PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

Autor: Miguel Ponce-de-Leon, Arnau Montagud, Vincent Noël, Annika Meert, Gerard Pradas, Emmanuel Barillot, Laurence Calzone, Alfonso Valencia

Publikováno v: npj Systems Biology and Applications, Vol 9, Iss 1, Pp 1-12 (2023)

Abstract In systems biology, mathematical models and simulations play a crucial role in understanding complex biological systems. Different modelling frameworks are employed depending on the nature and scales of the system under study. For instance,

Externí odkaz: https://doaj.org/article/cc0b2127b78a4b1b8228eea31db3bad1

Evaluating the policy of closing bars and restaurants in Cataluña and its effects on mobility and COVID19 incidence

Autor: Matthew Smith, Miguel Ponce-de-Leon, Alfonso Valencia

Publikováno v: Scientific Reports, Vol 12, Iss 1, Pp 1-19 (2022)

Abstract The world has gone through unprecedented changes since the global pandemic hit. During the early phase of the pandemic, the absence of known drugs or pharmaceutical treatments forced governments to introduce different policies in order to he

Externí odkaz: https://doaj.org/article/a459aa339ce34262aca9f77af4e43474

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Autor: 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 Frishman, Luis Cristóbal Monraz Gómez, 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 Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, 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 Grouès, 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 Peña‐Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Willighagen, 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

Publikováno v: Molecular Systems Biology, Vol 17, Iss 10, Pp 1-22 (2021)

Abstract We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS‐CoV‐2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe

Externí odkaz: https://doaj.org/article/07d2352966634fc58ef9a394d1092d67

Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth

Autor: Miguel Ponce-de-Leon, Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou, Alfonso Valencia

Publikováno v: Frontiers in Molecular Biosciences, Vol 9 (2022)

The emergence of cell resistance in cancer treatment is a complex phenomenon that emerges from the interplay of processes that occur at different scales. For instance, molecular mechanisms and population-level dynamics such as competition and cell–

Externí odkaz: https://doaj.org/article/ad585a2cdd25458f858a866dbad62f6a

Deriving policies from connection codes to ensure ongoing voltage stability

Autor: David Ryan, Miguel Ponce De Leon, Niall Grant, Bernard Butler, Steffen Vogel, Markus Mirz, Pádraig Lyons

Publikováno v: Energy Informatics, Vol 2, Iss S1, Pp 1-14 (2019)

Abstract The management and transmission networks is becoming increasingly complex due to the proliferation of renewables-based distributed energy resources (DER). Existing control systems for DER are based on static specifications from interdependen

Externí odkaz: https://doaj.org/article/939b4cddac5b4e04b0357fa0a286b52b