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Makrodimitris, S. (author), Pronk, I.B. (author), Abdelaal, T.R.M. (author), Reinders, M.J.T. (author)Multi-omic analyses are necessary to understand the complex biological processes taking place at the tissue and cell level, but also to make reliable predictions about, for example, disease outcome. Several linear methods exist that create a joint embedding using paired information per sample, but recently there has been a rise in the...review 2024
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Michielsen, L.C.M. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Most regulatory elements, especially enhancer sequences, are cell population-specific. One could even argue that a distinct set of regulatory elements is what defines a cell population. However, discovering which non-coding regions of the DNA are essential in which context, and as a result, which genes are expressed, is a difficult task. Some...journal article 2024
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Ghorbani, R. (author), Reinders, M.J.T. (author), Tax, D.M.J. (author)Photoplethysmography (PPG) signals, typically acquired from wearable devices, hold significant potential for continuous fitness-health monitoring. In particular, heart conditions that manifest in rare and subtle deviating heart patterns may be interesting. However, robust and reliable anomaly detection within these data remains a challenge...journal article 2024
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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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Zhang, M. (author), Bouland, G.A. (author), Holstege, H. (author), Reinders, M.J.T. (author)Background and Objectives - With age, somatic mutations accumulated in human brain cells can lead to various neurologic disorders and brain tumors. Because the incidence rate of Alzheimer disease (AD) increases exponentially with age, investigating the association between AD and the accumulation of somatic mutation can help understand the...journal article 2023
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Bizzarri, D. (author), Reinders, M.J.T. (author), Beekman, Marian (author), Slagboom, P. Eline (author), van den Akker, E.B. (author)1H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of 1H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies with repeated measures....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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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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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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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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de Bakker, Marie (author), Petersen, Teun B. (author), Rueten-Budde, Anja J. (author), Akkerhuis, K. Martijn (author), Umans, Victor A. (author), Brugts, Jasper J. (author), Germans, Tjeerd (author), Reinders, M.J.T. (author), Katsikis, Peter D. (author)Aims Risk assessment tools are needed for timely identification of patients with heart failure (HF) with reduced ejection fraction (HFrEF) who are at high risk of adverse events. In this study, we aim to derive a small set out of 4210 repeatedly measured proteins, which, along with clinical characteristics and established biomarkers, carry...journal article 2023
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Singh, A. (author), Biharie, K. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author), Abdelaal, T.R.M. (author)Motivation: Single-cell technologies allow deep characterization of different molecular aspects of cells. Integrating these modalities provides a comprehensive view of cellular identity. Current integration methods rely on overlapping features or cells to link datasets measuring different modalities, limiting their application to experiments...journal article 2023
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Keukeleire, P. (author), Makrodimitris, S. (author), Reinders, M.J.T. (author)Cell-free DNA (cfDNA) are DNA fragments originating from dying cells that are detectable in bodily fluids, such as the plasma. Accelerated cell death, for example caused by disease, induces an elevated concentration of cfDNA. As a result, determining the cell type origins of cfDNA molecules can provide information about an individual's health...journal article 2023
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Jongbloed, Elisabeth M. (author), Jansen, Maurice P.H.M. (author), de Weerd, Vanja (author), Helmijr, Jean A. (author), Beaufort, Corine M. (author), Reinders, M.J.T. (author), van Marion, Ronald (author), van IJcken, Wilfred F.J. (author), Makrodimitris, S. (author)Next generation sequencing of cell-free DNA (cfDNA) is a promising method for treatment monitoring and therapy selection in metastatic breast cancer (MBC). However, distinguishing tumor-specific variants from sequencing artefacts and germline variation with low false discovery rate is challenging when using large targeted sequencing panels...journal article 2023
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Biharie, K. (author), Michielsen, L.C.M. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Motivation: Knowing the relation between cell types is crucial for translating experimental results from mice to humans. Establishing cell type matches, however, is hindered by the biological differences between the species. A substantial amount of evolutionary information between genes that could be used to align the species is discarded by...journal article 2023
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Smit, J.M. (author), Krijthe, J.H. (author), van Bommel, Jasper (author), van Genderen, M. E. (author), Labrecque, J. A. (author), Komorowski, M. (author), Gommers, D.A.M.P.J. (author), Reinders, M.J.T. (author)Artificial intelligence (AI) research in the intensive care unit (ICU) mainly focuses on developing models (from linear regression to deep learning) to predict out-<br/>comes, such as mortality or sepsis [1, 2]. However, there is another important aspect of AI that is typically not framed as AI (although it may be more worthy of the name), which...journal article 2023
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Ghorbani, R. (author), Reinders, M.J.T. (author), Tax, D.M.J. (author)With the progress of sensor technology in wearables, the collection and analysis of PPG signals are gaining more interest. Using Machine Learning, the cardiac rhythm corresponding to PPG signals can be used to predict different tasks such as activity recognition, sleep stage detection, or more general health status. However, supervised...conference paper 2023
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Michielsen, L.C.M. (author), Lotfollahi, Mohammad (author), Strobl, Daniel (author), Sikkema, Lisa (author), Reinders, M.J.T. (author), Theis, Fabian J. (author), Mahfouz, A.M.E.T.A. (author)Single-cell genomics is now producing an ever-increasing amount of datasets that, when integrated, could provide large-scale reference atlases of tissue in health and disease. Such large-scale atlases increase the scale and generalizability of analyses and enable combining knowledge generated by individual studies. Specifically, individual...journal article 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