We strive to address the challenge of constructing a modeling language to write software which can take advantage of recent hardware developments (multicore, cloud) without compromising in its abstraction levels.

Promotor: Roeland M.H. Merks

Epithelial-mesenchymal plasticity (EMP) and tumor cell migration play an important role in cancer progression, and an improved understanding of the mechanisms underlying these concepts is essential for developing new targeted approaches.

Mathematical models of software systems enable characterizations, abstractions, simulations, and analysis of complex software during its development.

Real-life processes are characterized by dynamics involving time. Examples are walking, sleeping, disease progress in medical treatment, and events in a workflow.

In 2016, Dutch University Medical Centres (UMCs) developed the self-evaluation tool based on the PhD Competence Model. Our partners at Utrecht University are making a digital version of the tool available free of charge for our PhD candidates at Leiden University, including for candidates who are not…

Promotor: Prof.dr. E. Deprettere

Existing work in probabilistic language modeling can be mostly divided into two categories:

Promotores: Prof.dr. P.C.W. Hogendoorn & Prof.dr. H.P. Spaink, Co-promotor: Dr. B.E. Snaar-Jagalska

The aim of this thesis was to develop novel treatment strategies for different types of eye melanoma utilizing zebrafish models. We first establish orthotopic and ectopic xenograft models for uveal and conjunctival melanoma by engraftment of the immortalized cells derived from these tumors into zebrafish…

Immunotherapies for cancer are an emerging class of therapeutic strategies which aim to treat cancer via augmentation of the immune system.

Main challenges in skin vaccination are overcoming the stratum corneum (SC) barrier and targeting the antigen presenting cells (APC) in the epidermis and the dermis.

Arts and leisure, Arts and leisure

This research team is concerned with the measurement and modelling of behaviour, cognition, and unobserved traits (e.g., latent variables, missing data). Central aims include the distillation of a complex set of features into lower-dimensional representations (e.g., factor analysis, IRT), determining…

Industrial manufacturing processes, such as the production of steel or the stamping of car body parts, are complex semi-batch processes with many process steps, machine parameters and quality indicators.

Clinical development of drugs for central nervous system (CNS) disorders has been particularly challenging and still suffers from high attrition rates.

Death in all types of melanomas is generally caused by metastasis. Uveal melanoma (UM) is the most common intraocular melanoma, there are currently no (patient-derived) animal models that faithfully recapitulate metastatic dissemination of UM.

This dissertation studies the Asymptotics of Bayesian nonparametric inference for Gaussian linear models.

The molecular mechanisms that instigate a healthy cell to become malignant are fueled by (epi)genetic alterations in so-called driver genes.

In this thesis, we study systems of electrons in which strong correlations give rise to emergent exotic physics.

Promotor: Prof.dr. B. van de Water, Co-promotores: L.T.M. van der Ven, A.S. Kienhuis

This dissertation focuses on developing new mathematical and statistical methods to properly represent time-varying covariates and model them within the context of time-to-event analysis.

Promotor: Prof.dr. F.S. de Boer, Co-promotor: D. Clarke

Vandaag de dag liggen statistische methodes aan de grondslag van beslissingen in allerlei facetten van het leven, van de gezondheidszorg en agricultuur tot de financiële sector en marketing.

Promotor: Prof.dr. B. van de Water, Co-promotor: L.S. Price

Systems pharmacology aims to apply techniques from systems biology to pharmacological models.

Lipid formulations have demonstrated strong potential for nucleic acid delivery,particularly with the success of COVID-19 vaccines. Despite these advances, manyaspects of lipid formulations remain unclear.

To improve treatment of breast cancer patients it is important to understand all stages of breast cancer from initiation to in situ disease and progression to invasive disease. In this thesis we use intraductal injections of patient derived tissue to model ductal carcinoma in situ and invasive breast…

SDN (Software-Defined Networking) represents a revolutionary approach to network architecture that enables the dynamic and flexible management of network resources through software-based control. This dissertation introduces the idea of SDN and its southbound protocol OpenFlow, then presents the formal…

Lecture

Are predictive archaeological maps a reliable tool to play an important role in the spatial planning? One of the goals of this project was to develop best practices for the production and application of the models.

In this project, we aim to develop mathematical models to mechanistically and quantitatively predict the dynamics of cellular stress pathway activation and its relation with toxic effects when cells are exposed to various toxicants.

In this thesis, we extend the concept of null models as canonical ensembles of multi-graphs with given constraints and present new metrics able to characterize real-world layered systems based on their correlation patterns.

From surface science towards industrial practice using high-pressure scanning tunneling microscopy.

Promotor: M. Danhof, Co-promotores: J. Freijer, A. Yassen

Chemical reactions go hand-in-hand with an energy exchange with the environment in which they take place. Surfaces offer a variety of energy dissipation channels, constituted by the nuclear and electronic degrees of freedom of the atoms at the interface. Aiming at an improved future harvesting of energy,…

Lysosomal storage disorders (LSDs) are a group of orphan diseases characterized by lysosomal dysfunction or impaired lysosomal catabolism and affect collectively about 1 in 5000 live births.

ASLU 14

A research agenda

In this thesis, mathematical modeling and simulation was applied as a tool to inform quantitative decision making in oncology drug discovery and development.

Promotor: Prof.dr. W.J.G.M. Peijnenburg, Co-promotor: Dr. ing. M.G. Vijver

Growth hormone profiles are pulsatile and highly variable between individuals, limiting the implementation of mathemathical models to quantify an individual's secretion.

There is a need for alternative methods to replace, reduce and refine (3R) animal experimentation. Combining experimental data from high-throughput in vitro studies with in silico modeling is a promising approach to unravel the effect of chemicals on living cells and to gain a better understanding of…

The Agent Based Modelling for Archaeologists (ABMA) project is dedicated to developing Open Educational Resources (OERs) and accompanying materials for agent-based modelling (ABM) in Archaeology.

In this research project child language phonology is studied from the perspective of a psycholinguistic speech-production model and this model is in turn studied from the perspective of developmental phonology.

Decarbonizing the building stock is critical for realizing the climate-neutral target for the Netherlands.

Accurate prediction of the unbound drug concentration-time profile at the CNS target site is crucial for the assessment of the right drug concentration-effect relationship. PBPK models have supported the PK prediction of the CNS target sites and the translation of PK data between species and between…