Molecular Developmental Biology

Developmental Mechanisms Group
 

Gert Jan Veenstra

The group of Gert Jan Veenstra studies molecular mechanisms underlying stem cell differentiation and heart development, focusing on the dynamic changes in heart cells across the different time spans of embryonic development, adult life (disease), and evolution. The group examines heart development in different species and human stem cell-based models to understand fundamental principles of developmental competence and self-organisation, and the relationship between evolution and development. Deep conservation and differences among species are equally instructive to understand the heart better. With clinical partners, we also study tissue remodelling in human heart disease. By studying chromatin, gene regulation, and single cell trajectories, we aim to uncover fundamental biological principles and discover new avenues for treating disease and advancing regenerative medicine.  

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Computational Approaches to Understand Transcription Regulation Group

Simon van Heeringen

The group of Simon van Heeringen combines computational approaches with experimental data to unravel the intricate mechanisms that govern gene regulation and aims to shed light on the underlying processes that drive development, differentiation, and diseases. The research covers the interplay between primary DNA sequence and epigenetic mechanisms and their control of gene expression in two major themes: regulatory sequence analysis, and computational epigenetics.

Epidermal Stem Cell Fate Decisions Group

Klaas Mulder

The group of Klaas Mulder is dedicated to investigating the mechanisms underlying human skin stem cells renewal & differentiation. They focus on studying the epigenetic machinery, which involves chemical modifications of DNA and the role of non-coding RNA molecules. By exploring how different genes and cellular processes work together, they aim to uncover the secrets behind the robustness and precision of biological systems.

Comprehensive Model of Cell Behaviour Group

Rosemary Yu

The group of Rosemary Yu focuses on developing tools and mathematical models to understand the connections between gene expression, metabolism, and how cells function in both healthy and diseased states. We take a "vertical" approach, which means we aim to build a comprehensive model of cell behaviour at the molecular level. This model would allow us to simulate different cellular states and predict new strategies for treating diseases that may not have been obvious before. These predictions can then be tested in experiments.

Cell Fate Decisions of Epithelial Development and Disease Group

Jo Zhou

The group of Jo Zhou focuses on elucidating the fundamental mechanisms underlying stem cell fate determination, proliferation and differentiation, which are pivotal to human development and diseases pathology. Leveraging systems biology methodologies, including (single-cell) multi-omics and computational integrative analyses, we investigate gene regulation in human stem cells and derived organotypic models, in both healthy and diseased states. Through these studies, we uncover fundamental insights into the regulatory circuitry and mechanisms in stem cells, and offer powerful and effective tools for tissue regeneration and therapeutic intervention.

About Zhou's group

The Computational and Systems Biology Group

Federico Bocci

The group of Federico Bocci employs theoretical, computational, and bioinformatics tools to understand how cell fate is regulated in time and space, and how decisions about cell fate are propagated via cell-cell and cell-environment interactions. Using these multiscale models, we aim to address questions about causality in biology, regulatory networks underlying cellular decision-making, and the flow of information across biological scales.