Boolean modelling
Last updated on
Wed, 12 Jan 2022
Arnau Montagud
Researcher on Computational Systems Biology
My research interests include Boolean and multiscale modelling, data analyses and data integration.
Related
- PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
- Lessons learned from a performance analysis and optimization of a multiscale cellular simulation
- Multiscale model of the different modes of cancer cell invasion
- Parallel Model Exploration for Tumor Treatment Simulations
- Optimizing dosage-specific treatments in a multi-scale model of a tumor growth
Publications
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
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
Nikos Giatrakos,
David Arnu,
Theodoros Bitsakis,
Antonios Deligiannakis,
Minos Garofalakis,
Ralf Klinkenberg,
Aris Konidaris,
Antonis Kontaxakis,
Yannis Kotidis,
Vasilis Samoladas
Jonas Béal,
Arnau Montagud,
Pauline Traynard,
Emmanuel Barillot,
Laurence Calzone
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
Jonas Béal,
Arnau Montagud,
Pauline Traynard,
Emmanuel Barillot,
Laurence Calzone
This work is the result of an ongoing effort from SysBio group at Curie to organize a set of tools developed by us and others that have aligned phylosophies: Boolean modelling of biological systems, stochastic simulations using Gillespie algorithm and high-throughput study of the model possibilities. The paper is the tip of the iceberg of these efforts, as we also provided all the tools, scripts and a complete tutorial on several models on the GitHub repository and a Docker container to facilitate the use of these tools.
Arnau Montagud,
Pauline Traynard,
Loredana Martignetti,
Eric Bonnet,
Emmanuel Barillot,
Andrei Zinovyev,
Laurence Calzone