PEOPLE

Aurélie Carlier

Principal Investigator

Aurélie Carlier is associate professor at the Maastricht Centre for Systems Biology and Bioinformatics (MaCSBio), the Netherlands. She received her MSc in Biomedical Engineering in 2010 and her PhD degree in Biomedical Engineering in 2014, both at the KU Leuven, Belgium. During her PhD she also visited the Systems Biology Laboratory at the Johns Hopkins University in Baltimore, USA. Her research interests encompass the multiscale computational modelling of biological processes, with a particular focus on bone tissue engineering applications and cell-biomaterial interactions. Her research achievements have been awarded with a number of distinctions, including the Student Award of the European Society of Biomechanics (ESB, 2012), the Reinhart Heinrich Doctoral Thesis Award by the European Society for Mathematical and Theoretical Biology (ESMTB, 2015) and the Best Doctoral Thesis Award by the European Society of Biomechanics (ESB, 2015). She has also been elected as member of the Tissue Engineering Young Investigator Council (TEN YIC, 2016) and was also New Scientist Wetenschapstalent 2021 finalist. She received a prestigious VENI (2016) and VIDI (2025) career development grant from the Dutch Science Foundation, Dutch Kidney Foundation Success Accelerator grant (2021) and an ERC STG (2024) to develop new methodologies for automated model construction. She has been member of the ESB council for >6 years, currently in the role of Treasurer. Besides her research, she is co-founder of FEM (Female Empowerment Maastricht University), a network to discuss and tackle gender issues.

Leyla Noroozbabaee

Post doctoral fellow

leyla.noroozbabaee@maastrichtuniversity.nl

Leyla Noroozbabaee is a Research Fellow at the Maastricht Centre for Systems Biology and Bioinformatics (MaCSBio), Faculty of Science and Engineering, Maastricht University, the Netherlands. Her research focuses on computational biophysics and multiscale mechanistic modeling of kidney function, with particular emphasis on transporter-mediated toxin dynamics and bioartificial kidney systems.

She obtained her PhD in Computational Biophysics from the University of Waikato, New Zealand (2016), where she investigated the effects of anesthetic drugs on brain activity using mathematical modeling approaches. She subsequently held a Postdoctoral Research Fellow position at the University of Auckland (2019–2023), where she led the development of a modular and reproducible computational kidney model integrating experimental and theoretical insights.

Her current work centers on the development of physiologically based and mechanistic models to study toxin and drug transport in kidney and in bioartificial kidney devices. She combines parameter estimation, uncertainty quantification, and data integration techniques to bridge experimental observations with predictive modeling.

Her research aims to support the design and optimization of next-generation renal therapies and to improve the understanding of disease mechanisms in conditions such as chronic kidney disease, hypertension, and diabetes.

Matilde Marradi

PhD Candidate

matilde.marradi@maastrichtuniversity.nl

Matilde is from Italy and she studied Biomedical Engineering at Politecnico di Milano. Her Master’s degree focused on Biomechanics and Biomaterials. The course of study was centered in deeply understanding of mechanics

of both hard and soft biological tissues, including fluid dynamics. The second year was mainly dedicated to computational modelling of biological processes. Matilde graduated with a thesis entitled "A patient-specific agent-based modeling framework of restenosis after balloon angioplasty in a superficial femoral artery - effects of mechanical damage and hemodynamics on cellular dynamics". In August 2023, she joined MERLN for her PhD work, within the framework of the Material Driven Regeneration (MDR) consortium. The aim of her project is to develop in silico multiscale models to simulate cell-ECM interactions and fibrotic tissue remodeling.

Iga Skorupska

PhD Candidate

iga.skorupska@maastrichtuniversity.nl

Iga, originally from Poland, completed her Bachelor's degree in Data Science and Artificial Intelligence. Fascinated by intricate biological systems, she decided to continue her educational journey with a Master's in Systems Biology. Iga is now starting her Ph.D., focusing on Computational Modeling of cAMP Signaling in the context of Alzheimer's disease. Therefore, her research interest lies in uncovering the complexities of the brain on cell level and its connection to this challenging condition. Her PhD is a disciplinary project between MHeNs/ BIOMED (experimental work) and MERLN (computational work).

Yağmur Dogay

PhD Candidate

yagmur.dogay@maastrichtuniversity.nl

Yağmur is from Cyprus and she studied Biomedical Science at The University of Hull. She completed her master's degree in Data Science for Life Sciences at Hanze University of Applied Sciences. After completing her master's, she joined Trinity College Dublin/ ADAPT Centre, where she first worked on the HELICAL project and later contributed to the PARADISE project. Both projects focused on ANCA vasculitis. In April 2025, she joined MERLN for her PhD work and the focus of her work is Automated Knowledge Graphs for Kidney Physiology and Pathology.

Ali Aslan

PhD Candidate

ali.aslandemir@maastrichtuniversity.nl

aliadem@uio.no

Ali Aslan is from Turkey and is currently a visiting PhD researcher in the Carlier In Silico Lab at MERLN. He is pursuing his PhD at the University of Oslo, where his work combines biomineralization, biophysics, and computational modeling. He holds a bachelor's degree in physics from Middle East Technical University and a master's degree in Photonics from İzmir Institute of Technology, where he focused on computational imaging techniques (in-line lensless holography for cellular characterization). His current research aims to understand how bone forming cells differentiate to form biominerals within 2D and biomimetic hydrogel systems. By integrating experimental findings with cellular automaton–based models, he aims to evaluate the osteogenic potential of cells and build predictive frameworks for bone tissue engineering applications.

Alumni

Post-doctoral Researchers

Sangita Swapnasrita (2024) Sorbent-Assisted Continuous Flow Peritoneal Dialysis in silico
Hamidreza Jafarinia(2025) Modeling the cell-ECM interface using different computational techniques

PhD Candidates

Zeynep Karagöz (2024) Dynamic computational models of cell-extracellular matrix and cell-cell interactions
Jasia King (2022) Understanding toxin transport in the proximal tubule: coupling in vitro experiments with computational simulations
Kerbai Said Eroume (2021) In silico modelling of cell shape induced behavior - In silico modeling of cell shape induced behavior.

Master Students

Henrike Schulze (2023) Computational modeling of macrophage-fibroblast crosstalk.
River Hummel (2023) Image analysis of stretch-activated neuronal growth.
Honasoge K. (2022) Computational modeling of the force-dependent focal adhesion assembly and disassembly
Vanmeulebrouk C. (2022) Computational modeling of cAMP signalingng Computational modeling of cAMP signaling
Al-Baz A. (2022) Computational modeling of sodium handling in proximal tubule during menstrual cycles
Robeerst L. (2021) Computational model of cadherin-RTK crosstalk
Wagner A. (2021) Computational modeling of integrin adhesome dynamics
Vandelaer L. (2020) Stability analysis of cell polarization models
Gonzalez Ovalle A. (2020) Virtual Cell computational modelling of cAMP and phosphodiesterase signalling
Gomes Carvalho de Abreu M. (2020) Modeling TGF-β signaling
Hermans S. (2020) Computational modeling of cAMP signaling
Callens B. (2020) Computational modeling of cadherin signaling
Marques R. (2020) On the influence of hormonal levels on fallopian tube function: a computational study
Bengtsson del Barrio L. (2019) Regulation of mesenchymal stem cell nuclear architecture by micro-topographies
Nikody M. (2019) Optimisation of a proximal-tubule-function-on-chip device: unravelling toxin removal in the nephron
Shen F. (2018) In silico modeling of the YAP-TAZ signaling pathway
Wijnen I. (2017) Investigating mechanotransduction pathways involved in topography-induced cell behavior – the effect of cell culture conditions on EGR-1 and FOS expression
Van Steen B. (2017) Touch and go – topography induced changes in speed and direction of cell migration
Ricca V. (2015) In silico modeling of BMP driven bone formation
Homayounfar A. (2015) Mathematical modeling of blood flow
Jacobs M. (2014) Mathematical modeling of angiogenesis during tumor growth

Bachelor Students

Wiktoria Muzsik(2025)Developing a computational model to investigate toxin dynamics in the bioartificial kidney.
Jan Đurović(2025)Investigating the role of ERK signaling in ion channel regulation within the context of Alzheimer’s disease.
Lisa Robben(2025) Correcting metabolic tasks for a Genome-Scale Metabolic Model
Tess Ley (2024) Computational Modelling of P-Cresyl Sulfate Transport via OAT1 in the Human Proximal Tubule
Sakshi Mangala (2024) Computational Modelling of Sorbent-Assisted Peritoneal Dialysis: Modelling Blood Solute Concentrations for Improved Dialysis
Marjolein Ligtvoet (2024) Demographic Analysis of Sorbent-Assisted Peritoneal Dialysis
Andrea Pascaud (2023) Computational modeling of fibrosis
Liv Konrad (2023) Exploring sex differences in toxin transport kinetics in silico
Tien Pham (2023) Modeling sorbent-assisted peritoneal dialysis
Roy Erzurumluoğlu Roy (2023) Determining drug-toxin interaction kinetics via a combined in silico-in vitro approach

Harms M. (2022) Computational modeling of stretch-activated neuronal growth.
Loncol M. (2022) Modeling implant induced fibrosis.
Escarda-Castro E. (2021) Computational model of stretch-activated neuronal signaling.
Donis T. (2020) Computational modeling of isoform-specific PDE influence on cyclic cAMP input
Tomás AR. (2016) Profiling natural and synthetic surface topographies of osteogenic biomaterials

Visiting Researcher

Sakip Önder (2025) work on studying the impact of magnesium on bone healing mechanisms, particularly its role in immunomodulation, using an in silico approach

Collaborations

We work with a lot of wonderful scientists from around the world. We look forward to have a chat if you think we have common interests!

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