E-MUSE

ESR7 Anis Mansouri & ESR12 Muhammad Ahmed Ihsan

Anis Mansouri, Francesco Durazzi, Muhammad Ahmed Ihsan, Sholeem Griffin, Gerardo Manfreda, Vasilis P Valdramidis, Frédérique Pasquali, Daniel Remondini

"Identification of antimicrobial resistance genes in Escherichia coli through network diffusion",

Journal of Antimicrobial Chemotherapy, 2025, dkaf404.

DOI: 10.1093/jac/dkaf404

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ESR14 Huabin Luo:

Huabin Luo, Simen Akkermans, Wim Engels, Simon Jacobs, Herwig Bachmann, Jan F.M. Van Impe, Marjon H.J. Wells-Bennik

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

Food Chemistry, 2025, 146804.

DOI: 10.1016/j.foodchem.2025.146804​

 

ESR3 Hamza Faquir:

Hamza Faquir, Manuel Pajaro, Irene Otero-Muras

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

IEEE Transactions on Computational Biology and Bioinformatics.

DOI: 10.1109/TCBBIO.2025.3598449.

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ESR11 Jian Wang:

Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F M Van Impe

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

The ISME Journal, wraf 116.

DOI: 10.1093/ismejo/wraf116.

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ESR8 Gabriele Tazza & ESR9 Dario Ruggeri:

Gabriele Tazza, Dario Ruggeri, László Vidács

"Improving Microbiome-Based Disease Prediction With SuperTML and Data Augmentation",

IEEE Access, vol. 13, pp. 144505-144515, 2025.

DOI: 10.1109/ACCESS.2025.3598868.

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ESR8 Gabriele Tazza, ESR1 Francesco Moro, ESR9 Dario Ruggeri:

Gabriele Tazza, Francesco Moro, Dario Ruggeri, Bas Teusink, László Vidács

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

Computational and Structural Biotechnology Journal, vol 27, 2025, p3609-3617.

DOI: 10.1016/j.csbj.2025.08.004​​

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ESR9 Dario Ruggeri & ESR8 Gabriele Tazza:

D. Ruggeri, G. Tazza and László Vidács
"Introducing MLOps to Facilitate the Development of Machine Learning Models in Agronomy: A Case Study",
IEEE Access, vol. 13, pp. 122059-122070, 2025.
DOI: 10.1109/access.2025.3586691

 

ESR12 Muhammad Ahmed Ihsan:

Muhammad Ahmed Ihsan, Vasilis P. Valdramidis, Sholeem Griffin

"Bacterial and fungal profiling of Maltese sheep cheese with amplicon metabarcoding",

International Dairy Journal 170.

DOI: 10.1016/j.idairyj.2025.106362

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ESR11 Jian Wang & ESR14 Huabin Luo:

Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Davy Verheyen, Huabin Luo, Jan F.M. Van Impe

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

Food Research International 213.

DOI: 10.1016/j.foodres.2025.116408

 

ESR11 Jian Wang:

Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F.M. Van Impe

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

Chemical Engineering Science 319.

DOI: 10.1016/j.ces.2025.121962

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ESR11 Jian Wang:

Ihab Hashem, Jian Wang, Jan F.M. Van Impe

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

PLOS Computational Biology 21.

DOI: 10.1371/journal.pcbi.1012974

 

ESR14 Huabin Luo:

Huabin Luo, Simen Akkermans, Jan F. M. Van Impe

"Demystifying food flavor: Flavor data interpretation through machine learning",

Food Chemistry 483.

DOI: 10.1016/j.foodchem.2025.144000​

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ESR5 Rina Mekuli & ESR10 Mahtab Shoukat:

Rina Mekuli, Mahtab Shoukat, Eric Dugat-Bony, Pascal Bonnarme, Sophie Landaud, Dominique Swennen, Vincent Hervé

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

J Bacteriol 0:e00539-24.

DOI: 10.1128/jb.00539-24

 

​ESR3 Hamza Faquir:

Hamza Faquir, Manuel Pajaro, Irene Otero-Muras

"A computational framework for optimal and Model Predictive Control of stochastic gene regulatory networks",

arXiv:2409.11036, q-bio.QM.

DOI: 10.48550/arXiv.2409.11036

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ESR6 Mitja Briscik & ESR8 Gabriele Tazza:

Mitja Briscik, Gabriele Tazza, László Vidács, Marie-Agnès Dillies, Sébastien Déjean
"Supervised multiple kernel learning approaches for multi-omics data integration",

BioData Mining 17, article 53, 2024.

DOI: 10.1186/s13040-024-00406-9

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ESR10 Mahtab Shoukat:

Mahtab Shoukat, Vincent Hervé, Anne-Sophie Sarthou, Anne-Claire Peron, Alice Danel, Dominique Swennen, Pascal Bonnarme, Eric Dugat-Bony
"Iron fortification modifies the microbial community structure and metabolome of a model surface-ripened cheese",
International Journal of Food Microbiology, Volume 427, 110971.

DOI: 10.1016/j.ijfoodmicro.2024.110971

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ESR14 Huabin Luo & ESR11 Jian Wang:

Huabin Luo, Jian Wang, Simen Akkermans, Davy Verheyen, Monika Polanska, Jan F. M. Van Impe
"Tuning and modeling cheese flavor",
Comprehensive Reviews in Food Science and Food Safety, 2024, Volume 23, e13420.

DOI: 10.1111/1541-4337.13420

 

ESR15 Michèle Bou Habib:

​Michèle Bou Habib, Emmanuel Bernuau, Benjamín José Sánchez, Dominique Swennen, Ahmad A. Zeidan, Ioan-Cristian Trelea, Jannik Vindeloev

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

Journal of Food Engineering, Volume 387, 2025, 112329.

DOI: 10.1016/j.jfoodeng.2024.112329

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ESR1 Francesco Moro:

V. Somerville, P. Grigaitis, J. Battjes, F. Moro, B. Teusink
"Use and limitations of genome-scale metabolic models in food microbiology",
Current Opinion in Food Science, 2022, Volume 43, 225-231.

DOI: 10.1016/j.cofs.2021.12.010 

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ESR6 Mitja Briscik:

Mitja Briscik, Marie-Agnès Dillies, Sébastien Déjean

"Improvement of variables interpretability in kernel PCA"

BMC Bioinformatics, 2023, Volume 24, 282. DOI: 10.1186/s12859-023-05404-y

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ESR13 Alina Kyrylenko:

Alina Kyrylenko, Robyn T. Eijlander, Giovanni Alliner, Elly Lucas-van de Bos, Marjon H.J. Wells-Bennik

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

International Journal of Food Microbiology, 2023, Volume 407. DOI: 10.1016/j.ijfoodmicro.2023.110392

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