- document
-
Tesi, N. (author), Hulsman, M. (author), van der Lee, S.J. (author), Jansen, Iris E. (author), Stringa, N. (author), van Schoor, Natasja M. (author), Scheltens, Philip (author), Reinders, M.J.T. (author), Holstege, H. (author)Human longevity is influenced by the genetic risk of age-related diseases. As Alzheimer’s disease (AD) represents a common condition at old age, an interplay between genetic factors affecting AD and longevity is expected. We explored this interplay by studying the prevalence of AD-associated single-nucleotide-polymorphisms (SNPs) in...journal article 2021
- document
-
Groen, Nathalie (author), Leenders, Floris (author), Mahfouz, A.M.E.T.A. (author), Munoz-Garcia, Amadeo (author), Muraro, Mauro J. (author), de Graaf, Natascha (author), Rabelink, Ton J. (author), Hoeben, Rob (author), Reinders, M.J.T. (author)The maintenance of pancreatic islet architecture is crucial for proper β-cell function. We previously reported that disruption of human islet integrity could result in altered β-cell identity. Here we combine β-cell lineage tracing and single-cell transcriptomics to investigate the mechanisms underlying this process in primary human islet...journal article 2021
- document
-
Derks, Martijn F.L. (author), Groß, C. (author), Lopes, Marcos S. (author), Reinders, M.J.T. (author), Bosse, Mirte (author), Gjuvsland, Arne B. (author), de Ridder, Dick (author), Megens, Hendrik-Jan (author), Groenen, Martien A.M. (author)The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging...journal article 2021
- document
-
Reus, Lianne M. (author), Jansen, Iris E. (author), van Rooij, Jeroen (author), van Schoor, Natasja M. (author), Tesi, N. (author), Reinders, M.J.T. (author), Huisman, M.A. (author), van der Lugt, Aad (author), van der Lee, Sven J. (author)Genetic factors play a major role in frontotemporal dementia (FTD). The majority of FTD cannot be genetically explained yet and it is likely that there are still FTD risk loci to be discovered. Common variants have been identified with genome-wide association studies (GWAS), but these studies have not systematically searched for rare variants...journal article 2021
- document
-
Genetics Contributes to Concomitant Pathology and Clinical Presentation in Dementia with Lewy Bodiesvan der Lee, S.J. (author), van Steenoven, Inger (author), van de Beek, Marleen (author), Tesi, N. (author), Jansen, Iris E. (author), van Schoor, N.M. (author), Reinders, M.J.T. (author), Huisman, Martijn (author), Scheltens, Philip (author)Background: Dementia with Lewy bodies (DLB) is a complex, progressive neurodegenerative disease with considerable phenotypic, pathological, and genetic heterogeneity. Objective: We tested if genetic variants in part explain the heterogeneity in DLB. Methods: We tested the effects of variants previously associated with DLB (near APOE, GBA, and...journal article 2021
- document
-
Khatri, I. (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)Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be...journal article 2021
- document
-
de Jong, Sanne E. (author), van Unen, Vincent (author), Manurung, Mikhael D. (author), Jochems, Simon P. (author), Höllt, T. (author), Pezzotti, N. (author), Eisemann, E. (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)Controlled human infections provide opportunities to study the interaction between the immune system and malaria parasites, which is essential for vaccine development. Here, we compared immune signatures of malaria-naive Europeans and of Africans with lifelong malaria exposure using mass cytometry, RNA sequencing and data integration, before...journal article 2021
- document
-
Michielsen, L.C.M. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Supervised methods are increasingly used to identify cell populations in single-cell data. Yet, current methods are limited in their ability to learn from multiple datasets simultaneously, are hampered by the annotation of datasets at different resolutions, and do not preserve annotations when retrained on new datasets. The latter point is...journal article 2021
- document
-
Keo, D.L. (author), Dzyubachyk, Oleh (author), van der Grond, Jeroen (author), Hafkemeijer, Anne (author), van de Berg, Wilma D.J. (author), van Hilten, Jacobus J. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Structural covariance networks are able to identify functionally organized brain regions by gray matter volume covariance across a population. We examined the transcriptomic signature of such anatomical networks in the healthy brain using postmortem microarray data from the Allen Human Brain Atlas. A previous study revealed that a posterior...journal article 2021
- document
-
Bouland, G.A. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Single-cell RNA sequencing data is characterized by a large number of zero counts, yet there is growing evidence that these zeros reflect biological variation rather than technical artifacts. We propose to use binarized expression profiles to identify the effects of biological variation in single-cell RNA sequencing data. Using 16 publicly...journal article 2021
- document
-
Lähnemann, David (author), Köster, Johannes (author), Robinson, Mark D. (author), Vallejos, Catalina A. (author), Campbell, Kieran R. (author), Beerenwinkel, Niko (author), Pinello, Luca (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven...review 2020
- document
-
Mokveld, T.O. (author), Linthorst, J. (author), Al-Ars, Z. (author), Holstege, H. (author), Reinders, M.J.T. (author)The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of increasing pattern length and encoded variations inevitably leads to a combinatorial explosion of the search space. Instead of heuristic...journal article 2020
- document
-
Makrodimitris, S. (author), Reinders, M.J.T. (author), van Ham, R.C.H.J. (author)Physical interaction between two proteins is strong evidence that the proteins are involved in the same biological process, making Protein-Protein Interaction (PPI) networks a valuable data resource for predicting the cellular functions of proteins. However, PPI networks are largely incomplete for non-model species. Here, we tested to what...journal article 2020
- document
-
Villegas Morcillo, A.O. (author), Makrodimitris, S. (author), van Ham, R.C.H.J. (author), Gomez, A.M. (author), Sanchez, Victoria (author), Reinders, M.J.T. (author)Motivation: Protein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict function from these. Deep supervised models require a lot of labeled training data which are not available for this task. However, a very large amount of protein...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
-
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
-
Groß, C. (author), Derks, Martijn (author), Megens, Hendrik Jan (author), Bosse, Mirte (author), Groenen, Martien A.M. (author), Reinders, M.J.T. (author), de Ridder, D. (author)Background: In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by...journal article 2020
- 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