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Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients
Jonas Béal, Arnau Montagud, Pauline Traynard, Emmanuel Barillot, Laurence Calzone
Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling
Several omics were gathered from a collection of medulloblastoma samples and we applied different pathway analyses to characterise different subgorups, notably the usually amalgamated group 3 and 4.
Antoine Forget, Loredana Martignetti, Stéphanie Puget, Laurence Calzone, Sebastian Brabetz, Daniel Picard, Arnau Montagud, Stéphane Liva, Alexandre Sta, Florent Dingli, Guillaume Arras, Jaime Rivera, Damarys Loew, Aurore Besnard, Joëlle Lacombe, Mélanie Pagès, Pascale Varlet, Christelle Dufour, Hua Yu, Audrey L. Mercier, Emilie Indersie, Anaïs Chivet, Sophie Leboucher, Laura Sieber, Kevin Beccaria, Michael Gombert, Frauke D. Meyer, Nan Qin, Jasmin Bartl, Lukas Chavez, Konstantin Okonechnikov, Tanvi Sharma, Venu Thatikonda, Franck Bourdeaut, Celio Pouponnot, Vijay Ramaswamy, Andrey Korshunov, Arndt Borkhardt, Guido Reifenberger, Patrick Poullet, Michael D. Taylor, Marcel Kool, Stefan M. Pfister, Daisuke Kawauchi, Emmanuel Barillot, Marc Remke, Olivier Ayrault
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases
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
Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites
Filipe Pinto, Catarina C Pacheco, Paulo Oliveira, Arnau Montagud, Andrew Landels, Narciso Couto, Phillip C Wright, Javier F Urchueguía, Paula Tamagnini
Synechocystis sp. PCC6803 metabolic models for the enhanced production of biofuels
Arnau Montagud, Daniel Gamermann, Pedro Fernández de Córdoba, Javier F Urchueguía
Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942
Julián Triana, Arnau Montagud, Maria Siurana, David Fuente, Arantxa Urchueguía, Daniel Gamermann, Javier Torres, Jose Tena, Pedro Fernández de Córdoba, Javier F Urchueguía
Herramienta para la optimización de flujos metabólicos en un sistema biológico
RA Jaime-Infante, Z Hernández-Martínez, J Triana-Dopico, O Fosado-Tellez, Arnau Montagud, Daniel Gamermann, Pedro Fernández de Córdoba, Javier F Urchueguía
New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks
Daniel Gamermann, Arnau Montagud, Jose Alberto Conejero, Javier F. Urchueguía, Pedro Fernández de Córdoba
PyNetMet: Python tools for efficient work with networks and metabolic models
Daniel Gamermann, Arnau Montagud, RA Jaime-Infante, Julián Triana, Javier F Urchueguía, Pedro Fernández de Córdoba
A Modular Synthetic Device To Calibrate Promoters
Daniel Gamermann, Arnau Montagud, Pablo Aparicio, Emilio Navarro, Julián Triana, Francisco R Villatoro, Javier F Urchueguía, Pedro Fernández de Córdoba