Cokelaer, Thomas; Chandran, Deepak; Kim, Kyung Hyuk; Loh, Po-Ru; Tucker, George; Lipson, Mark; Berger, Bonnie; Kreutz, Clemens; Raue, Andreas; Steiert, Bernhard; Timmer, Jens; et al. (BMC Syst. Biol., 2014)

8th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2014, 4-6 June, 2014, Salamanca, Spain (Springer, 2014)

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. - Villaverde, Alejandro Fernández; Henriques, David; Smallbone, Kieran; Bongard, Sophia; Schmid, Joachim; Cicin-Sain, Damjan; Crombach, Anton; Saez-Rodriguez, Julio; Mauch, Klaus; Balsa-Canto, Eva; Mendes, Pedro; Jaeger, Johannes; et al. (CoRR, 2014)

Using Python to Dive into Signalling Data with CellNOpt and BioServices. - Cokelaer, Thomas; Saez-Rodriguez, Julio (CoRR, 2014)

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. - Pacini, Clare; Iorio, Francesco; Gonçalves, Emanuel J. V.; Iskar, Murat; Klabunde, Thomas; Bork, Peer; Saez-Rodriguez, Julio (Bioinform., 2013)

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. - Guziolowski, Carito; Videla, Santiago; Eduati, Federica; Thiele, Sven; Cokelaer, Thomas; Siegel, Anne; Saez-Rodriguez, Julio (Bioinform., 2013)

BioServices: a common Python package to access biological Web Services programmatically. - Cokelaer, Thomas; Pultz, Dennis; Harder, Lea M.; Serra-Musach, Jordi; Saez-Rodriguez, Julio (Bioinform., 2013)

CySBGN: A Cytoscape plug-in to integrate SBGN maps. - Gonçalves, Emanuel J. V.; Iersel, Martijn P. van; Saez-Rodriguez, Julio (BMC Bioinform., 2013)

Path2Models: large-scale generation of computational models from biochemical pathway maps. - Büchel, Finja; Rodriguez, Nicolas; Swainston, Neil; Wrzodek, Clemens; Czauderna, Tobias; Keller, Roland; Mittag, Florian; Schubert, Michael; Glont, Mihai; Golebiewski, Martin; Iersel, Martijn P. van; Keating, Sarah M.; et al. (BMC Syst. Biol., 2013)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M.; Naldi, Aurélien; Iersel, Martijn P. van; Rodriguez, Nicolas; Dräger, Andreas; Büchel, Finja; Cokelaer, Thomas; Kowal, Bryan M.; Wicks, Benjamin; Gonçalves, Emanuel J. V.; et al. (BMC Syst. Biol., 2013)

Network based elucidation of drug response: from modulators to targets. - Iorio, Francesco; Saez-Rodriguez, Julio; Bernardo, Diego di (BMC Syst. Biol., 2013)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Egea, Jose A.; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro Fernández; Banga, Julio R.; Saez-Rodriguez, Julio (CoRR, 2013)

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages. - Gonçalves, Emanuel J. V.; Saez-Rodriguez, Julio (F1000Research, 2013)

Integrating literature-constrained and data-driven inference of signalling networks. - Eduati, Federica; Rivas, Javier De Las; Camillo, Barbara Di; Toffolo, Gianna; Saez-Rodriguez, Julio (Bioinform., 2012)

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. - Kirouac, Daniel C.; Saez-Rodriguez, Julio; Swantek, Jennifer; Burke, John M.; Lauffenburger, Douglas A.; Sorger, Peter K. (BMC Syst. Biol., 2012)

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. - Terfve, Camille; Cokelaer, Thomas; Henriques, David; MacNamara, Aidan; Gonçalves, Emanuel J. V.; Morris, Melody K.; Iersel, Martijn P. van; Lauffenburger, Douglas A.; Saez-Rodriguez, Julio (BMC Syst. Biol., 2012)

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. - Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Grabe, Niels; Saez-Rodriguez, Julio; Siegel, Anne (2012)

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming - Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Grabe, Niels; Saez-Rodriguez, Julio; Siegel, Anne (CoRR, 2012)

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties - Menden, Michael P.; Iorio, Francesco; Garnett, Mathew; McDermott, Ultan; Benes, Cyril; Ballester, Pedro J.; Saez-Rodriguez, Julio (CoRR, 2012)

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. - Morris, Melody K.; Saez-Rodriguez, Julio; Clarke, David C.; Sorger, Peter K.; Lauffenburger, Douglas A. (PLoS Comput. Biol., 2011)

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. - Wittmann, Dominik M.; Krumsiek, Jan; Saez-Rodriguez, Julio; Lauffenburger, Douglas A.; Klamt, Steffen; Theis, Fabian J. (BMC Syst. Biol., 2009)

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. - Aldridge, Bree B.; Saez-Rodriguez, Julio; Muhlich, Jeremy; Sorger, Peter K.; Lauffenburger, Douglas A. (PLoS Comput. Biol., 2009)

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. - Samaga, Regina; Saez-Rodriguez, Julio; Alexopoulos, Leonidas G.; Sorger, Peter K.; Klamt, Steffen (PLoS Comput. Biol., 2009)

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. - Mitsos, Alexander; Melas, Ioannis N.; Siminelakis, Paraskeuas; Chairakaki, Aikaterini D.; Saez-Rodriguez, Julio; Alexopoulos, Leonidas G. (PLoS Comput. Biol., 2009)

Flexible informatics for linking experimental data to mathematical models via DataRail. - Saez-Rodriguez, Julio; Goldsipe, Arthur; Muhlich, Jeremy; Alexopoulos, Leonidas G.; Millard, Bjorn; Lauffenburger, Douglas A.; Sorger, Peter K. (Bioinform., 2008)

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. - Saez-Rodriguez, Julio; Gayer, Stefan; Ginkel, Martin; Gilles, Ernst Dieter (2008)

Structural and functional analysis of cellular networks with CellNetAnalyzer. - Klamt, Steffen; Saez-Rodriguez, Julio; Gilles, Ernst Dieter (BMC Syst. Biol., 2007)

A Logical Model Provides Insights into T Cell Receptor Signaling. - Saez-Rodriguez, Julio; Simeoni, Luca; Lindquist, Jonathan A.; Hemenway, Rebecca; Bommhardt, Ursula; Arndt, Boerge; Haus, Utz-Uwe; Weismantel, Robert; Gilles, Ernst Dieter; Klamt, Steffen; Schraven, Burkhart (PLoS Comput. Biol., 2007)

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. - Conzelmann, Holger; Saez-Rodriguez, Julio; Sauter, Thomas; Kholodenko, Boris N.; Gilles, Ernst Dieter (BMC Bioinform., 2006)

A methodology for the structural and functional analysis of signaling and regulatory networks. - Klamt, Steffen; Saez-Rodriguez, Julio; Lindquist, Jonathan A.; Simeoni, Luca; Gilles, Ernst Dieter (BMC Bioinform., 2006)

Visual setup of logical models of signaling and regulatory networks with ProMoT. - Saez-Rodriguez, Julio; Mirschel, Sebastian; Hemenway, Rebecca; Klamt, Steffen; Gilles, Ernst Dieter; Ginkel, Martin (BMC Bioinform., 2006)

Dissecting the puzzle of life: modularization of signal transduction networks. - Saez-Rodriguez, Julio; Kremling, Andreas; Gilles, Ernst Dieter (Comput. Chem. Eng., 2005)

Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems. - Behrendt, Knut; Politzer, Andreas; Saez-Rodriguez, Julio; Reuss, Matthias; Mauch, Klaus (2001)