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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
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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
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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
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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
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Raz, Yotam (author), van den Akker, E.B. (author), Roest, Tijmen (author), Riaz, Muhammad (author), van de Rest, Ondine (author), Suchiman, H. Eka D. (author), Lakenberg, Nico (author), Stassen, Stefanie A. (author), Reinders, M.J.T. (author)Skeletal muscles control posture, mobility and strength, and influence whole-body metabolism. Muscles are built of different types of myofibers, each having specific metabolic, molecular, and contractile properties. Fiber classification is, therefore, regarded the key for understanding muscle biology, (patho-) physiology. The expression of...journal article 2020
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Kwakkel, J.H. (author)Even though real options analysis (ROA) is often thought as the best tool available for evaluating flexible strategies, there are profound problems with the assumptions underpinning ROA rendering it unsuitable for use in supporting planning and decision-making on climate adaptation. In the face of dynamic and deep uncertainty about the future...journal article 2020
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Anyansi, C.A. (author), Keo, D. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Manson, Abigail L. (author), Earl, Ashlee M. (author), Abeel, T.E.P.M.F. (author)Background: Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In...journal article 2020
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Anyansi, C.A. (author), Straub, Timothy J. (author), Manson, Abigail L. (author), Earl, Ashlee M. (author), Abeel, T.E.P.M.F. (author)Metagenomic sequencing is a powerful tool for examining the diversity and complexity of microbial communities. Most widely used tools for taxonomic profiling of metagenomic sequence data allow for a species-level overview of the composition. However, individual strains within a species can differ greatly in key genotypic and phenotypic...review 2020
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Rentroia Pacheco, Barbara (author)Due to their altered genetic context, cancer cells can become dependent on specific genes for their survival. Such cancer-specific dependencies may represent promising therapeutic targets. However, knowledge on which molecular features of cancer cells induce specific dependencies is still limited and hampers the development of effective targeted...master thesis 2019
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van Dijk, Mick (author)Global medical use of azole antifungals and echinocandins has led to an enormous increase in resistant <i>Candida</i> species, that are most commonly associated with fungal infections. A possible mechanism causing resistance are single or simultaneous point mutations in the genes responsible for encoding antifungal target enzymes. The aim of...master thesis 2019
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Allahyar, A. (author)In the last two decades, our understanding of the molecular mechanisms within the cell has witnessed a great leap forward. For the most part this is due to the fast innovation of the genomic measurements technologies and wide spread usage of computational methods which enables knowledge extraction from the massive datasets produced by these...doctoral thesis 2018
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Uljee, Jasper (author), de Vries, Yorick (author)Accurate diagnosis and treatment of patients infected with multiple strains of a pathogen is a challenging task. The use of whole genome sequencing techniques provide high potential to give proper insight into the microbial composition of human metagenomic samples. Distinguishing multiple strains of a certain species is difficult due to the high...bachelor thesis 2018
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van Dijk, Lucas (author)Capturing all genetic variation within a polyploid organism is a challenge. Most current de novo assemblers have no notion of the concept “ploidy”. Consequently, when assembling the genome of diploid or higher ploidy organisms, the assembler mixes reads coming from either chromosome copy and builds a single DNA sequence representing an arbitrary...master thesis 2017
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Thomaidou, Eftychia (author)In this research, we studied the impact of the 5'UTR sequences on translation. This is done by generating various features describing the 5'UTR. Those features are then used as input in regression and classification models, that have the Translation Initiation Rates as target. The reason why it is of such importance, is dual. Because is very...master thesis 2017
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van Gelder, Celia W.G. (author), Hooft, Rob W.W. (author), van Rijswijk, Merlijn N. (author), van den Berg, Linda (author), Kok, Ruben G. (author), Reinders, M.J.T. (author), Mons, Barend (author), Heringa, Jaap (author)This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics...journal article 2017
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van Unen, Vincent (author), Höllt, T. (author), Pezzotti, N. (author), Li, Na (author), Reinders, M.J.T. (author), Eisemann, E. (author), Koning, Frits (author), Vilanova Bartroli, A. (author), Lelieveldt, B.P.F. (author)Mass cytometry allows high-resolution dissection of the cellular composition of the immune system. However, the high-dimensionality, large size, and non-linear structure of the data poses considerable challenges for the data analysis. In particular, dimensionality reduction-based techniques like t-SNE offer single-cell resolution but are...journal article 2017
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)DNA read alignment is a major step in genome analysis. However, as DNA reads continue to become longer, new approaches need to be developed to effectively use these longer reads in the alignment process. Modern aligners commonly use a two-step approach for read alignment: 1. seeding, 2. extension. In this paper, we have investigated various...conference paper 2016
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Van Dyk, H.O. (author), Hoogstraat, M (author), ten Hoeve, J (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)The frequent recurrence of copy number aberrations across tumour samples is a reliable hallmark of certain cancer driver genes. However, state-of-the-art algorithms for detecting recurrent aberrations fail to detect several known drivers. In this study, we propose RUBIC, an approach that detects recurrent copy number breaks, rather than...journal article 2016
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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array...conference paper 2015
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Timal, N.R.N. (author)Detecting similarities between (RNA, DNA, and protein) sequences is an important part of bioinformatics. Among the algorithms used to accomplish this, the Smith-Waterman algorithm is very popular. A sequential implementation of Smith-Waterman requires quadratic running time with respect to the length of the sequences. As the amount of data in...master thesis 2015