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Bourgonje, Arno R. (author), Hu, Shixian (author), Spekhorst, Lieke M. (author), Zhernakova, Daria V. (author), Vila, Arnau Vich (author), Li, Yanni (author), Charrout, M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Background and Aims: Protein profiling in patients with inflammatory bowel diseases [IBD] for diagnostic and therapeutic purposes is underexplored. This study analysed the association between phenotype, genotype, and the plasma proteome in IBD. Methods: A total of 92 inflammation-related proteins were quantified in plasma of 1028 patients...journal article 2022
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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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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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De Ridder, D. (author), Li, Y. (author), De Groot, M.J.L. (author), Reinders, M.J.T. (author)Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the...journal article 2008