Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration.

Project Information

E-MUSE

Grant agreement ID: 956126

DOI

10.3030/956126

Project closed

EC signature date 28 August 2020

Start date 1 January 2021

End date 30 June 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 901 305,60

EU contribution

€ 3 901 305,60

Coordinated by

INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT
France

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (2)

Vacancies advertising

Vacancies advertizing

Dissemination of project results

Websites, patent fillings, videos etc. (1)

Social networks

Website LinkedIn and social media accounts implemented

Publications

Peer reviewed articles (18)

Levels and types of microbial contaminants in different plant-based ingredients used in dairy alternatives

Author(s): Alina Kyrylenko, Robyn T. Eijlander, Giovanni Alliney, Elly Lucas-van de Bos, Marjon H.J. Wells-Bennik
Published in: International Journal of Food Microbiology, Issue Volume 407, 2023, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2023.110392

MINN: A metabolic-informed neural network for integrating omics data into genome-scale metabolic modeling

Author(s): Gabriele Tazza, Francesco Moro, Dario Ruggeri, Bas Teusink, László Vidács
Published in: Computational and Structural Biotechnology Journal, Issue 27, 2025, Page(s) 3609-3617, ISSN 2001-0370
Publisher: Elsevier BV
DOI: 10.1016/j.csbj.2025.08.004

Bacterial and fungal profiling of Maltese sheep cheese with amplicon metabarcoding

Author(s): Muhammad Ahmed Ihsan, Vasilis P. Valdramidis, Sholeem Griffin
Published in: International Dairy Journal, Issue 170, 2025, Page(s) 106362, ISSN 0958-6946
Publisher: Elsevier BV
DOI: 10.1016/j.idairyj.2025.106362

Introducing MLOps to Facilitate the Development of Machine Learning Models in Agronomy: A Case Study

Author(s): Dario Ruggeri, Gabriele Tazza, László Vidács
Published in: IEEE Access, 2025, Page(s) 1-1, ISSN 2169-3536
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2025.3586691

Signaling dynamics in microbial communities: A reduced-complexity mathematical analysis

Author(s): Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F.M. Van Impe
Published in: Chemical Engineering Science, Issue 319, 2025, Page(s) 121962, ISSN 0009-2509
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.ces.2025.121962

Improvement of variables interpretability in kernel PCA

Author(s): Mitja Briscik, Marie-Agnès Dillies, Sébastien Déjean
Published in: BMC Bioinformatics, 2023, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-023-05404-y

Demystifying food flavor: Flavor data interpretation through machine learning

Author(s): Huabin Luo, Simen Akkermans, Jan F.M. Van Impe
Published in: Food Chemistry, Issue 483, 2025, Page(s) 144000, ISSN 0308-8146
Publisher: Elsevier BV
DOI: 10.1016/j.foodchem.2025.144000

Tuning and modeling cheese flavor

Author(s): Huabin Luo,Simen Akkermans,Davy Verheyen,Jian Wang,Monika Polanska,Jan F. M. Van Impe
Published in: Comprehensive Reviews in Food Science and Food Safety, Issue Volume 23, Issue 5, 2024, ISSN 1541-4337
Publisher: International Life Sciences Institute
DOI: 10.1111/1541-4337.13420

Iron fortification modifies the microbial community structure and metabolome of a model surface-ripened cheese

Author(s): Mahtab Shoukat,Vincent Hervé,Anne-Sophie Sarthou,Anne-Claire Peron,Alice Danel,Dominique Swennen,Pascal Bonnarme,Eric Dugat-Bony
Published in: International Journal of Food Microbiology, Issue Volulme 427, 2024, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2024.110971

Mechanistic modeling of the dynamics of phage attack during milk acidification in the cheese-making process

Author(s): Michèle Bou Habib, Emmanuel Bernuau, Benjamín José Sánchez, Dominique Swennen, Ahmad A. Zeidan, Ioan-Cristian Trelea, Jannik Vindeloev
Published in: Journal of Food Engineering, Issue 387, 2024, Page(s) 112329, ISSN 0260-8774
Publisher: Elsevier BV
DOI: 10.1016/j.jfoodeng.2024.112329

A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes

Author(s): Ihab Hashem, Jian Wang, Jan F.M. Van Impe
Published in: PLOS Computational Biology, Issue 21, 2025, Page(s) e1012974, ISSN 1553-7358
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012974

Supervised multiple kernel learning approaches for multi-omics data integration

Author(s): Mitja Briscik, Gabriele Tazza, László Vidács, Marie-Agnès Dillies, Sébastien Déjean
Published in: BioData Mining, Issue 17, 2024, ISSN 1756-0381
Publisher: BioMed Central
DOI: 10.1186/s13040-024-00406-9

Iron-based microbial interactions: the role of iron metabolism in the cheese ecosystem

Author(s): Rina Mekuli, Mahtab Shoukat, Eric Dugat-Bony, Pascal Bonnarme, Sophie Landaud, Dominique Swennen, Vincent Hervé
Published in: Journal of Bacteriology, 2025, ISSN 0021-9193
Publisher: American Society for Microbiology
DOI: 10.1128/jb.00539-24

Use and limitations of genome-scale metabolic models in food microbiology

Author(s): Vincent Somerville, Pranas Grigaitis, Julius Battjes, Francesco Moro, BasTeusink
Published in: Current Opinion in Food Science, Issue Volume 43, 2022, Page(s) 225-231, ISSN 2214-7993
Publisher: Elsevier BV
DOI: 10.1016/j.cofs.2021.12.010

Individual-based modeling (IbM) unravels spatial and social interactions in bacterial communities

Author(s): Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F M Van Impe
Published in: The ISME Journal, 2025, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1093/ismejo/wraf116

Individual-based modelling (IbM) in food microbiology: A comprehensive guideline

Author(s): Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Davy Verheyen, Huabin Luo, Jan F.M. Van Impe
Published in: Food Research International, Issue 213, 2025, Page(s) 116408, ISSN 0963-9969
Publisher: Elsevier BV
DOI: 10.1016/j.foodres.2025.116408

A computational framework for Optimal and Model Predictive Control of stochastic gene regulatory networks

Author(s): Hamza Faquir, Manuel Pájaro, Irene Otero-Muras
Published in: IEEE Transactions on Computational Biology and Bioinformatics, 2025, Page(s) 1-13, ISSN 2998-4165
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/tcbbio.2025.3598449

Improving Microbiome-Based Disease Prediction With SuperTML and Data Augmentation

Author(s): Gabriele Tazza, Dario Ruggeri, László Vidács
Published in: IEEE Access, Issue 13, 2025, Page(s) 144505-144515, ISSN 2169-3536
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2025.3598868

Conference proceedings (2)

Feedback control of stochastic gene switches using PIDE models

Author(s): Christian Fernández, Hamza Faquir, Manuel Pájaro, Irene Otero-Muras
Published in: IFAC-PapersOnLine, Issue Volume 55, 2022, Page(s) Issue 18, 2022, Pages 62-67, ISSN 2405-8963
Publisher: Elsevier
DOI: 10.1016/j.ifacol.2022.08.031

Vulnerability of Microbial Communities to Dishonest Signals: A biology driven complexity reduced model.

Author(s): Jian Wang, Ihab Hashem, Satyajeet S. Bhonsale, Jan F.M. Van Impe
Published in: Computer Aided Chemical Engineering, 34th European Symposium on Computer Aided Process Engineering / 15th International Symposium on Process Systems Engineering, 2025, Page(s) 769-774
Publisher: Elsevier
DOI: 10.1016/b978-0-443-28824-1.50129-0

Thesis and dissertations (4)

Development of kernel approaches for the integration of biological data from heterogeneous sources.

Author(s): Mitja Briscik
Published in: 2025
Publisher: Université de Toulouse

Development and analysis of a dynamic model of phage attack in milk acidification for cheese-making.

Author(s): Michèle Bou Habib
Published in: 2025
Publisher: Université Paris-Saclay

Integrative analysis of iron availability on metabolism and interaction dynamics of Hafnia alvei and Brevibacterium aurantiacum.

Author(s): Rina Mekuli
Published in: 2025
Publisher: Université Paris-Saclay

Iron as a modulator of the cheese microbial ecosystem.

Author(s): Mahtab Shoukat
Published in: 2025
Publisher: Université Paris-Saclay

Book chapters (1)

Systems Biology

Author(s): Bas Teusink
Published in: Applied food science, Issue 01/11/2022, 2022, Page(s) 141-155, ISBN 9789086869336
Publisher: Wageningen Academic Publishers
DOI: 10.3920/978-90-8686-933-6_8

Other (1)

E-MUSE - Data management plan

Author(s): Balsa-Canto Eva, Bou Habib Michèle, Briscik Mitja, Déjean Sébastien, Dugat-Bony Eric, Faquir Hamza, Hervé Vincent, Ihsan Muhammad Ahmed, Koduru Lokamand, Kyrylenko Alina, Luo Huabin, Mansouri Anis, Mekuli Rina, Moro Francesco, Osset Ojea Teresa, Otero-Muras Irene, Remondini Daniel, Roudaut Geoffrey, Ruggeri Dario, Shoukat Mahtab, Tazza Gabriele, Teusink Bas, Trelea Cristian, Valdramidis Vasili
Published in: 2025
Publisher: INRAE