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Research Themes

Nutrigenomics

Toxicogenomics

Toxicogenomics 
In the theme of Toxicogenomics, we bring together genomics, transcriptomics and advanced bioinformatics to understand how chemicals perturb human biology. We assess molecular changes directly in human-relevant cell models, instead of using animal experiments. We generate genomics data across thousands of genes simultaneously, to discover relevant molecular pathways, modes of action and early biomarkers of effect. Where possible, we validate these molecular signatures in human population studies, human interventions or in clinical settings.

Our research focus: 
The goal of our toxicogenomics research is to understand how exposure to chemical substances and environmental factors affects gene expression and other molecular processes, and how these changes relate to adverse health outcomes. In essence, it combines toxicology with functional genomics to:

  • Identify molecular signatures of toxicity (e.g., gene expression profiles, epigenetic changes, microRNA patterns);
  • Clarify mechanisms of action for chemicals and environmental stressors at the genomic level;
  • Predict toxicity and risk before adverse effects occur, using biomarkers and computational models;
  • Improve safety assessments by moving beyond traditional animal testing toward mechanistic, high-throughput approaches;

  • Support personalized risk evaluation, considering genetic variability in responses to toxicants.

     

Our approach is based on: 

  • The development of New Approach Methodologies (NAMs) to predict toxicity of chemicals without the traditional use of animal experiments;
  • Studying genomics responses to environmental exposures in human population studies (population-based toxicogenomics);
  • Cross-validation of findings in human studies versus in vitro models to establish robust mechanisms of action. 

We focus on FAIR and reproducible science: standardising study reporting, containerised analysis pipelines, and open training so that high-quality omics data can be trusted in decision-making. We co-create methods with regulators and industrial partners to ensure results are interpretable, auditable and suitable for use in safety dossiers. 

Collaboration and Networks
We have an extensive (inter)national network of collaboration in the toxicogenomics domain, having been involved in more than 15 consortia both as partner and as coordinator. Some key collaborations include: 

  • Involvement in national and international research consortia, currently including ONTOX, VHP4Safety, ASPIS, ELIXIR;
  • Strong interaction with safety regulators and authorities such as EFSA, the Dutch Food and Safety Authority and the OECD.
  • Strong involvement in the European Federation of Toxicology (EUROTOX) and the Dutch society of Toxicology

Members:

Toxicogenomics

Clinical Genomics

The Clinical Genomics theme within the Department of Translational Genomics brings together researchers working at the intersection of genomics, computation and human disease modelling to transform scientific discoveries into novel therapeutic approaches based on profound understanding of the molecular pathophysiology.. ​

Our research focuses on:​

  • Personalized therapy development for genetic muscle diseases​

  • Identification of molecular mechanisms of (rare) genetic diseases​

  • Patient-specific in vitro and in silico modelling​

  • Biomarker discovery​

Our approach:​

Rare genetic diseases are inherently heterogeneous. The same genetic mutation can result in diverse phenotypic outcomes depending on genetic background and environmental exposure. Conversely, distinct genetic variants or even different rare diseases may converge on shared clinical or molecular features. We deliberately incorporate this complexity into our research strategy.​

A central goal of our work is to develop therapeutic strategies to combat mitochondrial and LAMA2 muscular disease using (genetically corrected) myogenic stem cells. By integrating gene correction approaches with advanced stem cell technologies and functional validation models, we aim to translate mechanistic insights into tangible therapeutic innovation.​

In parallel, we elucidate molecular processes in (rare) metabolic and neurodevelopmental disorders using in vitro models and computational approaches. Through patient-specific modelling, deep phenotyping, and multi-omics profiling, we characterise disease mechanisms within and across tissues, and across developmental or differentiation stages.​

By merging advanced in vitro systems, capturing spatial and temporal aspects of disease development, with sophisticated in silico modelling, we relate information across datasets and disease conditions. This integrated strategy enables us to extract maximal insight from diseases with inherently small patient populations.​

In addition, we actively contribute to the curation and development of reliable digital resources for disease pathways and molecular interactions, facilitating knowledge sharing and automated integration of emerging insights across the scientific community.​

Collaboration and networks:​

  • Close collaboration with universities (UHasselt, KU Leuven, CHU Liege, RWTH Aachen) and companies (Milocron, Revatis, Scinus, Rewrite, Bramverbrugge.nl) within EuregioMR on development of myogenic cell therapy (FIT project)​

  • Partnership with Cardiff University (UK) to investigate the  molecular and cellular interactions that underlie genetic risk for psychiatric conditions​

  • Active membership in the European Rare Disease Alliance (ERDERA), European mitochondrial society (EuroMIT), Dutch communities for Neuromuscular(SZN) and Metabolic (ESN) diseases.

  • FIT Project

  • Patient-centered by active involvement of patients and patient-societies (Voor Sara, LAMA2-Europe, Ride4Kids, Join4Energy) in our therapeutic research.

  • Part of the biotech ecosystem in the RegioMR with a spin-out of the UM, supported by Brightlands.

Members:

Clingen

Bioinformatics

The Research Theme Bioinformatics studies and develops computing science algorithms to answer biological questions. Our ambition is with each new study to find more informative answers to biological challenges. The research can roughly be divided into two subthemes: data analysis and knowledge representation. The first includes image analysis, multi-omics data integration, machine learning, network and pathways analysis, and the use of large-language models. The second includes the use of open standards, like knowledge graphs, ontologies, and linked, and the development of innovative knowledge bases.

Our research focuses on:
· Biological and chemical knowledge presentation
· Integration of knowledge and experimental data
· Sharing of data and knowledge, for reuse and education
· Applications in metabolism, rare diseases, drug repurposing, and toxicology and safety

Our approach
Our approach is based on open science principles: collaboration, inclusiveness, transparency, and scientific quality. This is done by controlling and minimizing error, open licensing, FAIR principles, systematic adoption of the most demanding community standards, and routinely applying these to new biological questions.

Our laboratory where we run our experiments is oriented around multiple local and international projects, including:

· Knowledge bases and Linked Data: WikiPathways, AOP Wiki RDF, ChEMBL RDF, SBD4Nano
· Webservices: BridgeDb, ArrayAnalysis, Virtual Human Platform, Scholia
· Research software: BridgeDb, Chemistry Development Kit (CDK), BioDataFuse, CyTargetLinker, R-ODAF, ToxTempAssistant
· Bioinformatics education at FHML and FSE

Collaboration and networks
· Collaboration with other TGX Themes and other Maastricht University Departments
· Active membership in ELIXIR Europe and contributions of several services
· Contribution of bioinformatics education to BioSB
· Collaborations with other bioinformatics centers, including the SIB and EBI
· Coordination of various international open science projects, like the CDK and WikiPathways
· Co-organizer of the ByteMAL symposium (Maastricht, Aachen, Liege)
· Co-organizer of the BioSB conference in 2026 (TGX and MaCSBio)
· Advisory roles in international bodies like IUPAC, NFDI, and OECD
· Participation in (inter)national research consortia, currently including VHP4Safety, TGX-MAPr, NUTRIOME and ERDERA

Members:

bio

Omics- and in vitro models

In vitro models and Omics
The in vitro models and Omics theme aims to advance the understanding of human biology and disease by integrating innovative cell and tissue models with state-of-the-art omics technologies. By combining advanced in vitro systems with high-throughput sequencing approaches and phenotypic analyses, in vitro models and Omics seeks to translate molecular insights into improved disease modelling, toxicity assessment, and personalized therapeutic strategies. 

Our research focuses on: 

  • Development and application of advanced cell and tissue models of muscle, liver, brain, heart, and colon;
  • Investigation of cellular and organ behaviour under physiological and disease conditions;
  • Personalized, preclinical testing of therapeutic interventions using patient-derived tissue models (with a focus on muscle);
  • Development of next-generation cell models that better capture the complexity of human tissues.

Our approach 
A central principle of our work is that human diseases and therapeutic responses are best understood in biologically relevant model systems. We therefore combine innovative cell and tissue engineering approaches with comprehensive (single-cell) omics technologies. 

To study these complex systems, we apply a broad range of sequencing-based omics approaches using the Illumina NovaSeq platform, enabling: 

  • In-depth analysis of gene regulation and molecular pathways,
  • Identification of disease mechanisms and toxicity pathways,
  • Evaluation of therapeutic efficacy in preclinical models,
  • Integration of multi-omics data to gain systems-level insights. 

Collaboration and networks 

Members

omics