- document
-
Mokveld, T.O. (author)Genomics is a field devoted to understanding the differences in genetics between populations, individuals, and even within individuals. By constantly comparing and contrasting data from diverse sources, genomics can refine our understanding of life and identify new ways to improve our lives. However, this often presents technical and biological...doctoral thesis 2023
- document
-
Agrawal, Isha (author)Metagenomic Next-Generation Sequencing (mNGS) presents a promising avenue to generate massive volume of sequence reads in a short period of time. This has opened opportunities for disease diagnosis based on individual variations and mutations by considering the microbiome profile of each patient. However, the effective use of this data requires...master thesis 2023
- document
-
d' Abreu de Paulo, Gedeon (author)Cancer is one of the leading causes of death in the world. While there have been many studies investigating the development and progression of cancer in human tissues using host omics data or microbial data, there is a lack of research combining both types of data, even though both modalities have been shown to affect cancer morphology and...master thesis 2023
- document
-
van Graft, Tijmen (author)Metabolic engineering is an important field in biotechnology, aimed at optimizing cellular processes to produce desired compounds. In this thesis, we focus on predicting the metabolome from the proteome, as understanding this relationship is crucial for understanding cellular metabolism. We investigate the usage of additional biological...master thesis 2023
- document
-
Sharman, Kavya (author), Patterson, Nathan Heath (author), Weiss, Andy (author), Neumann, Elizabeth K. (author), Guiberson, Emma R. (author), Ryan, Daniel J. (author), Gutierrez, Danielle B. (author), Spraggins, Jeffrey M. (author), Van de Plas, Raf (author), Skaar, Eric P. (author), Caprioli, Richard M. (author)Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate...journal article 2023
- document
-
Florescu, Stefanos (author)Over the past 20 years, the cost of sequencing genomes has reduced drastically. As DNA data grows at an unprecedented rate, the need for fast and affordable software and hardware solutions for DNA analysis is higher than ever. A critical and time-consuming component in any DNA analysis pipeline is sequence alignment, which refers to mapping...master thesis 2022
- document
-
Drummer, Francesca (author)Single-cell sequencing allows measuring individual cells' molecular features and their responses to perturbations. Understanding which cells respond to a particular perturbation and how these responses vary across populations can be used to, for example, improve vaccine immunogenicity. However, an exhaustive exploration of single-cell...master thesis 2022
- document
-
Keukeleire, Pia (author)Cell-free DNA (cfDNA) are DNA fragments originating from dying cells that enter the plasma. Uncontrolled cell death, for example caused by cancer, induces an elevated concentration of cfDNA. As a result, determining the cell type origins of cfDNA can provide information about an individual's health. This research looks into how to increase the...master thesis 2022
- document
-
van der Toorn, Eric (author)Next-Generation Sequencing (NGS) has made it possible to perform metagenomic sequencing of environmental microbiome samples. Colorectal cancer (CRC) benefits from early detection, and many studies find correlations between disease presence and abundance of species in samples of the microbiome. However, these studies are hard to reproduce and...master thesis 2022
- document
- Mikuš, Matus (author) master thesis 2022
- document
-
Ma, Yunjian (author), Liang, Hongjing (author), Zhao, Zexin (author), Wu, Bin (author), Lan, Dongming (author), Hollmann, F. (author), Wang, Yonghua (author)Unspecific peroxygenases (UPOs, EC 1.11.2.1) are promising oxyfunctionalization catalysts because of their unique stereoselectivity. However, so far only a few UPOs have been reported. In this study, gene mining was used to identify a gene from Galerina marginata that coded for a novel UPO (GmaUPO). GmaUPO was expressed in Pichia pastoris X...journal article 2022
- document
-
Bogaards, Fatih A. (author), Gehrmann, Thies (author), Beekman, Marian (author), van den Akker, E.B. (author), van de Rest, Ondine (author), Hangelbroek, Roland W.J. (author), Noordam, Raymond (author), Mooijaart, Simon P. (author), Reinders, M.J.T. (author)The response to lifestyle intervention studies is often heterogeneous, especially in older adults. Subtle responses that may represent a health gain for individuals are not always detected by classical health variables, stressing the need for novel biomarkers that detect intermediate changes in metabolic, inflammatory, and immunity-related...journal article 2022
- document
-
Hinrichs-Krapels, S. (author), Ditewig, Bor (author), Boulding, Harriet (author), Chalkidou, Anastasia (author), Erskine, Jamie (author), Shokraneh, Farhad (author)Objectives To systematically review academic literature for studies on any processes, procedures, methods or approaches to purchasing high-cost medical devices and equipment within hospitals in high-income countries. Methods On 13 August 2020, we searched the following from inception: Cost-Effectiveness Analysis Registry, EconLit and ProQuest...review 2022
- document
-
Anyansi, C.A. (author)This thesis represents one small step in the battle with TB, where we apply WGS approaches to explore different topics of TB research. Here we offer the global community a method to diagnose complex TB infections consisting of multiple distinct strains. We show that this functionality is necessary and has been overlooked by the TB community in...doctoral thesis 2021
- document
-
Ruighaver, Ewoud (author)In recent years the advent of multi-omic techniques have shown great promise in the field of oncology. In light of these advancements, this thesis focuses on the use of multiple data types to find methylation markers around transcription start site regions for colorectal cancer in the cell-free DNA (cfDNA) domain. It combines several methods of...master thesis 2021
- document
-
Abdelaal, T.R.M. (author)Single-cell technologies have emerged as powerful tools to analyze complex tissues at the single-cell resolution, resolving the cellular heterogeneity within a tissue through the discovery of different cell populations. Over the past decade, single-cell technologies have greatly developed allowing the profiling of various molecular features...doctoral thesis 2021
- document
-
Singh, Akash (author)Single-cell multi-modal omics promises to open new doors in bioinformatics by measuring different aspects of cells, thus offering multiple perspectives on the underlying biological phenomenon. Although simultaneous multi-modal measurement protocols do exist, their inherent technical limitations necessitate focus on single modality measurements....master thesis 2021
- document
-
Salami, Nima (author)Context: The study and analysis of (meta-)genomics have been providing scientists with valuable insights into the functioning and composition of microbial communities. Latest advancements in next-gen and high throughput sequencing technologies have resulted in significant growth in the data produced and made available for further research. These...bachelor thesis 2021
- document
-
Makrodimitris, S. (author)Billions of people world-wide rely on plant-based food for their daily energy intake. As global warming and the spread of diseases (such as the banana Panama disease) is substantially hindering the cultivation of plants, the need to develop temperature- and/or disease-resistant varieties is getting more and more pressing. The field of plant...doctoral thesis 2021
- document
-
Agahari, W. (author)Data sharing facilitated by data marketplaces enable companies to generate meaningful insights and discover new opportunities. However, enterprises are reluctant to share data over platforms due to lack of trust, fear of losing control over data and concerns regarding privacy violations. Multi-party computation (MPC) is a cryptographic technique...conference paper 2020