Saran Pankaew and Vincent Noel and Loic Pauleve and Denis Thieffry and Emmanuel Barillot and Laurence Calzone, AstroLogics: A simulation-based analysis framework for monotonous Boolean model ensemble, bioRxiv, 2025.11. 17.688236, 2025
Thaleia Ntiniakou and James Osborne and Jieling Zhao and Jules Dichamp and Nicolò Cogno and Randy Heiland and Kwabena Amponsah and Jiri Pesek and Tobias Duswald and Othmane Hayoun-Mya and Jack Jennings and Matteo Pedrazzi and Ryan Bournes and Marco Ruscone and Fergus Cooper and Vincent Noël and Matthew I Leach and Alejandro Madrid-Valiente and Jose Estragués-Muñoz and Adam Smelko and Taghi Aliyev and Marco Manca and Joe Pitt-Francis and Gary Mirams and Paul Macklin and Alexander G Fletcher and Vasileios Vavourakis and Stefan Hoehme and Jose Carbonell-Caballero and Roman Bauer and Van Paul Liedekerke and Dirk Drasdo and Alfonso Valencia and Arnau Montagud, Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative, bioRxiv, 2025.07. 16.664358, 2025
Stéphanie Chevalier and Julia Becker and Yujuan Gui and Vincent Noël and Cui Su and Sascha Jung and Laurence Calzone and Andrei Zinovyev and Antonio Del Sol and Jun Pang and Lasse Sinkkonen and Thomas Sauter and Loïc Paulevé, Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming, npj Systems Biology and Applications 11 (1), 105, 2025
Vincent Noel and Marco Ruscone and Randy Heiland and Arnau Montagud and Alfonso Valencia and Emmanuel Barillot and Paul Macklin and Laurence Calzone, PhysiBoSS-Models: A database for multiscale models, arXiv preprint arXiv:2508.05550, 2025
Vincent Noël, Aurélien Naldi, Laurence Calzone, Loic Paulevé, Denis Thieffry; Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial. Interface Focus 22 August 2025; 15 (3): 20250002. , doi: 10.1098/rsfs.2025.0002
Adam Šmelko and Miroslav Kratochvíl and Emmanuel Barillot and Vincent Noël, Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators, BMC bioinformatics 25 (1), 199, 2024
Anna Niarakis and Marek Ostaszewski and Alexander Mazein and Inna Kuperstein and Martina Kutmon and Marc E Gillespie and Akira Funahashi and Marcio Luis Acencio and Ahmed Hemedan and Michael Aichem and Karsten Klein and Tobias Czauderna and Felicia Burtscher and Takahiro G Yamada and Yusuke Hiki and Noriko F Hiroi and Finterly Hu and Nhung Pham and Friederike Ehrhart and Egon L Willighagen and Alberto Valdeolivas and Aurelien Dugourd and Francesco Messina and Marina Esteban-Medina and Maria Peña-Chilet and Kinza Rian and Sylvain Soliman and Sara Sadat Aghamiri and Bhanwar Lal Puniya and Aurelien Naldi and Tomáš Helikar and Vidisha Singh and Marco Fariñas Fernández and Viviam Bermudez and Eirini Tsirvouli and Arnau Montagud and Vincent Noël and Miguel Ponce-de-Leon and Dieter Maier and Angela Bauch and Benjamin M Gyori and John A Bachman and Augustin Luna and Janet Piñero and Laura I Furlong and Irina Balaur and Adrien Rougny and Yohan Jarosz and Rupert W Overall and Robert Phair and Livia Perfetto and Lisa Matthews and Devasahayam Arokia Balaya Rex and Marija Orlic-Milacic and Luis Cristobal Monraz Gomez and Bertrand De Meulder and Jean Marie Ravel and Bijay Jassal and Venkata Satagopam and Guanming Wu and Martin Golebiewski and Piotr Gawron and Laurence Calzone and Jacques S Beckmann and Chris T Evelo and Peter D’Eustachio and Falk Schreiber and Julio Saez-Rodriguez and Joaquin Dopazo and Martin Kuiper and Alfonso Valencia and Olaf Wolkenhauer and Hiroaki Kitano and Emmanuel Barillot and Charles Auffray and Rudi Balling and Reinhard Schneider and COVID-19 Disease Map Community, Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches, Frontiers in immunology 14, 1282859, 2024
Marco Ruscone and Andrea Checcoli and Randy Heiland and Emmanuel Barillot and Paul Macklin and Laurence Calzone and Vincent Noël, Building multiscale models with PhysiBoSS, an agent-based modeling tool, Briefings in Bioinformatics 25 (6), bbae509, 2024
Eirini Tsirvouli and Vincent Noel and Åsmund Flobak and Laurence Calzone and Martin Kuiper, Dynamic Boolean modeling of molecular and cellular interactions in psoriasis predicts drug target candidates, Iscience 27 (2), 2024
Vincent Noël and Marco Ruscone and Robyn Shuttleworth and Cicely K Macnamara, PhysiMeSS-a new physiCell addon for extracellular matrix modelling, Gigabyte 2024, gigabyte135-0, 2024
Anna Niarakis and Reinhard Laubenbacher and Gary An and Yaron Ilan and Jasmin Fisher and Åsmund Flobak and Kristin Reiche and María Rodríguez Martínez and Liesbet Geris and Luiz Ladeira and Lorenzo Veschini and Michael L Blinov and Francesco Messina and Luis L Fonseca and Sandra Ferreira and Arnau Montagud and Vincent Noël and Malvina Marku and Eirini Tsirvouli and Marcella M Torres and Leonard A Harris and TJ Sego and Chase Cockrell and Amanda E Shick and Hasan Balci and Albin Salazar and Kinza Rian and Ahmed Abdelmonem Hemedan and Marina Esteban-Medina and Bernard Staumont and Esteban Hernandez-Vargas and Shiny Martis B and Alejandro Madrid-Valiente and Panagiotis Karampelesis and Luis Sordo Vieira and Pradyumna Harlapur and Alexander Kulesza and Niloofar Nikaein and Winston Garira and Rahuman S Malik Sheriff and Juilee Thakar and Van Du T Tran and Jose Carbonell-Caballero and Soroush Safaei and Alfonso Valencia and Andrei Zinovyev and James A Glazier, Immune digital twins for complex human pathologies: applications, limitations, and challenges, NPJ systems biology and applications 10 (1), 141, 2024
Randy Heiland and Daniel Bergman and Blair Lyons and Grant Waldow and Julie Cass and Heber Lima da Rocha and Marco Ruscone and Vincent Noël and Paul Macklin, PhysiCell Studio: a graphical tool to make agent-based modeling more accessible, GigaByte 2024, 2024
Marco Ruscone and Arnau Montagud and Philippe Chavrier and Olivier Destaing and Isabelle Bonnet and Andrei Zinovyev and Emmanuel Barillot and Vincent Noël and Laurence Calzone, Multiscale model of the different modes of cancer cell invasion, Bioinformatics 39 (6), btad374, 2023
Miguel Ponce-de-Leon and Arnau Montagud and Vincent Noël and Annika Meert and Gerard Pradas and Emmanuel Barillot and Laurence Calzone and Alfonso Valencia, PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks, npj Systems Biology and Applications 9 (1), 54, 2023
Anna Niarakis and Dagmar Waltemath and James Glazier and Falk Schreiber and Sarah M Keating and David Nickerson and Claudine Chaouiya and Anne Siegel and Vincent Noël and Henning Hermjakob and Tomáš Helikar and Sylvain Soliman and Laurence Calzone, Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology, Briefings in bioinformatics 23 (4), bbac212, 2022
Laurence Calzone and Vincent Noël and Emmanuel Barillot and Guido Kroemer and Gautier Stoll, Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells, Computational and Structural Biotechnology Journal 20, 5661-5671, 2022
Gautier Stoll and Aurélien Naldi and Vincent Noël and Eric Viara and Emmanuel Barillot and Guido Kroemer and Denis Thieffry and Laurence Calzone, UPMaBoSS: a novel framework for dynamic cell population modeling, Frontiers in molecular biosciences 9, 800152, 2022
Anna Niarakis and Martin Kuiper and Marek Ostaszewski and Rahuman S Malik Sheriff and Cristina Casals-Casas and Denis Thieffry and Tom C Freeman and Paul Thomas and Vasundra Touré and Vincent Noël and Gautier Stoll and Julio Saez-Rodriguez and Aurélien Naldi and Eugenia Oshurko and Ioannis Xenarios and Sylvain Soliman and Claudine Chaouiya and Tomáš Helikar and Laurence Calzone, Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC] 2 2019 CoLoMoTo/SysMod Workshop, Briefings in bioinformatics 22 (2), 1848-1859, 2021
Jonas Béal and Lorenzo Pantolini and Vincent Noël and Emmanuel Barillot and Laurence Calzone, Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers, PLOS Computational Biology 17 (1), e1007900, 2021
Vincent Noël and Marco Ruscone and Gautier Stoll and Eric Viara and Andrei Zinovyev and Emmanuel Barillot and Laurence Calzone, Webmaboss: a web interface for simulating boolean models stochastically, Frontiers in molecular biosciences 8, 754444, 2021
Marek Ostaszewski and Anna Niarakis and Alexander Mazein and Inna Kuperstein and Robert Phair and Aurelio Orta‐Resendiz and Vidisha Singh and Sara Sadat Aghamiri and Marcio Luis Acencio and Enrico Glaab and Andreas Ruepp and Gisela Fobo and Corinna Montrone and Barbara Brauner and Goar Frishman and Luis Cristobal Monraz Gomez and Julia Somers and Matti Hoch and Shailendra Kumar Gupta and Julia Scheel and Hanna Borlinghaus and Tobias Czauderna and Falk Schreiber and Arnau Montagud and Miguel Ponce de Leon and Akira Funahashi and Yusuke Hiki and Noriko Hiroi and Takahiro G Yamada and Andreas Dräger and Alina Renz and Muhammad Naveez and Zsolt Bocskei and Francesco Messina and Daniela Börnigen and Liam Fergusson and Marta Conti and Marius Rameil and Vanessa Nakonecnij and Jakob Vanhoefer and Leonard Schmiester and Muying Wang and Emily E Ackerman and Jason E Shoemaker and Jeremy Zucker and Kristie Oxford and Jeremy Teuton and Ebru Kocakaya and Gökçe Yağmur Summak and Kristina Hanspers and Martina Kutmon and Susan Coort and Lars Eijssen and Friederike Ehrhart and Devasahayam Arokia Balaya Rex and Denise Slenter and Marvin Martens and Nhung Pham and Robin Haw and Bijay Jassal and Lisa Matthews and Marija Orlic‐Milacic and Andrea Senff-Ribeiro and Karen Rothfels and Veronica Shamovsky and Ralf Stephan and Cristoffer Sevilla and Thawfeek Varusai and Jean‐Marie Ravel and Rupsha Fraser and Vera Ortseifen and Silvia Marchesi and Piotr Gawron and Ewa Smula and Laurent Heirendt and Venkata Satagopam and Guanming Wu and Anders Riutta and Martin Golebiewski and Stuart Owen and Carole Goble and Xiaoming Hu and Rupert W Overall and Dieter Maier and Angela Bauch and Benjamin M Gyori and John A Bachman and Carlos Vega and Valentin Groues and Miguel Vazquez and Pablo Porras and Luana Licata and Marta Iannuccelli and Francesca Sacco and Anastasia Nesterova and Anton Yuryev and Anita De Waard and Denes Turei and Augustin Luna and Ozgun Babur and Sylvain Soliman and Alberto Valdeolivas and Marina Esteban‐Medina and Maria Peña‐Chilet and Kinza Rian and Tomáš Helikar and Bhanwar Lal Puniya and Dezso Modos and Agatha Treveil and Marton Olbei and Bertrand De Meulder and Stephane Ballereau and Aurelien Dugourd and Aurelien Naldi and Vincent Noel and Laurence Calzone and Chris Sander and Emek Demir and Tamas Korcsmaros and Tom C Freeman and Franck Auge and Jacques S Beckmann and Jan Hasenauer and Olaf Wolkenhauer and Egon L Willighagen and Alexander R Pico and Chris T Evelo and Marc E Gillespie and Lincoln D Stein and Henning Hermjakob and Peter D'eustachio and Julio Saez‐Rodriguez and Joaquin Dopazo and Alfonso Valencia and Hiroaki Kitano and Emmanuel Barillot and Charles Auffray and Rudi Balling and Reinhard Schneider and COVID‐19 Disease Map Community, COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms, Molecular systems biology 17 (10), e10387, 2021
Stéphanie Chevalier and Vincent Noël and Laurence Calzone and Andrei Zinovyev and Loïc Paulevé, Synthesis and simulation of ensembles of boolean networks for cell fate decision, International Conference on Computational Methods in Systems Biology, 193-209, 2020
Vincent Noël and Jose Carbonell and Miguel Ponce de Leon and Sylvain Soliman and Anna Niarakis and Laurence Calzone and Emmanuel Barillot and Alfonso Valencia and Arnau Montagud, PhysiBoSS-COVID: the Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework allows for the uncovering of mechanistic insights,
Andrea Checcoli and Jonathan G Pol and Aurelien Naldi and Vincent Noel and Emmanuel Barillot and Guido Kroemer and Denis Thieffry and Laurence Calzone and Gautier Stoll, Dynamical boolean modeling of immunogenic cell death, Frontiers in Physiology 11, 590479, 2020
Mihály Koltai and Vincent Noel and Andrei Zinovyev and Laurence Calzone and Emmanuel Barillot, Exact solving and sensitivity analysis of stochastic continuous time Boolean models, BMC bioinformatics 21 (1), 241, 2020
Matheus H Dias and Cecília S Fonseca and Julianna D Zeidler and Layra L Albuquerque and Marcelo S da Silva and Eduardo Cararo‐Lopes and Marcelo S Reis and Vincent Noël and Edmilson O Dos Santos and Ian A Prior and Hugo A Armelin, Fibroblast Growth Factor 2 lethally sensitizes cancer cells to stress‐targeted therapeutic inhibitors, Molecular oncology 13 (2), 290-306, 2019
Marcelo S Reis and Vincent Noël and Matheus H Dias and Layra L Albuquerque and Amanda S Guimaraes and Lulu Wu and Junior Barrera and Hugo A Armelin, An interdisciplinary approach for designing kinetic models of the RAS/MAPK signaling pathway, Kinase Signaling Networks, 455-474, 2017
Vincent Noel and Marcelo da Silva Reis and Matheus Henrique dos Santos Dias and Lulu Wu and Amanda S Guimarães and Daniel F Reverbel and Júnior Barrera and Hugo Aguirre Armelin, SigNetSim: a web-based framework for designing kinetic models of molecular signaling networks, Abstracts, 2016
Vincent Noel and Marcelo da Silva Reis and Matheus Henrique dos Santos Dias and Layra Lucy Albuquerque and Ricardo Pariona-Llanos and Raphael Souza Pavani and Ariel Mariano Silber and Maria Isabel Nogueira Cano and Maria Carolina Elias and Fabio Nakano and Júnior Barrera and Hugo Aguirre Armelin, Design and analysis of dynamical models of biochemical reaction networks, Abstracts Book, 2015
Ricardo Pariona-Llanos and Raphael Souza Pavani and Marcelo Reis and Vincent Noel and Ariel Mariano Silber and Hugo Aguirre Armelin and Maria Isabel Nogueira Cano and Maria Carolina Elias, Glyceraldehyde 3-Phosphate Dehydrogenase-Telomere Association Correlates with Redox Status in Trypanosoma cruzi, Plos one 10 (3), e0120896, 2015
Vincent Noel and Dima Grigoriev and Sergei Vakulenko and Ovidiu Radulescu, Tropicalization and tropical equilibration of chemical reactions, Tropical and Idempotent Mathematics and Applications 616, 261-277, 2014
Marcelo S Reis and Matheus HS Dias and Fábio Nakano and Vincent Noël and Junior Barrera and Hugo A Armelin, Modeling the kinetics of Ras/MAPK and PI3K/AKT signaling pathways in the K-Ras-driven mouse Y1 adrenocortical tumor cells: novel insights into the mechanisms of FGF2-driven cell cycle arrest, Program and Index, 2014
Marcelo S Reis and Matheus HS Dias and Layra L Albuquerque and Fábio Nakano and Vincent Noël and Junior Barrera and Hugo A Armelin, Mathematical modeling of the Ras/MAPK and PI3K/Akt signaling networks in the K-Ras-driven mouse Y1 adrenocortical tumor cells, Program and Index, 2014
Vincent Noël and Sergey Vakulenko and Ovidiu Radulescu, A hybrid mammalian cell cycle model, arXiv preprint arXiv:1309.0870, 2013
Ovidiu Radulescu and Alexander N Gorban and Andrei Zinovyev and Vincent Noel, Reduction of dynamical biochemical reaction networks in computational biology, Frontiers in Genetics 3 (131), 2012
Vincent Noel and Dima Grigoriev and Sergei Vakulenko and Ovidiu Radulescu, Hybrid models of the cell cycle molecular machinery, arXiv preprint arXiv:1208.3854, 2012
Vincent Noël, Modèles réduits et hybrides de réseaux de réactions biochimiques: applications à la modélisation du cycle cellulaire, Université Rennes 1, 2012
Vincent Noel, Dima Grigoriev, Sergei Vakulenko and Ovidiu Radulescu, Tropical geometries and dynamics of biochemical networks application to hybrid cell cycle models, Electronic Notes in Theoretical Computer Science 284, 75-91, 2012
Vincent Noel, Sergei Vakulenko and Ovidiu Radulescu, Algorithm for identification of piecewise smooth hybrid systems: application to eukaryotic cell cycle regulation, International Workshop on Algorithms in Bioinformatics, 225-236, 2011
Vincent Noël, Sergei Vakulenko and Ovidiu Radulescu, Piecewise smooth hybrid systems as models for networks in molecular biology, Proceedings of JOBIM, 2010
Conference proceedings talk at Testing Institute of America 2014 Annual Conference, Los Angeles, CA, USA
Talk at London School of Testing, London, UK
Tutorial at UC-Berkeley Institute for Testing Science, Berkeley, CA, USA
Talk at UC San Francisco, Department of Testing, San Francisco, CA, USA