Traditional drug discovery approaches have been hampered by (in vitro) cell-culture models that poorly represent the situation in the human body.

Promotor: B. van de Water, Co-promotor: E.H.J. Danen

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

There is an urgent need for more physiologically relevant cell culture methods to guide compound selection in pre-clinical stages of the drug development pipeline.

Promotor: Prof.dr. J.N. Kok

Pharmaceutical companies, governments and the general public have become increasingly aware that animal models used in drug testing lack vital aspects to serve as an accurate representation of human biology. As models of the human body should become more physiologically relevant, animal models no longer…

Endothelial dysfunction and microvascular diseases are key drivers of cardiovascular disease, the world's leading cause of death.

In design optimization problems, engineers typically handcraft design representations based on personal expertise, which leaves a fingerprint of the user experience in the optimization data. Thus, learning this notion of experience as transferrable design features has potential to improve the performance…

Optical projection tomography (OPT) is a tomographic 3D imaging technique used for specimens in the millimetre scale.

A new type of tripodal squaramide-based supramolecular hydrogels is developed and studied.

In this thesis, we investigate how deep generative models (AI models that can create new designs) can be better utilized for technical and industrial design. Our goal is to generate designs that are not only realistic (plausible), but also efficient, reliable, and usable in complex 2D and 3D applica…

Promotor: Prof.dr. J.N. Kok, Co-promotor: F.J. Verbeek

De onderzoeksgroep Digital Archaeology beheert twee computerlaboratoria voor verschillende doeleinden: een onderwijslab en een onderzoekslab.

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.

This thesis tackles the difficulty of predicting the liver’s clinical response to novel therapies, a challenge arising from interspecies differences and limitations of existing in vitro models.

Promotor: Roeland M.H. Merks

Professor Jan Pieter Abrahams gaat onderzoek doen naar de 3D structuur van biomoleculen om uiteindelijk ziektes als tuberculose, malaria en kanker beter te kunnen begrijpen. Hiervoor heeft de Technologiestichting STW een subsidie toegekend van € 25.000,-

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.

We have studied shape with a particular focus on the zebrafish model system. The shape is an essential appearance of the phenotype of a biological specimen and it can be used to read out a current state or response or to study gene expression.

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 hebben Universitaire Medische Centra (UMC's) van Nederland de zelfevaluatie-tool ontwikkeld gebaseerd op het PhD Competence Model. Onze partners van de Universiteit Utrecht stellen een digitale versie van de tool kosteloos beschikbaar voor onze promovendi binnen de Universiteit Leiden, ook voor…

Promotor: Prof.dr. E. Deprettere

De Leidse promovendus Sreenivasa Ramaiahgari ontwikkelde voor het eerst een 3D-model van de lever. Zijn model kan een hoop besparen: schade bij patiënten, dierenleed en veel geld. Promotie 4 juni.

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

Het LLMC is een Leids expertisecentrum dat kennis over taal en AI inzet om het gebruik van taalmodellen verantwoord, transparant en effectief te maken.

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…

During the development of the (human) body from a single fertilized egg, organs and structures must form. The development and growth of biological forms is called morphogenesis.

Promotor: Prof.dr. V. Icke, Co-Promotor: T.I. Madura

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

Breast cancer (BC) is a clinically and biologically heterogeneous disease.

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

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

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.

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…

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.

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…

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

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.

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

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

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

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.

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…