Personalized signaling models for personalized treatments

by Julio Saez‐Rodriguez, Nils Blüthgen
Published 2020-01-01

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
Published 2013-09-01

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
Published 2014-07-01

Looking beyond the cancer cell for effective drug combinations

by Jonathan R. Dry, Mi Yang, Julio Saez-Rodriguez
Published 2016-11-01

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
Published 2018-11-01

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
Published 2019-10-01

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
Published 2018-09-01

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
Published 2018-10-01

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
Published 2009-08-01

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
Published 2017-02-01

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
Published 2018-01-01

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
Published 2009-04-01

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
Published 2011-03-01

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.

by David R Penas, David Henriques, Patricia González, Ramón Doallo, Julio Saez-Rodriguez, Julio R Banga
Published 2017-01-01

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

by Alexander Mitsos, Ioannis N Melas, Paraskeuas Siminelakis, Aikaterini D Chairakaki, Julio Saez-Rodriguez, Leonidas G Alexopoulos
Published 2009-12-01

Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

by Federica Eduati, Patricia Jaaks, Jessica Wappler, Thorsten Cramer, Christoph A Merten, Mathew J Garnett, Julio Saez‐Rodriguez
Published 2020-06-01

Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

by Federica Eduati, Patricia Jaaks, Jessica Wappler, Thorsten Cramer, Christoph A Merten, Mathew J Garnett, Julio Saez‐Rodriguez
Published 2020-02-01

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

by Alexander Mitsos, Ioannis N Melas, Melody K Morris, Julio Saez-Rodriguez, Douglas A Lauffenburger, Leonidas G Alexopoulos
Published 2012-01-01

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

by Francesco Iorio, Roshan L Shrestha, Nicolas Levin, Viviane Boilot, Mathew J Garnett, Julio Saez-Rodriguez, Viji M Draviam
Published 2015-01-01

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

by Emanuel Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrao, Julio Saez-Rodriguez
Published 2017-01-01