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PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
In this paper, we present the re-implementation of a stochastic simulation of Boolean models using MaBoSS in an agent-based model simulator using PhysiCell. We propose this work as a suitable framework to capture macroscopic phenotypical changes from environment and genetic perturbations.
Miguel Ponce-de-Leon, Arnau Montagud, Vincent Noel, Gerard Pradas, Annika Meert, Emmanuel Barillot, Laurence Calzone, Alfonso Valencia
Multiscale model of the different modes of cancer cell invasion
Marco Ruscone, Arnau Montagud, Philippe Chavrier, Olivier Destaing, Isabelle Bonnet, Andrei Zinovyev, Emmanuel Barillot, Vincent Noel, Laurence Calzone
Parallel Model Exploration for Tumor Treatment Simulations
Charilaos Akasiadis, Miguel Ponce-de-Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
Optimizing dosage-specific treatments in a multi-scale model of a tumor growth
Miguel Ponce-de-Leon, Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou, Alfonso Valencia
Patient-specific Boolean models of signaling networks guide personalized treatments
We present a tool to uncover personalised drug treatments. First, we personalised prostate models to 488 TCGA patients and 8 cell lines. Then, we study the effect of single and combined drugs for each of these models. In one particular cell-line, we identified 15 actionable points of which 9 were tested and found a dose-dependent effect on four of them.
Arnau Montagud, Jonas Béal, Luis Tobalina, Pauline Traynard, Vigneshwari Subramanian, Bence Szalai, Robert Alfoldi, Laszlo Puskas, Alfonso Valencia, Emmanuel Barillot, Julio Saez-Rodriguez, Laurence Calzone
Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems
An overview of where is the multiscale modelling field and what it needs to have complex, giga-scale simulations
Arnau Montagud, Miguel Ponce-de-Leon, Alfonso Valencia
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristobal Monraz Gomez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce-de-Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Drager, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Bornigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gokce Yagmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. a. B. Rex, Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Groues, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Pena-Chilet, Tomas Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Auge, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community
Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development
Enrico Santus, Nicola Marino, Davide Cirillo, Emmanuele Chersoni, Arnau Montagud, Antonella Santuccione Chadha, Alfonso Valencia, Kevin Hughes, Charlotta Lindvall
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction
Daniel Gamermann, Arnau Montagud, J. Alberto Conejero, Pedro Fernández de Córdoba, Javier F. Urchueguía
PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling
In this paper, we present the implementation of a stochastic simulation of Boolean models using MaBoSS in an agent-based model simulator using PhysiCell. We propose this work as a suitable framework to capture macroscopic phenotypical changes from environment and genetic perturbations.
Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, Laurence Calzone