- 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
-
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
- 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), 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
- document
-
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
- document
-
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
- document
-
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
- 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
- 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
- document
- 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
- document
-
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
- 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
-
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
-
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
-
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
-
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
- 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