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Naseri Jahfari, A. (author), Tax, D.M.J. (author), van der Harst, Pim (author), Reinders, M.J.T. (author), van der Bilt, Ivo (author)Background: Smartwatches enable continuous and noninvasive time series monitoring of cardiovascular biomarkers like heart rate (from photoplethysmograms), step counter, skin temperature, et cetera; as such, they have promise in assisting in early detection and prevention of cardiovascular disease. Although these biomarkers may not be directly...journal article 2023
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Mokveld, T.O. (author), Al-Ars, Z. (author), Sistermans, Erik A. (author), Reinders, M.J.T. (author)Background<br/><br/>Non-Invasive Prenatal Testing is often performed by utilizing read coverage-based profiles obtained from shallow whole genome sequencing to detect fetal copy number variations. Such screening typically operates on a discretized binned representation of the genome, where (ab)normality of bins of a set size is judged relative...journal article 2023
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Bouland, G.A. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets increasing exponentially and concurrent increased sparsity due to more zero counts being measured for many genes, we demonstrate here that downstream analyses on binary-based gene expression give similar results as count-based analyses. Moreover, a binary...journal article 2023
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Khan, Abdul Rehman (author), Reinders, M.J.T. (author), Khatri, Indu (author)SUMMARY: T-cell receptors (TCRs) on T cells recognize and bind to epitopes presented by the major histocompatibility complex in case of an infection or cancer. However, the high diversity of TCRs, as well as their unique and complex binding mechanisms underlying epitope recognition, make it difficult to predict the binding between TCRs and...journal article 2023
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Smit, J.M. (author), Krijthe, J.H. (author), Kant, W. M.R. (author), Labrecque, J. A. (author), Komorowski, M. (author), Gommers, D.A.M.P.J. (author), van Bommel, J. (author), Reinders, M.J.T. (author), van Genderen, M. E. (author)This scoping review focuses on the essential role of models for causal inference in shaping actionable artificial intelligence (AI) designed to aid clinicians in decision-making. The objective was to identify and evaluate the reporting quality of studies introducing models for causal inference in intensive care units (ICUs), and to provide...review 2023
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Mourragui, S.M.C. (author), Loog, M. (author), van Nee, Mirrelijn (author), de Wiel, Mark A.van (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)Motivation: Anti-cancer drugs may elicit resistance or sensitivity through mechanisms which involve several genomic layers. Nevertheless, we have demonstrated that gene expression contains most of the predictive capacity compared to the remaining omic data types. Unfortunately, this comes at a price: gene expression biomarkers are often hard...conference paper 2023
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Reinders, J.S. (author)Compilers transform a human readable source language into machine readable target language. Nanopass compilers simplify this approach by breaking up this transformation into small steps that are more understandable, maintainable, and extensible. We propose a semantics-driven variant of the nanopass compiler architecture exploring the use a...conference paper 2023
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Zhang, M. (author), Ganz, Andrea B. (author), Rohde, Susan (author), Lorenz, Linda (author), Rozemuller, Annemieke J.M. (author), Reinders, M.J.T. (author), Hulsman, M. (author), Hoozemans, Jeroen J.M. (author), Holstege, H. (author)INTRODUCTION: Neuropathological substrates associated with neurodegeneration occur in brains of the oldest old. How does this affect cognitive performance?. METHODS: The 100-plus Study is an ongoing longitudinal cohort study of centenarians who self-report to be cognitively healthy; post mortem brain donation is optional. In 85 centenarian...journal article 2023
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van der Lee, S.J. (author), De Rojas, I. (author), Holstege, H. (author), Hulsman, M. (author), Reinders, M.J.T. (author), Tesi, N. (author), van Rooij, Jeroen (author), Zhao, Y. (author), Zhang, X. (author)Characterization of the genetic landscape of Alzheimer’s disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage<br/>genome-wide association study totaling 111,326 clinically diagnosed/‘proxy’ AD cases and 677,663 controls. We found...journal article 2022
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Bongaerts, Michiel (author), Bonte, Ramon (author), Demirdas, Serwet (author), Huidekoper, Hidde H. (author), Langendonk, Janneke (author), Wilke, Martina (author), de Valk, Walter (author), Blom, Henk J. (author), Reinders, M.J.T. (author), Ruijter, George J.G. (author)The integration of metabolomics data with sequencing data is a key step towards improving the diagnostic process for finding the disease-causing genetic variant(s) in patients suspected of having an inborn error of metabolism (IEM). The measured metabolite levels could provide additional phenotypical evidence to elucidate the degree of...journal article 2022
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Smit, J.M. (author), Krijthe, J.H. (author), Tintu, Andrei N. (author), Endeman, Henrik (author), Ludikhuize, Jeroen (author), van Genderen, Michel E. (author), Gommers, D.A.M.P.J. (author), Arbous, M.S. (author), Reinders, M.J.T. (author)Background: Timely identification of deteriorating COVID-19 patients is needed to guide changes in clinical management and admission to intensive care units (ICUs). There is significant concern that widely used Early warning scores (EWSs) underestimate illness severity in COVID-19 patients and therefore, we developed an early warning model...journal article 2022
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Mulder, S.T. (author), Omidvari, Amir-Houshang (author), Rueten-Budde, A.J. (author), Hai, R. (author), Akgün, O.C. (author), Tax, D.M.J. (author), Reinders, M.J.T. (author), Reinders, Marcel (author), Visch, V.T. (author)A digital twin (DT), originally defined as a virtual representation of a physical asset, system, or process, is a new concept in health care. A DT in health care is not a single technology but a domain-adapted multimodal modeling approach incorporating the acquisition, management, analysis, prediction, and interpretation of data, aiming to...journal article 2022
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Cordes, Martijn (author), Canté-Barrett, Kirsten (author), van den Akker, E.B. (author), Moretti, Federico A. (author), Kiełbasa, Szymon M. (author), Vloemans, Sandra A. (author), Garcia-Perez, Laura (author), Teodosio, Cristina (author), van Dongen, Jacques J.M. (author), Pike-Overzet, K. (author), Reinders, M.J.T. (author), Staal, F.J.T. (author)T cell development in the mouse thymus has been studied extensively, but less is known regarding T cell development in the human thymus. We used a combination of single-cell techniques and functional assays to perform deep immune profiling of human T cell development, focusing on the initial stages of prelineage commitment. We identified...journal article 2022
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Bizzarri, D. (author), Reinders, M.J.T. (author), Beekman, M. (author), Slagboom, P. E. (author), van den Akker, E.B. (author)Motivation: 1H-NMR metabolomics is rapidly becoming a standard resource in large epidemiological studies to acquire metabolic profiles in large numbers of samples in a relatively low-priced and standardized manner. Concomitantly, metabolomics-based models are increasingly developed that capture disease risk or clinical risk factors. These...journal article 2022
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Niehues, Anna (author), Bizzarri, Daniele (author), Reinders, M.J.T. (author), Slagboom, P. Eline (author), van Gool, Alain J. (author), van den Akker, E.B. (author), 't Hoen, Peter A.C. (author)Population-scale expression profiling studies can provide valuable insights into biological and disease-underlying mechanisms. The availability of phenotypic traits is essential for studying clinical effects. Therefore, missing, incomplete, or inaccurate phenotypic information can make analyses challenging and prevent RNA-seq or other omics...journal article 2022
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Naseri Jahfari, A. (author), Tax, D.M.J. (author), Reinders, M.J.T. (author), van der Bilt, Ivo (author)Background: Wearable technology has the potential to improve cardiovascular health monitoring by using machine learning. Such technology enables remote health monitoring and allows for the diagnosis and prevention of cardiovascular diseases. In addition to the detection of cardiovascular disease, it can exclude this diagnosis in symptomatic...review 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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Eltager, M.A.M.E. (author), Abdelaal, T.R.M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Motivation: Single-cell multi-omics assays simultaneously measure different molecular features from the same cell. A key question is how to benefit from the complementary data available and perform cross-modal clustering of cells. Results: We propose Single-Cell Multi-omics Clustering (scMoC), an approach to identify cell clusters from data...journal article 2022
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Bizzarri, D. (author), Reinders, M.J.T. (author), Beekman, M. (author), Slagboom, P. E. (author), van den Akker, E.B. (author)Background: Missing or incomplete phenotypic information can severely deteriorate the statistical power in epidemiological studies. High-throughput quantification of small-molecules in bio-samples, i.e. ‘metabolomics’, is steadily gaining popularity, as it is highly informative for various phenotypical characteristics. Here we aim to leverage...journal article 2022
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Mokveld, T.O. (author), Al-Ars, Z. (author), Sistermans, Erik A. (author), Reinders, M.J.T. (author)In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the...journal article 2022