Vincent Noël

Vincent Noël

Research scientist in the Computation Systems Biology of Cancer group at Institut Curie

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portfolio

publications

A hybrid mammalian cell cycle model

Published in arXiv preprint arXiv:1309.0870, 2013, 2013

Recommended citation: Vincent Noël and Sergey Vakulenko and Ovidiu Radulescu, A hybrid mammalian cell cycle model, arXiv preprint arXiv:1309.0870, 2013
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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

Published in Program and Index, 2014, 2014

Recommended citation: 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
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Tropicalization and tropical equilibration of chemical reactions

Published in Tropical and Idempotent Mathematics and Applications 616, 261-277, 2014, 2014

Recommended citation: 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
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Glyceraldehyde 3-Phosphate Dehydrogenase-Telomere Association Correlates with Redox Status in Trypanosoma cruzi

Published in Plos one 10 (3), e0120896, 2015, 2015

Recommended citation: 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
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Design and analysis of dynamical models of biochemical reaction networks

Published in Abstracts Book, 2015, 2015

Recommended citation: 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
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Fibroblast Growth Factor 2 lethally sensitizes cancer cells to stress‐targeted therapeutic inhibitors

Published in Molecular oncology 13 (2), 290-306, 2019, 2019

Recommended citation: 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
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Dynamical boolean modeling of immunogenic cell death

Published in Frontiers in Physiology 11, 590479, 2020, 2020

Recommended citation: 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
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PhysiBoSS-COVID: the Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework allows for the uncovering of mechanistic insights

Published in , 2020

Recommended citation: 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,
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Synthesis and simulation of ensembles of boolean networks for cell fate decision

Published in International Conference on Computational Methods in Systems Biology, 193-209, 2020, 2020

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

Published in Molecular systems biology 17 (10), e10387, 2021, 2021

Recommended citation: 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
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Webmaboss: a web interface for simulating boolean models stochastically

Published in Frontiers in molecular biosciences 8, 754444, 2021, 2021

Recommended citation: 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
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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

Published in Briefings in bioinformatics 22 (2), 1848-1859, 2021, 2021

Recommended citation: 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
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UPMaBoSS: a novel framework for dynamic cell population modeling

Published in Frontiers in molecular biosciences 9, 800152, 2022, 2022

Recommended citation: 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
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Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells

Published in Computational and Structural Biotechnology Journal 20, 5661-5671, 2022, 2022

Recommended citation: 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
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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Published in Briefings in bioinformatics 23 (4), bbac212, 2022, 2022

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

Published in npj Systems Biology and Applications 9 (1), 54, 2023, 2023

Recommended citation: 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
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Multiscale model of the different modes of cancer cell invasion

Published in Bioinformatics 39 (6), btad374, 2023, 2023

Recommended citation: 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
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Immune digital twins for complex human pathologies: applications, limitations, and challenges

Published in NPJ systems biology and applications 10 (1), 141, 2024, 2024

Recommended citation: 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
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Building multiscale models with PhysiBoSS, an agent-based modeling tool

Published in Briefings in Bioinformatics 25 (6), bbae509, 2024, 2024

Recommended citation: 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
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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Published in Frontiers in immunology 14, 1282859, 2024, 2024

Recommended citation: 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
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PhysiBoSS-Models: A database for multiscale models

Published in arXiv preprint arXiv:2508.05550, 2025, 2025

Recommended citation: 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
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Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming

Published in npj Systems Biology and Applications 11 (1), 105, 2025, 2025

Recommended citation: 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
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Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative

Published in bioRxiv, 2025.07. 16.664358, 2025, 2025

Recommended citation: 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
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talks

teaching

PerMedCoE Summer School: From pathway modelling tools to cell-level simulations

Thematic School, Hotel Montanyà, 2023

The course combined lectures and hands-on exercises to introduce attendees to key practicalities of working with HPC clusters, build first-hand experience in using PerMedCoE modelling tools and develop a practical appreciation of using workflow managers and containerised PerMedCoE modelling tools to execute biomedical workflows.