Logic-Based Models for the Analysis of Cell Signaling Networks

by Morris, Melody Kay, Saez-Rodriguez, Julio, Sorger, Peter K., Lauffenburger, Douglas A.
Published 2012

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

by Samaga, Regina, Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Sorger, Peter K., Klamt, Steffen
Published 2010

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

by Aldridge, Bree B., Saez-Rodriguez, Julio, Muhlich, Jeremy L., Sorger, Peter K., Lauffenburger, Douglas A.
Published 2010

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

by Morris, Melody Kay, Saez-Rodriguez, Julio, Clarke, David C., Sorger, Peter K., Lauffenburger, Douglas A.
Published 2011

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

by Cosgrove, Benjamin D., Alexopoulos, Leonidas G., Saez-Rodriguez, Julio, Griffith, Linda G., Lauffenburger, Douglas A.
Published 2010

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

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

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

by Wittmann, Dominik M., Krumsiek, Jan, Saez-Rodriguez, Julio, Lauffenburger, Douglas A., Klamt, Steffen, Theis, Fabian J.
Published 2010

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

by Kirouac, Daniel C, Saez-Rodriguez, Julio, Swantek, Jennifer, Burke, John M., Lauffenburger, Douglas A., Sorger, Peter K
Published 2012

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

by Mitsos, Alexander, Melas, Ioannis N., Morris, Melody Kay, Saez-Rodriguez, Julio, Lauffenburger, Douglas A., Alexopoulos, Leonidas G.
Published 2013

Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models

by Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Zhang, MingSheng, Morris, Melody Kay, Lauffenburger, Douglas A., Sorger, Peter K.
Published 2013

Discrete logic modelling as a means to link protein signalling networks functional analysis of mammalian signal transduction

by Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Epperlein, Jonathan, Samaga, Regina, Lauffenburger, Douglas A., Klamt, Steffen, Sorger, Peter K.
Published 2011

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

by Melas, Ioannis N., Sakellaropoulos, Theodore, Iorio, Francesco, Alexopoulos, Leonidas G., Loh, Wei-Yin, Saez-Rodriguez, Julio, Bai, Jane P. F., Lauffenburger, Douglas A
Published 2017

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

by Terfve, Camille, Cokelaer, Thomas, Henriques, David, MacNamara, Aidan, Goncalves, Emanuel, Iersel, Martijn van, Saez-Rodriguez, Julio, Morris, Melody Kay, Lauffenburger, Douglas A.
Published 2013

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

by Holland, Christian H, Tanevski, Jovan, Perales-Patón, Javier, Gleixner, Jan, Kumar, Manu Prajapati, Mereu, Elisabetta, Joughin, Brian Alan, Stegle, Oliver, Lauffenburger, Douglas A, Heyn, Holger, Szalai, Bence, Saez-Rodriguez, Julio
Published 2020

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

by Meyer, Pablo, Cokelaer, Thomas, Chandran, Deepak, Kim, Kyung H., Loh, Po-Ru, Lipson, Mark, Berger, Bonnie, Kreutz, Clemens, Raue, Andreas, Steiert, Bernhard, Timmer, Jens, Bilal, Erhan, DREAM 6&7 Parameter Estimation consortium, Sauro, Herbert M., Stolovitzky, Gustavo, Saez-Rodriguez, Julio, Tucker, George Jay
Published 2014