Personalized signaling models for personalized treatments by Julio Saez‐Rodriguez, Nils Blüthgen

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Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] by Emanuel Gonçalves, Julio Saez-Rodriguez

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Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v2; ref status: indexed, http://f1000r.es/3hl] by Emanuel Gonçalves, Franz Mirlach, Julio Saez-Rodriguez

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Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury by Terezinha Souza, Panuwat Trairatphisan, Janet Piñero, Laura I. Furlong, Julio Saez-Rodriguez, Julio Saez-Rodriguez, Jos Kleinjans, Danyel Jennen

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Looking beyond the cancer cell for effective drug combinations by Jonathan R. Dry, Mi Yang, Julio Saez-Rodriguez

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Enablers and challenges of spatial omics, a melting pot of technologies by Theodore Alexandrov, Julio Saez‐Rodriguez, Sinem K Saka

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Molecular causality in the advent of foundation models by Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, Julio Saez-Rodriguez

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In silico Prioritization of Transporter–Drug Relationships From Drug Sensitivity Screens by Adrián César-Razquin, Enrico Girardi, Mi Yang, Mi Yang, Marc Brehme, Marc Brehme, Julio Saez-Rodriguez, Julio Saez-Rodriguez, Giulio Superti-Furga, Giulio Superti-Furga

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Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis by Damien Arnol, Denis Schapiro, Bernd Bodenmiller, Julio Saez-Rodriguez, Oliver Stegle

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Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks by Martin Garrido‐Rodriguez, Katharina Zirngibl, Olga Ivanova, Sebastian Lobentanzer, Julio Saez‐Rodriguez

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A systematic atlas of chaperome deregulation topologies across the human cancer landscape. by Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas A Schuppert, Marc Brehme

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Explainable multiview framework for dissecting spatial relationships from highly multiplexed data by Jovan Tanevski, Ricardo Omar Ramirez Flores, Attila Gabor, Denis Schapiro, Julio Saez-Rodriguez

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Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. by David Henriques, Alejandro F Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R Banga

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Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. by Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski

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The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. by Regina Samaga, Julio Saez-Rodriguez, Leonidas G Alexopoulos, Peter K Sorger, Steffen Klamt

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DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics by Arezou Rahimi, Luis A. Vale-Silva, Maria Fälth Savitski, Jovan Tanevski, Julio Saez-Rodriguez

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Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease by Ricardo Omar Ramirez Flores, Jan David Lanzer, Daniel Dimitrov, Britta Velten, Julio Saez-Rodriguez

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Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. by Melody K Morris, Julio Saez-Rodriguez, David C Clarke, Peter K Sorger, Douglas A Lauffenburger

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Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. by Bree B Aldridge, Julio Saez-Rodriguez, Jeremy L Muhlich, Peter K Sorger, Douglas A Lauffenburger

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Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival by Abel Sousa, Aurelien Dugourd, Danish Memon, Borgthor Petursson, Evangelia Petsalaki, Julio Saez‐Rodriguez, Pedro Beltrao

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