- document
-
Ugwuoke, C.I. (author), Erkin, Z. (author), Reinders, M.J.T. (author), Lagendijk, R.L. (author)Genome sequencing has rapidly advanced in the last decade, making it easier for anyone to obtain digital genomes at low costs from companies such as Helix, MyHeritage, and 23andMe. Companies now offer their services in a direct-to-consumer (DTC) model without the intervention of a medical institution. Thereby, providing people with direct...conference paper 2020
- document
-
Makrodimitris, S. (author), Reinders, M.J.T. (author), van Ham, R.C.H.J. (author)Motivation: Co-expression of two genes across different conditions is indicative of their involvement in the same biological process. However, when using RNA-Seq datasets with many experimental conditions from diverse sources, only a subset of the experimental conditions is expected to be relevant for finding genes related to a particular...journal article 2020
- document
-
Raz, Yotam (author), van den Akker, E.B. (author), Roest, Tijmen (author), Riaz, Muhammad (author), van de Rest, Ondine (author), Suchiman, H. Eka D. (author), Lakenberg, Nico (author), Stassen, Stefanie A. (author), Reinders, M.J.T. (author)Skeletal muscles control posture, mobility and strength, and influence whole-body metabolism. Muscles are built of different types of myofibers, each having specific metabolic, molecular, and contractile properties. Fiber classification is, therefore, regarded the key for understanding muscle biology, (patho-) physiology. The expression of...journal article 2020
- document
-
Keo, D.L. (author), Mahfouz, A.M.E.T.A. (author), Ingrassia, Angela M.T. (author), Meneboo, Jean Pascal (author), Villenet, Celine (author), Mutez, Eugénie (author), Comptdaer, Thomas (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)The molecular mechanisms underlying caudal-to-rostral progression of Lewy body pathology in Parkinson’s disease remain poorly understood. Here, we identified transcriptomic signatures across brain regions involved in Braak Lewy body stages in non-neurological adults from the Allen Human Brain Atlas. Among the genes that are indicative of...journal article 2020
- document
- van den Akker, E.B. (author), Makrodimitris, S. (author), Hulsman, M. (author), Brugman, Martijn H. (author), Nikolic, Tatjana (author), Bradley, Ted (author), Waisfisz, Quinten (author), Baas, Frank (author), Reinders, M.J.T. (author), Holstege, H. (author) journal article 2020
- document
-
Tesi, N. (author), van der Lee, S.J. (author), Hulsman, M. (author), Jansen, Iris E. (author), Stringa, N. (author), van Schoor, N.M. (author), Scheltens, Philip (author), van der Flier, Wiesje M. (author), Huisman, Martijn (author), Reinders, M.J.T. (author), Holstege, H. (author)Developing Alzheimer’s disease (AD) is influenced by multiple genetic variants that are involved in five major AD-pathways. Per individual, these pathways may differentially contribute to the modification of the AD-risk. The pathways involved in the resilience against AD have thus far been poorly addressed. Here, we investigated to what...journal article 2020
- document
-
Groß, C. (author), Bortoluzzi, Chiara (author), de Ridder, Dick (author), Megens, Hendrik-Jan (author), Groenen, Martien A.M. (author), Reinders, M.J.T. (author), Bosse, Mirte (author)The availability of genomes for many species has advanced our understanding of the non-protein-coding fraction of the genome. Comparative genomics has proven itself to be an invaluable approach for the systematic, genome-wide identification of conserved non-protein-coding elements (CNEs). However, for many non-mammalian model species,...journal article 2020
- document
-
Makrodimitris, S. (author), van Ham, R.C.H.J. (author), Reinders, M.J.T. (author)The current rate at which new DNA and protein sequences are being generated is too fast to experimentally discover the functions of those sequences, emphasizing the need for accurate Automatic Function Prediction (AFP) methods. AFP has been an active and growing research field for decades and has made considerable progress in that time....review 2020
- document
-
Linthorst, J. (author), Meert, Wim (author), Hestand, Matthew S. (author), Korlach, Jonas (author), Vermeesch, Joris Robert (author), Reinders, M.J.T. (author), Holstege, H. (author)The human genome harbors numerous structural variants (SVs) which, due to their repetitive nature, are currently underexplored in short-read whole-genome sequencing approaches. Using single-molecule, real-time (SMRT) long-read sequencing technology in combination with FALCON-Unzip, we generated a de novo assembly of the diploid genome of a...journal article 2020
- document
-
Abdelaal, T.R.M. (author), Mourragui, S.M.C. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome expression of single cells, it lacks their spatial localization. Novel spatial transcriptomics methods do retain cells spatial information but some methods can...journal article 2020
- document
-
Bongaerts, Michiel (author), Bonte, Ramon (author), Demirdas, Serwet (author), Jacobs, Edwin H. (author), Oussoren, Esmee (author), van der Ploeg, Ans T. (author), Wagenmakers, Margreet A.E.M. (author), Hofstra, Robert M.W. (author), Blom, Henk J. (author), Reinders, M.J.T. (author), Ruijter, George J.G. (author)Untargeted metabolomics is an emerging technology in the laboratory diagnosis of inborn errors of metabolism (IEM). Analysis of a large number of reference samples is crucial for correcting variations in metabolite concentrations that result from factors, such as diet, age, and gender in order to judge whether metabolite levels are abnormal....journal article 2020
- document
-
Reinders, Brian (author)Supply chains are to be found in almost every corporation around the world. When tryingto manage a supply chain often two types of disturbance can jeopardize the effectiveness of a supply chain. These are supply and demand uncertainty. This thesis tries to investigate the effects of those two types of disturbances in a supply chain and seeks to...master thesis 2019
- document
-
Hagenbeek, Fiona A. (author), Bomer, N. (author), van Hilten, J. A. (author), Fu, J. (author), van der Heijden, A. A.W.A. (author), van der Spek, A. (author), Boersma, E. (author), van den Akker, E.B. (author), Reinders, M.J.T. (author)Metabolomics examines the small molecules involved in cellular metabolism. Approximately 50% of total phenotypic differences in metabolite levels is due to genetic variance, but heritability estimates differ across metabolite classes. We perform a review of all genome-wide association and (exome-) sequencing studies published between November...journal article 2019
- document
-
Reinders, Anne (author)Investing in urban transit is necessary to fuel urban growth and sustainable mobility. Decision making for public transport projects usually involves long term forecasts of travel demand. Future development of factors that influence those forecasts and hence the expected net societal benefits of the investments are uncertain. Decision makers may...master thesis 2019
- document
-
Makrodimitris, S. (author), van Ham, R.C.H.J. (author), Reinders, M.J.T. (author)Motivation: Most automatic functional annotation methods assign Gene Ontology (GO) terms to proteins based on annotations of highly similar proteins. We advocate that proteins that are less similar are still informative. Also, despite their simplicity and structure, GO terms seem to be hard for computers to learn, in particular the Biological...journal article 2019
- document
-
Abdelaal, T.R.M. (author), van Unen, Vincent (author), Höllt, T. (author), Koning, Frits (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Mass cytometry by time-of-flight (CyTOF) is a valuable technology for high-dimensional analysis at the single cell level. Identification of different cell populations is an important task during the data analysis. Many clustering tools can perform this task, which is essential to identify “new” cell populations in explorative experiments....journal article 2019
- document
-
Mourragui, S.M.C. (author), Loog, M. (author), van der Wiel, Mark A. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)Motivation: Cell lines and patient-derived xenografts (PDXs) have been used extensively to understand the molecular underpinnings of cancer. While core biological processes are typically conserved, these models also show important differences compared to human tumors, hampering the translation of findings from pre-clinical models to the human...journal article 2019
- document
-
Abdelaal, T.R.M. (author), Michielsen, L.C.M. (author), Cats, Davy (author), Hoogduin, Dylan (author), Mei, Hailiang (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Background: Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growth in the number of...journal article 2019
- document
-
Abdelaal, T.R.M. (author), Höllt, T. (author), van Unen, Vincent (author), Lelieveldt, B.P.F. (author), Koning, Frits (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Motivation: High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single-cell level, providing a comprehensive view of cell compositions.<br/>However, the power of CyTOF to explore the full heterogeneity of a biological sample at the singlecell level is currently limited by the number of...journal article 2019
- document
-
van der Lee, S.J. (author), Conway, Olivia J. (author), Hansen, Iris (author), Carrasquillo, Minerva M. (author), Kleineidam, Luca (author), van den Akker, E.B. (author), Hulsman, M. (author), Tesi, N. (author), Reinders, M.J.T. (author)The genetic variant rs72824905-G (minor allele) in the PLCG2 gene was previously associated with a reduced Alzheimer’s disease risk (AD). The role of PLCG2 in immune system signaling suggests it may also protect against other neurodegenerative diseases and possibly associates with longevity. We studied the effect of the rs72824905-G on seven...journal article 2019