E-MUSE

Eva Balsa-Canto received her doctorate in 2001 at the University of Vigo. MSc in Physics, during her Ph.D. she focused on modeling and optimization of dynamic systems. She is the leader of the group on Biosystems and Bioprocess engineering at IIM-CSIC. Her team, Applied Systems Biology, focuses on the mathematical modeling, optimization, and control of biological systems and bioprocesses, with applications in the food industry. The team has contributed with methods and tools to automate model identification and systematize process optimization. Currently, they are studying the dynamics of fermentation processes led by single or multiple microbial species. 

Irene Otero Muras is a researcher at the CSIC (Spanish National Research Council), where she is starting a new group at I2SysBio Valencia, The Institute for Integrative Systems Biology in Valencia. The group research will focus on the design, analysis and control of biosystems, with particular interest in biomolecular networks (which are nonlinear, stochastic, complex systems) with relevance in cell regulation and metabolic processes. In this context, the group's research will aim at advance fundamental understanding and to address innovative applications for systems and synthetic biology.

Sophie Landaud is a professor in Industrial Microbiology at AgroParisTech and Vice President of the Department of Food and Biological Sciences and Processes (SPAB). She has expertise in fermentation applied to food matrices (alcoholic fermentation, dairy and plant-based fermented products), food microbial communities (fungi, bacteria), microbial metabolism (sulfur in particular) and biochemistry. She has a specific expertise in metabolomics (including volatilomics) applied to fermented products.
She coordinated several projects to understand and control the aromatic quality of fermented food, and more recently the metabolism of complex microbial communities in relation to aromatic compounds production and regulation. An important part of its projects was carried out in connection with associations of companies producing ferments or fermented foods, which created links and job opportunities for the students supervised in Master's or thesis.

Research scientist at INRAE in the Paris-Saclay Food and Bioproduct Engineering Research Unit (SayFood), Eric Dugat-Bony is a microbial ecologist working on the structure and functioning of microbial ecosystems. During his PhD at Blaise Pascal University with Dr Corinne Petit (2008-2011, Clermont-Ferrand, France), he developed functional DNA microarrays and related bioinformatic solutions in order to monitor microbial populations involved in the bioremediation of contaminated groundwater. Then, he moved to the University of Lethbridge (2012-2013, Alberta, Canada) for a postdoctoral position with Pr Brent Selinger to study the relationship between disbyosis of the cattle intestinal microbiota and the shedding of Escherichia coli O157:H7 with metagenomic tools. Since his recruitment at INRAE in 2013, he developed research projects to understand the effect of biotic (e.g. diversity level, microbial interactions, bacteriophages) and abiotic (e.g. NaCl content, temperature, oxygen level) factors inducing perturbations of the stability and functioning of the microbial ecosystem involved in food fermentation. His favorite model ecosystem is the cheese surface.

Pascal Bonnarme is a research director at INRAE and deputy director of the SayFood (Food and Bioproducts Engineering) Unit. He has expertise in fermentation of protein-based matrices, food microbial communities (fungi, bacteria), microbial biochemistry, metabolism related to the fermentation/ripening process (e.g. proteolysis, sulfur metabolism, amino acids catabolism, deacidification), development of a foodomics approach (e.g. metagenomics, metatranscriptomics, metabolomics, volatilomics) in fermented products, microbial and functional ecology, synthetic ecology, biodiversity of fermented foods ecosystems, control/formulation of microbial communities adapted to the food matrix to get desired functionalities.

Pascal Bonnarme coordinated several projects in which dynamic, functional meta-omic approaches - including (meta)-transcriptome and metagenome analyses - together with metabolome and aroma compounds analyses of cheese-ripening ecosystems were successfully developed to get an integrated view of microbial consortia functioning. More recently, he developed expertise in the fermentation of alternative sources of proteins (eg leguminous). He is currently involved in the Knowledge Hub SYSTEMIC (2020 - 2023).

Prof. Jan F.M. Van Impe obtained a master's degree in electrical and mechanical engineering from the University of Gent in 1988, and a doctorate in applied sciences from the KU Leuven in 1993. Immediately thereafter he founded the BioTeC (Chemical and Biochemical Process Technology and Control) research group. In the period 2005-2011, he has served as Departmental Head, while during the period 2006-2015 he was a visiting professor at the UAntwerpen. Currently, he is coordinating the European Master of Science in Food Science, Technology and Business (BIFTEC), co-funded by the Erasmus+ Programme of the European Union.

Prof Bas Teusink is head of the Systems Bioinformatics group, which he runs together with prof Frank Bruggeman. Prof Teusink's main research interest is the design principles of biological networks. He studies how fundamental constraints and functional purposes of networks lead to the system specifications that determine the fittest designs. He combines excellence in such fundamental studies with industrially-oriented applied research, as is evident from the Midterm Career Award he received in 2014 from the Lactic Acid Bacteria Industrial Platform for excellent research with industrial relevance.

Prof. Vasilis P. Valdramidis (PhD) graduated from the Aristotle University of thessaloniki at the Department of Food Science and Techonology (Greece). He was awarded his PhD at Catholic University of Leuven (Department of Chemical Engineering), Belgium, for research on Predictive Modelling in Foods. He undertook post doctoral research at the Agricultural University of Athens (Greece) in Predictive Modelling, the Agri-Food and Bioscience Institute (Nothern Ireland) in non-thermal technologies and the French National Institute for Agricultural Research (France) in food equipment Hygiene. He was also a research and teaching fellow at the Dublin Institute of Technology (Ireland), the University College Dublin (Ireland) and Associate Prof at University of Malta at the Department of Food Sciences and Nutrition. He is currently Associate Prof at National and Kapodistrian University of Athens. Prof. Valdramidis is leading a strong group in the area of food safety and processing.

Dr. Ahmad Zeidan holds an MSc degree in Pharmaceutical Sciences from Ain Shams University in Cairo, Egypt and a PhD degree in Bioengineering from Lund University in Sweden. He has more than 15 years of international expertise in the fields of microbiology, biotechnology and systems biology in both academia and industry. Dr. Zeidan is currently the R&D Director of Systems Biology and the Head of the Bioinformatics & Modeling Department at Chr. Hansen A/S, a global bioscience company that develops natural solutions for the food, nutritional, pharmaceutical and agricultural industries. His main research interest is bridging the gap between computational biology and industrial biotechnology. His current research activities at Chr. Hansen are centered on the application of integrative systems biology approaches for decoding the molecular mechanisms underlying desirable microbial traits and generating comprehensive knowledge on the company’s strain collection, which is employed in the continuous development of superior bacterial strains as ingredients of novel and innovative products. Dr. Zeidan is coordinating and/or participating in several active collaborations with academic partners and acts as reviewer for various peer-reviewed journals. In addition, he has (co)supervised several PhD and MSc students on their degree projects in the areas of microbiology, bioinformatics, systems biology, biotechnology and food engineering

Sébastien Déjean is a research engineer in statistics at the Université Toulouse III - Paul Sabatier. He is a member of the Institut de Mathématiques de Toulouse, mixed research unit of the University of Toulouse and the French National Centre for Scientific Research (CNRS). He was awarded his PhD title in applied mathematics and statistics in 2002, after 4 years in a biometry lab of the French National Research Institute for Agriculture, Food and Environment (INRAE). He was then recruited as a research engineer, its current position, to develop interdisciplinary research projects associating mathematics and other domains. In 2019, he defended his habilitation thesis based on 15 years of applied research in data science. He has contributed to many interdisciplinary research projects in different research fields including high-throughput biology and chemistry. His research interests focus on statistical data analysis and data integration to extract knowledge from data. He also contributes to the development of several R packages including mixOmics, a package dedicated to data integration, freely available on the international repository Bioconductor.

Daniel Remondini (Ph.D.) is a full professor at the Department of Physics and Astronomy at Bologna University. He has been working for more than 20 years on the analysis and modelling of biological data in medicine (multi-omics, imaging) applying Network Theory, Machine Learning and Artificial Intelligence methods.

He teaches Biomedical Courses (Physics for Medicine and Biotechnology, School of Specialization in Medical Physics) and on Applied Physics Master Course (Complex Networks, Pattern Recognition).

He has participated and is still participating in several national and EU projects on genomics of ageing and cancer (EU EUROBONET, PROTHETS, Mark-Age, T-CIA, NU-AGE, MissionT2D, NGS-PTL projects), on models of Data Analysis and Artificial Intelligence (EU MIMOMICS, Artificial Intelligence in Medicine INFN AIM, INFN next_AIM, COST INC) and on Data Analysis on food production and public health (foodborne diseases, epidemiology) encompassing Digital Health, genome and metagenome analysis and Machine Learning (EU Fibebiotics, COMPARE, VEO, ITN E-MUSE). He supervised more than 50 Thesis students (undergraduate and master in Physics) and 10 Ph.D. students in Physics. He is the author of more than 120 publications on high-impact peer-reviewed journals, has an H-index of 35 with >3600 citations (scholar).

Ioan-Cristian Trelea is professor at AgroParisTech, Paris-Saclay University. He holds an MSc in automatic control and a PhD in process modelling and control. He is head of the Modelling and computer-aided design group in the SayFood research unit, supervised 20 PhD students and is author of more than 70 papers in peer-reviewed journals. Prof. Trelea’s teaching and research interests are in mechanistic modelling of food and biological processes as well as in model-based optimization and control. He participated in several national and European collaborative research programmes as team leader, workpackage leader and PhD supervisor.

László Vidács is a senior research fellow, head of the Applied Artificial Intelligence Research Group at the Department of Software Engineering, University of Szeged, Hungary. He received his PhD in 2010 from the University of Szeged.
He received best paper awards at the IEEE ICPC 2009 and the IEEE CSMR-WCRE 2014 conferences. He continuously takes part in research projects based on academia/industry collaborations with leading national and international companies. Building on program analysis and testing research background, he is recently working at the intersection of artificial intelligence and software engineering, finding AI methods that help solving software-related problems with special interest in natural language processing and deep learning.

As a Principal Scientist in the section Food Safety and Fermentation at NIZO, Dr. Marjon Wells-Bennik works on preventing and solving food safety and quality issues. Her main focus is on the control of undesirable bacteria in foods, which slow an enormous diversity and cause foodborne illness or spoilage. Effective solutions to protect safety and quality of foods include traditional processes such as food fermentation, heat processing, and formulation of products to prevent outgrowth of undesirable microbes. This requires knowledge about microbes and their functionalities and properties, the food ingredients and their sources, the manufacturing process, and finished product composition. Together with the NIZO team, this is tackled using multidisciplinary approaches which range from trouble shooting activities, predictive modelling, challenge testing, process validations, microbial and chemical risk assessments, to in-depth genomics analysis of microbes and gene-trait matching. She has been the daily supervisor of seven PhD students over the past 15 years.

Tibor Gyimóthy is a corresponding member of the Hungarian Academy of Sciences (MTA), full professor at the Software Engineering Department at the University of Szeged in Hungary and the head of the MTA-SZTE Research Group on Artificial Intelligence. His research interests are concentrated on high-quality software development and maintenance, natural language processing and applied machine learning. His main contributions are methods and tools for identifying and predicting harmful program elements in the source code. He published over 210 research papers with more than 2600 independent citations. The software maintenance tools developed in his team are used by numerous software companies in the world. His scientific contributions were awarded with the Széchenyi Professor Grant, László Kalmár Award, HAS Academic Prize, Gábor Dénes Award and Szent-Györgyi Albert Prize. Tibor Gyimóthy is four-time program committee member of the International Conference on Software Engineering (ICSE), which is the most significant software engineering conference in the world. In 2011, Tibor Gyimóthy was elected the Conference Chair of the European Software Engineering Conference (ESEC)/ ACM Foundations of Software Engineering (FSE) .