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Ferraro, F. (author), Fevga, Christina (author), Bonifati, Vincenzo (author), Mandemakers, Wim (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Several studies have analyzed gene expression profiles in the substantia nigra to better understand the pathological mechanisms causing Parkinson’s disease (PD). However, the concordance between the identified gene signatures in these individual studies was generally low. This might have been caused by a change in cell type composition as loss...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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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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- Smit, J. M. (author), van Genderen, M. E. (author), Reinders, M.J.T. (author), Gommers, D. A.M.P.J. (author), Krijthe, J.H. (author), Van Bommel, J. (author) journal article 2021
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Coutinho de Almeida, Rodrigo (author), Mahfouz, A.M.E.T.A. (author), Mei, Hailiang (author), Houtman, Evelyn (author), den Hollander, Wouter (author), Soul, Jamie (author), Suchiman, Eka (author), Nelissen, R.G.H.H. (author), Reinders, M.J.T. (author)OBJECTIVE: To identify OA subtypes based on cartilage transcriptomic data in cartilage tissue and characterize their underlying pathophysiological processes and/or clinically relevant characteristics. METHODS: This study includes n = 66 primary OA patients (41 knees and 25 hips), who underwent a joint replacement surgery, from which...journal article 2021
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Tesi, N. (author), van der Lee, S.J. (author), Hulsman, M. (author), Holstege, H. (author), Reinders, M.J.T. (author)Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which...journal article 2021
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Yu, W. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)The power of single-cell RNA sequencing (scRNA-seq) in detecting cell heterogeneity or developmental process is becoming more and more evident every day. The granularity of this knowledge is further propelled when combining two batches of scRNA-seq into a single large dataset. This strategy is however hampered by technical differences between...journal article 2021
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Ju, Jie (author), Wismans, Leonoor V. (author), Mustafa, Dana A.M. (author), Reinders, M.J.T. (author), van Eijck, Casper H.J. (author), Li, Yunlei (author)A major challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is the unpredictability of their prognoses due to high heterogeneity. We present Multi-Omics DEep Learning for Prognosis-correlated subtyping (MODEL-P) to identify PDAC subtypes and to predict prognoses of new patients. MODEL-P was trained on autoencoder...journal article 2021
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Tesi, N. (author), van der Lee, S.J. (author), Hulsman, M. (author), Jansen, Iris E. (author), Stringa, N. (author), van Schoor, N.M. (author), Huisman, Martijn (author), Reinders, M.J.T. (author), Holstege, H. (author)Studying the genome of centenarians may give insights into the molecular mechanisms underlying extreme human longevity and the escape of age-related diseases. Here, we set out to construct polygenic risk scores (PRSs) for longevity and to investigate the functions of longevity-associated variants. Using a cohort of centenarians with...journal article 2021
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Reinders, K.J. (author), van Leijen, F.J. (author), Hanssen, R.F. (author), Korff, M. (author)This paper investigates the use of InSAR data during shield tunnel construction when short-term settlements occur within a few days. Additionally, the long-term settlement, which occur over several years, in the vicinity of these tunnels are evaluated with inSAR. The North-South Line in Amsterdam is used as a case study for this research. We...conference paper 2021
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Khatri, I. (author), Diks, Annieck M. (author), van den Akker, E.B. (author), Oosten, Liesbeth E. M. (author), Zwaginga, Jaap Jan (author), Reinders, M.J.T. (author), van Dongen, Jacques J. M. (author), Berkowska, Magdalena A. (author)To mount an adequate immune response against pathogens, stepwise mutation and selection processes are crucial functions of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single-cell transcriptome as well as the B...journal article 2021
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- Khatri, Indu (author), Berkowska, Magdalena A. (author), van den Akker, E.B. (author), Teodosio, Cristina (author), Reinders, M.J.T. (author), van Dongen, Jacques J.M. (author) journal article 2021
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Transcriptomic Signatures Associated With Regional Cortical Thickness Changes in Parkinson’s DiseaseKeo, D.L. (author), Dzyubachyk, Oleh (author), Van Der Grond, Jeroen (author), van Hilten, Jacobus J. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Cortical atrophy is a common manifestation in Parkinson’s disease (PD), particularly in advanced stages of the disease. To elucidate the molecular underpinnings of cortical thickness changes in PD, we performed an integrated analysis of brain-wide healthy transcriptomic data from the Allen Human Brain Atlas and patterns of cortical thickness...journal article 2021
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Reinders, K.J. (author), Hanssen, R.F. (author), van Leijen, F.J. (author), Korff, M. (author)In this work, we investigate if, when, and how satellite InSAR can be used for evaluating surface settlements that occur during shield tunnelling in soft soil areas. We evaluate the applicability of InSAR prior, during, and after tunnel construction. Special emphasis is placed on the influence of the InSAR phase ambiguities in relation to short...journal article 2021
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van den Bent, Irene (author), Makrodimitris, S. (author), Reinders, M.J.T. (author)Computationally annotating proteins with a molecular function is a difficult problem that is made even harder due to the limited amount of available labeled protein training data. Unsupervised protein embeddings partly circumvent this limitation by learning a universal protein representation from many unlabeled sequences. Such embeddings...journal article 2021