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

Información del proyecto

E-MUSE

Identificador del acuerdo de subvención: 956126

DOI

10.3030/956126

Proyecto cerrado

Fecha de la firma de la CE 28 Agosto 2020

Fecha de inicio 1 Enero 2021

Fecha de finalización 30 Junio 2025

Financiado con arreglo a

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coste total

€ 3 901 305,60

Aportación de la UE

€ 3 901 305,60

Coordinado por

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

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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

Publicaciones

Peer reviewed articles (20)

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

Autores: Alina Kyrylenko, Robyn T. Eijlander, Giovanni Alliney, Elly Lucas-van de Bos, Marjon H.J. Wells-Bennik
Publicado en: International Journal of Food Microbiology, Edición Volume 407, 2023, ISSN 0168-1605
Editor: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2023.110392

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

Autores: Gabriele Tazza, Francesco Moro, Dario Ruggeri, Bas Teusink, László Vidács
Publicado en: Computational and Structural Biotechnology Journal, Edición 27, 2025, Página(s) 3609-3617, ISSN 2001-0370
Editor: Elsevier BV
DOI: 10.1016/j.csbj.2025.08.004

Bacterial and fungal profiling of Maltese sheep cheese with amplicon metabarcoding

Autores: Muhammad Ahmed Ihsan, Vasilis P. Valdramidis, Sholeem Griffin
Publicado en: International Dairy Journal, Edición 170, 2025, Página(s) 106362, ISSN 0958-6946
Editor: Elsevier BV
DOI: 10.1016/j.idairyj.2025.106362

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

Autores: Dario Ruggeri, Gabriele Tazza, László Vidács
Publicado en: IEEE Access, 2025, Página(s) 1-1, ISSN 2169-3536
Editor: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2025.3586691

Hybrid plant-dairy cheese: Effects of lactic acid bacteria and plant proteins on composition, proteolysis, and flavor profile

Autores: Huabin Luo, Simen Akkermans, Wim Engels, Simon Jacobs, Herwig Bachmann, Jan F.M. Van Impe, Marjon H.J. Wells-Bennik
Publicado en: Food Chemistry, 2025, Página(s) 146804, ISSN 0308-8146
Editor: Elsevier BV
DOI: 10.1016/j.foodchem.2025.146804

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

Autores: Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F.M. Van Impe
Publicado en: Chemical Engineering Science, Edición 319, 2025, Página(s) 121962, ISSN 0009-2509
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.ces.2025.121962

Improvement of variables interpretability in kernel PCA

Autores: Mitja Briscik, Marie-Agnès Dillies, Sébastien Déjean
Publicado en: BMC Bioinformatics, 2023, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-023-05404-y

Demystifying food flavor: Flavor data interpretation through machine learning

Autores: Huabin Luo, Simen Akkermans, Jan F.M. Van Impe
Publicado en: Food Chemistry, Edición 483, 2025, Página(s) 144000, ISSN 0308-8146
Editor: Elsevier BV
DOI: 10.1016/j.foodchem.2025.144000

Tuning and modeling cheese flavor

Autores: Huabin Luo,Simen Akkermans,Davy Verheyen,Jian Wang,Monika Polanska,Jan F. M. Van Impe
Publicado en: Comprehensive Reviews in Food Science and Food Safety, Edición Volume 23, Edición 5, 2024, ISSN 1541-4337
Editor: International Life Sciences Institute
DOI: 10.1111/1541-4337.13420

Identification of antimicrobial resistance genes in <i>Escherichia coli</i> through network diffusion

Autores: Anis Mansouri, Francesco Durazzi, Muhammad Ahmed Ihsan, Sholeem Griffin, Gerardo Manfreda, Vasilis P Valdramidis, Frédérique Pasquali, Daniel Remondini
Publicado en: Journal of Antimicrobial Chemotherapy, 2025, ISSN 0305-7453
Editor: Oxford University Press
DOI: 10.1093/jac/dkaf404

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

Autores: Mahtab Shoukat,Vincent Hervé,Anne-Sophie Sarthou,Anne-Claire Peron,Alice Danel,Dominique Swennen,Pascal Bonnarme,Eric Dugat-Bony
Publicado en: International Journal of Food Microbiology, Edición Volulme 427, 2024, ISSN 0168-1605
Editor: 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

Autores: Michèle Bou Habib, Emmanuel Bernuau, Benjamín José Sánchez, Dominique Swennen, Ahmad A. Zeidan, Ioan-Cristian Trelea, Jannik Vindeloev
Publicado en: Journal of Food Engineering, Edición 387, 2024, Página(s) 112329, ISSN 0260-8774
Editor: 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

Autores: Ihab Hashem, Jian Wang, Jan F.M. Van Impe
Publicado en: PLOS Computational Biology, Edición 21, 2025, Página(s) e1012974, ISSN 1553-7358
Editor: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012974

Supervised multiple kernel learning approaches for multi-omics data integration

Autores: Mitja Briscik, Gabriele Tazza, László Vidács, Marie-Agnès Dillies, Sébastien Déjean
Publicado en: BioData Mining, Edición 17, 2024, ISSN 1756-0381
Editor: BioMed Central
DOI: 10.1186/s13040-024-00406-9

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

Autores: Rina Mekuli, Mahtab Shoukat, Eric Dugat-Bony, Pascal Bonnarme, Sophie Landaud, Dominique Swennen, Vincent Hervé
Publicado en: Journal of Bacteriology, 2025, ISSN 0021-9193
Editor: American Society for Microbiology
DOI: 10.1128/jb.00539-24

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

Autores: Vincent Somerville, Pranas Grigaitis, Julius Battjes, Francesco Moro, BasTeusink
Publicado en: Current Opinion in Food Science, Edición Volume 43, 2022, Página(s) 225-231, ISSN 2214-7993
Editor: Elsevier BV
DOI: 10.1016/j.cofs.2021.12.010

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

Autores: Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F M Van Impe
Publicado en: The ISME Journal, 2025, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1093/ismejo/wraf116

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

Autores: Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Davy Verheyen, Huabin Luo, Jan F.M. Van Impe
Publicado en: Food Research International, Edición 213, 2025, Página(s) 116408, ISSN 0963-9969
Editor: Elsevier BV
DOI: 10.1016/j.foodres.2025.116408

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

Autores: Hamza Faquir, Manuel Pájaro, Irene Otero-Muras
Publicado en: IEEE Transactions on Computational Biology and Bioinformatics, 2025, Página(s) 1-13, ISSN 2998-4165
Editor: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/tcbbio.2025.3598449

Improving Microbiome-Based Disease Prediction With SuperTML and Data Augmentation

Autores: Gabriele Tazza, Dario Ruggeri, László Vidács
Publicado en: IEEE Access, Edición 13, 2025, Página(s) 144505-144515, ISSN 2169-3536
Editor: 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

Autores: Christian Fernández, Hamza Faquir, Manuel Pájaro, Irene Otero-Muras
Publicado en: IFAC-PapersOnLine, Edición Volume 55, 2022, Página(s) Edición 18, 2022, Pages 62-67, ISSN 2405-8963
Editor: Elsevier
DOI: 10.1016/j.ifacol.2022.08.031

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

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

Thesis and dissertations (5)

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

Autores: Mitja Briscik
Publicado en: 2025
Editor: Université de Toulouse

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

Autores: Michèle Bou Habib
Publicado en: 2025
Editor: Université Paris-Saclay

Machine Learning and network-based methods for the analysis of biological systems involved in food processing.

Autores: Anis Mansouri
Publicado en: 2025
Editor: UNIBO

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

Autores: Rina Mekuli
Publicado en: 2025
Editor: Université Paris-Saclay

Iron as a modulator of the cheese microbial ecosystem.

Autores: Mahtab Shoukat
Publicado en: 2025
Editor: Université Paris-Saclay

Book chapters (1)

Systems Biology

Autores: Bas Teusink
Publicado en: Applied food science, Edición 01/11/2022, 2022, Página(s) 141-155, ISBN 9789086869336
Editor: Wageningen Academic Publishers
DOI: 10.3920/978-90-8686-933-6_8

Other (1)

E-MUSE - Data management plan

Autores: 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
Publicado en: 2025
Editor: INRAE