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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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van de Kamp, Lars (author), Reinders, Joey (author), Hunnekens, Bram (author), Oomen, T.A.E. (author), van de Wouw, Nathan (author)Patient-ventilator asynchrony is one of the largest challenges in mechanical ventilation and is associated with prolonged ICU stay and increased mortality. The aim of this paper is to automatically detect and classify the different types of patient-ventilator asynchronies during a patient's breath using the typically available data on...journal article 2024
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Karakaslar, E.O. (author), Severens, J.F. (author), Sánchez-López, Elena (author), van Veelen, Peter A. (author), Zlei, Mihaela (author), van Dongen, Jacques J.M. (author), Otte, Annemarie M. (author), Reinders, M.J.T. (author), van den Akker, E.B. (author)The diagnostic spectrum for AML patients is increasingly based on genetic abnormalities due to their prognostic and predictive value. However, information on the AML blast phenotype regarding their maturational arrest has started to regain importance due to its predictive power for drug responses. Here, we deconvolute 1350 bulk RNA-seq...journal article 2024
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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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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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Reinders, L.G.A.J. (author)Doing architecture is an act of bricolage. New things take shape out of the existing. The architect makes do with the materials at hand. Accidents happen, incidents occur, circumstances meet. The site-specific nature of the architectural project opens up questions on how to work with materials at hand and as found, and how to capture, approach...conference paper 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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Reinders, Joey (author), Giaccagli, Mattia (author), Hunnekens, Bram (author), Astolfi, Daniele (author), Oomen, T.A.E. (author), Van De Wouw, Nathan (author)Repetitive control (RC) has shown to achieve superior rejection of periodic disturbances. Many nonlinear systems are subject to repeating disturbances. The aim of this article is to develop a continuous-time RC design with stability guarantees for nonlinear Lur'e-type systems. Approximate output tracking is achieved by combining an internal...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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Kuiper, L.M. (author), Polinder-Bos, Harmke A. (author), Bizzarri, D. (author), Vojinovic, Dina (author), Vallerga, Costanza L. (author), Reinders, M.J.T. (author), Slagboom, P. Eline (author), van den Akker, E.B. (author)Biological age captures a person's age-related risk of unfavorable outcomes using biophysiological information. Multivariate biological age measures include frailty scores and molecular biomarkers. These measures are often studied in isolation, but here we present a large-scale study comparing them. In 2 prospective cohorts (n = 3 222), we...journal article 2023
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Eltager, M.A.M.E. (author), Abdelaal, T.R.M. (author), Charrout, M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author), Makrodimitris, S. (author)Deep generative models, such as variational autoencoders (VAE), have gained increasing attention in computational biology due to their ability to capture complex data manifolds which subsequently can be used to achieve better performance in downstream tasks, such as cancer type prediction or subtyping of cancer. However, these models are...journal article 2023
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Bongaerts, Michiel (author), Kulkarni, Purva (author), Zammit, Alan (author), Bonte, Ramon (author), Kluijtmans, Leo A. J. (author), Blom, Henk J. (author), Engelke, Udo F. H. (author), Tax, D.M.J. (author), Ruijter, George J.G. (author), Reinders, M.J.T. (author)Untargeted metabolomics (UM) is increasingly being deployed as a strategy for screening patients that are suspected of having an inborn error of metabolism (IEM). In this study, we examined the potential of existing outlier detection methods to detect IEM patient profiles. We benchmarked 30 different outlier detection methods when applied to...journal article 2023