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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
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Koorneef, Lisa L. (author), Bogaards, Marit (author), Reinders, M.J.T. (author), Meijer, Onno C. (author), Mahfouz, A.M.E.T.A. (author)
Metabolic status impacts on the emotional brain to induce behavior that maintains energy balance. While hunger suppresses the fear circuitry to promote explorative food-seeking behavior, satiety or obesity may increase fear to prevent unnecessary risk-taking. Here we aimed to unravel which metabolic factors, that transfer information about...
journal article 2018
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Gehrmann, T. (author), Pelkmans, Jordi F. (author), Ohm, Robin A. (author), Vos, A.M. (author), Sonnenberg, Anton S.M. (author), Baars, Johan J.P. (author), Wösten, Han A.B. (author), Reinders, M.J.T. (author), Abeel, T.E.P.M.F. (author)
Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroom Agaricus bisporus contains two to 25 nuclei of...
journal article 2018
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Derks, Martijn F.L. (author), Megens, Hendrik-Jan (author), Bosse, Mirte (author), Visscher, Jeroen (author), Peeters, Katrijn (author), Bink, Marco C.A.M. (author), Vereijken, Addie (author), Groß, C. (author), de Ridder, D. (author), Reinders, M.J.T. (author), Groenen, Martien A.M. (author)
Background: Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken...
journal article 2018
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Coutinho de Almeida, Rodrigo (author), Ramos, Yolande F.M. (author), Mahfouz, A.M.E.T.A. (author), den Hollander, Wouter (author), Lakenberg, Nico (author), Houtman, Evelyn (author), van Hoolwerff, Marcella (author), Suchiman, H. Eka D. (author), Rodriguez-Ruiz, Alejandro (author), Slagboom, P. Eline (author), Mei, Hailiang (author), Kielbasa, Szymon M. (author), Nelissen, R.G.H.H. (author), Reinders, M.J.T. (author), Meulenbelt, Ingrid (author)
Objective To uncover the microRNA (miRNA) interactome of the osteoarthritis (OA) pathophysiological process in the cartilage.
Methods We performed RNA sequencing in 130 samples (n=35 and n=30 pairs for messenger RNA (mRNA) and miRNA, respectively) on macroscopically preserved and lesioned OA cartilage from the same patient and performed...
journal article 2018
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Groß, C. (author), de Ridder, D. (author), Reinders, M.J.T. (author)
Background: Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealth of available human genomic information. This raises the question whether it can be done with less data for non-human...
journal article 2018
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van Beek, Daphne M (author), Straver, R. (author), Weiss, Marjan M. (author), Boon, Elles M.J. (author), Huijsdens-van Amsterdam, Karin (author), Oudejans, Cees B.M. (author), Reinders, M.J.T. (author), Sistermans, Erik A. (author)
Objective: To compare available analysis methods for determining fetal fraction on single read next generation sequencing data. This is important as the performance of non-invasive prenatal testing (NIPT) procedures depends on the fraction of fetal DNA. Methods: We tested six different methods for the detection of fetal fraction in NIPT...
journal article 2017
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Obinna, U.P. (author), Joore, J.P. (author), Wauben, L.S.G.L. (author), Reinders, A.H.M.E. (author)
Two residential Smart Grid pilots, PowerMatching City, Groningen (NL) and Pecan Street, Austin Texas (USA) have been compared regarding their energy performance and the experiences of users in these pilots. The objective of the comparison was to gain new insights that could support the successful deployment of future residential Smart Grids....
journal article 2017
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van Unen, V. (author), Hollt, T. (author), Pezzotti, N. (author), Li, Na (author), Reinders, M.J.T. (author), Eisemann, E. (author), Koning, F. (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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Straver, R. (author), Weiss, Marjan M. (author), Waisfisz, Quinten (author), Sistermans, Erik A. (author), Reinders, M.J.T. (author)
In clinical genetics, detection of single nucleotide polymorphisms (SNVs) as well as copy number variations (CNVs) is essential for patient genotyping. Obtaining both CNV and SNV information from WES data would significantly simplify clinical workflow. Unfortunately, the sequence reads obtained with WES vary between samples, complicating...
journal article 2017
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Holstege, H. (author), van der Lee, S.J. (author), Hulsman, M. (author), Hang Wong, Tsz (author), van Rooij, Jeroen (author), Weiss, Marjan M. (author), Louwersheimer, Eva (author), Wolters, Frank J, (author), Amin, Najaf (author), Reinders, M.J.T. (author), More Authors (author)
Accumulating evidence suggests that genetic variants in the SORL1 gene are associated with Alzheimer disease (AD), but a strategy to identify which variants are pathogenic is lacking. In a discovery sample of 115 SORL1 variants detected in 1908 Dutch AD cases and controls, we identified the variant characteristics associated with SORL1...
journal article 2017
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Keo, D.L. (author), Aziz, N. Ahmad (author), Dzyubachyk, Oleh (author), Van Der Grond, Jeroen (author), van Roon-Mom, WMC (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)
Cytosine-adenine-guanine (CAG) repeat expansions in the coding regions of nine polyglutamine (polyQ) genes (HTT, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATN1, AR, and TBP) are the cause of several neurodegenerative diseases including Huntington’s disease (HD), six different spinocerebellar ataxias (SCAs), dentatorubral-pallidoluysian atrophy, and...
journal article 2017
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Doorenweerd, Nathalie (author), Mahfouz, A.M.E.T.A. (author), van Putten, Maaike (author), Kaliyaperumal, Rajaram (author), 't Hoen, P.A.C. (author), Hendriksen, Jos G.M. (author), Aartsma-Rus, Annemieke M. (author), Verschuuren, Jan J.G.M. (author), Niks, Erik H. (author), Reinders, M.J.T. (author), Kan, Hermien E. (author), Lelieveldt, B.P.F. (author)
Duchenne muscular dystrophy (DMD) is a muscular dystrophy with high incidence of learning and behavioural problems and is associated with neurodevelopmental disorders. To gain more insights into the role of dystrophin in this cognitive phenotype, we performed a comprehensive analysis of the expression patterns of dystrophin isoforms across...
journal article 2017
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Eising, Else (author), Shyti, Reinald (author), 't Hoen, P.A.C. (author), Vijfhuizen, L.S. (author), Huisman, S.M.H. (author), Broos, Ludo A. M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author), Ferrari, M.D. (author), Tolner, Else A. (author), de Vries, Boukje (author), van den Maagdenberg, Arn M.J.M. (author)
Familial hemiplegic migraine type 1 (FHM1) is a rare monogenic subtype of migraine with aura caused by mutations in CACNA1A that encodes the α1A subunit of voltage-gated CaV2.1 calcium channels. Transgenic knock-in mice that carry the human FHM1 R192Q missense mutation (‘FHM1 R192Q mice’) exhibit an increased susceptibility to cortical spreading...
journal article 2017
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Mahfouz, A.M.E.T.A. (author), Huisman, S.M.H. (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)
The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases allow researchers to probe the molecular mechanisms...
journal article 2017
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Pelkmans, Jordi F. (author), Patil, Mohini B. (author), Gehrmann, T. (author), Reinders, M.J.T. (author), Wösten, Han A.B. (author), Lugones, Luis G. (author)
Mushrooms are the most conspicuous fungal structures. Transcription factors (TFs) Bri1 and Hom1 of the model fungus Schizophyllum commune are involved in late stages of mushroom development, while Wc-2, Hom2, and Fst4 function early in development. Here, it is shown that Bri1 and Hom1 also stimulate vegetative growth, while biomass formation...
journal article 2017
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Huisman, S.M.H. (author), Van Lew, B. (author), Mahfouz, A.M.E.T.A. (author), Pezzotti, N. (author), Hollt, T. (author), Michielsen, Lieke C.M. (author), Vilanova Bartroli, A. (author), Reinders, M.J.T. (author), Lelieveldt, B.P.F. (author)
Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present BrainScope: A web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human...
journal article 2017
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van Gelder, Celia W.G. (author), Hooft, Rob (author), van Rijswijk, Merlijn (author), van den Berg, Linda (author), Kok, Ruben (author), Reinders, M.J.T. (author), Mons, Barend (author), Heringa, Jaap (author)
This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics...
journal article 2017
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Scholma, Jetse (author), Fuhler, G.M. (author), Joore, Jos (author), Hulsman, M. (author), Schivo, Stefano (author), List, Alan F. (author), Reinders, M.J.T. (author), Peppelenbosch, M.P. (author), Post, Janine N. (author)
Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often...
journal article 2016
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Taskesen, E. (author), Huisman, S.M.H. (author), Mahfouz, A.M.E.T.A. (author), Krijthe, J.H. (author), de Ridder, J. (author), van de Stolpe, A (author), van den Akker, E.B. (author), Verhaegh, Wim (author), Reinders, M.J.T. (author)
The use of genome-wide data in cancer research, for the identification of groups of patients with similar molecular characteristics, has become a standard approach for applications in therapy-response, prognosis-prediction, and drug-development. To progress in these applications, the trend is to move from single genome-wide measurements in a...
journal article 2016
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