Searched for: subject%3A%22bioinformatics%22
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Shahroodi, T. (author)
Modern applications like Genomics and Machine Learning (ML) hold the potential to reshape our understanding of diseases’ genetic origins and guide machines in executing tasks and making predictions without our explicit programming. The successful, widespread integration of these modern applications can usher in advancements in di-agnostics,...
doctoral thesis 2024
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Firtina, Can (author), Pillai, Kamlesh (author), Kalsi, Gurpreet S. (author), Suresh, Bharathwaj (author), Cali, Damla Senol (author), Kim, Jeremie S. (author), Shahroodi, Taha (author), Cavlak, Meryem Banu (author), Lindegger, Joël (author)
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented as graph structures, where states and edges capture modifications (i.e., insertions, deletions, and substitutions) by...
journal article 2024
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van der Voort, Niels (author)
Heart rate data and other data collected by consumer-grade wearable devices can give away quite useful information about the user. It can for example be used by machine learning algorithms such as Deep Neural Networks (DNN) to learn patterns about cardiovascular disease and fitness, or be used for identification. Heart rate patterns can also...
bachelor thesis 2023
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Das, Aratrika (author)
Type 2 Diabetes is a very prevalent disease in current times and leads to significant adverse effects. Recently, there has been a growing interest in the association of the human gut microbiome with respect to chronic diseases like Type 2 Diabetes with the aim to identify biomarkers. In this study, we researched the effect of different machine...
bachelor thesis 2023
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Dorrestijn, Eljo (author)
Horizontal gene transfer (HGT) trough plasmids is one of the main contributors to the rapid increase of antimicrobial resistance (AMR). Studying wastewater from wastewater treatment plants (WWTPs) allows us new insights into HGT as bacteria from different sources come together. Currently the analysis of HGT is limited, as plasmids cannot be...
master thesis 2023
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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
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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
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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
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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
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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
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Simons, L.P.A. (author)
Four areas make up 75% of our healthcare costs: cardio-, onco-, neuro- and metabolic diseases. These are largely preventable, even reversible. Instead, they are currently often ‘managed’ and made chronic, not cured. This is too costly. Research is showing new opportunities for enhancing our body’s self-repair in a matter of hours or days. Our...
journal article 2023
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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
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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
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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
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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
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Mikuš, Matus (author)
master thesis 2022
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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
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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
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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
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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
Searched for: subject%3A%22bioinformatics%22
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