From human cellular atlases to human experimental models
We integrate single-cell and spatial omics with patient-derived human models to uncover how mucosal tissues are organized, disrupted in disease, and restored.
The LMB Discovery Framework
Our research follows a continuous framework that transforms observations from human tissues into mechanistic insights and translational opportunities through cellular atlases, systems biology and atlas-guided human experimental models.
Human Tissues
Human Cellular Atlases
Systems Biology
Human Experimental Models
Mechanistic Discovery
Translation
Research Highlights
INTERNATIONAL CONSORTIA
Selected studies highlighting our contributions to international collaborative efforts.
Human Gut Cell Atlas Roadmap
A coordinated framework for building a comprehensive, spatially resolved atlas of the human gastrointestinal tract.
Nature Reviews Gastroenterology Hepatology (2023)
RNA-Rescue Spatial Transcriptomics
A spatial transcriptomics workflow enabling robust transcriptomic profiling of degraded and challenging tissue samples.
Nature Communications (2023)
Regional Epithelial Programs in GI Disease
Single-cell and spatial transcriptomics define region-specific epithelial programs and reveal how they are remodeled in GI disease.
Preprint – ResearchSquare (2025)
RESEARCH FROM OUR LAB
Selected studies highlighting research developed within the Laboratory of Mucosal Biology.
Regional Epithelial Programs in GI Disease
Single-cell and spatial transcriptomics define region-specific epithelial programs and reveal how they are remodeled in GI disease.
Preprint – ResearchSquare (2025)
Hydrogen Sulfide Protects the Intestinal Barrier
Hydrogen sulfide restores cytokine-induced epithelial barrier dysfunction by enhancing mitochondrial oxidative phosphorylation.
Scientific Reports (2026)
Cirrhosis Associated Immune Dysfunction
Cirrhosis disrupts the intestinal immune barrier through loss of CCR9⁺ intraepithelial lymphocyte compartmentalization.
bioRxiv (2026)
LMB at a Glance
A snapshot of the people, platforms and human data that power our research.
2022
Established
€2M+
Research Funding
1M+
Single Cells Mapped
50+
Organoid Lines
15+
Collaborators
Our Research
Our research integrates human cellular atlases, patient-derived models and systems biology to uncover the mechanisms that govern mucosal health and disease.
Human Cellular Atlases
Building comprehensive cellular reference maps of human tissues across health and disease.
Atlas-Guided Human Models
Developing patient-derived human organoid models guided by cellular atlases to investigate tissue biology and disease.
Mucosal Systems Biology
Deciphering how epithelial, immune and microbial interactions shape tissue homeostasis and disease.
Our Team
Our team combines expertise in experimental biology, single-cell and spatial omics, computational biology, and human organoid systems to advance our understanding of human mucosal biology.
Laboratory Leadership
Alexandre Denadai-Souza
Principal Investigator
Building human cellular atlases that guide the next generation of human experimental models.
Research Focus
We build human cellular atlases and use them to develop atlas-guided human experimental models that uncover the mechanisms governing mucosal health and disease across the gut–liver axis.
Expertise
PhD Researchers
Matthias van Sligtenhorst
PhD Candidate
Research Focus
Developing and applying patient-derived organoid models to investigate epithelial biology, tissue homeostasis and diseases of the gut–liver axis.
Expertise
Femke van Geest
PhD Candidate
Research Focus
Investigating the role of long non-coding RNAs in cellular metabolism using advanced molecular biology approaches.
Expertise
Shi Gao
PhD Candidate
Research Focus
Novel bile acid immunoregulatory networks in chronic inflammatory disease
Expertise
Justine Fiefvet
PhD Candidate (co-supervision)
Research Focus
Developing advanced multicellular models to understand tissue regeneration in health and its impairment in disease.
Expertise
Gabriel Henrique Caxali
PhD Candidate (International Scholar)
Research Focus
Using computational biology to understand colorectal cancer progression and liver metastasis.
Expertise
Master's Students
Vedika Kapoor
Master’s student
Research Focus
Developing intestinal organoid models that preserve regional identity to study tissue function in health and disease.