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Taskesen, E. (author), Reinders, M.J.T. (author)The GTEx Consortium reported that hierarchical clustering of RNA profiles from 25 unique tissue types among 1641 individuals accurately distinguished the tissue types, but a multidimensional scaling failed to generate a 2D projection of the data that separates tissue-subtypes. In this study we show that a projection by t-Distributed Stochastic...journal article 2016
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Apostolou, G. (author), Reinders, A.H.M.E. (author), Verwaal, M. (author)This article presents a simple comparative model which has been developed for the estimation of the performance of photovoltaic (PV) products' cells in indoor environments. The model predicts the performance of PV solar cells, as a function of the distance from a spectrum of artificial (fluorescent light, halogen light, and light-emitting diodes...journal article 2016
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Apostolou, G. (author), Reinders, A.H.M.E. (author), Verwaal, M. (author)This article presents a simple comparative model which has been developed for the estimation of the performance of photovoltaic (PV) products' cells in indoor environments. The model predicts the performance of PV solar cells, as a function of the distance from a spectrum of artificial (fluorescent light, halogen light, and light-emitting diodes...journal article 2016
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- Gehrmann, T. (author), Pelkmans, Jordi F. (author), Wösten, Han A.B. (author), Ohm, Robin (author), Sonnenberg, Anton (author), Baars, Johan J.P. (author), Reinders, M.J.T. (author), Abeel, T.E.P.M.F. (author) poster 2016
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Straver, R. (author), Oudejans, Cees B.M. (author), Sistermans, Erik A. (author), Reinders, M.J.T. (author)Objective While large fetal copy number aberrations can generally be detected through sequencing of DNA in maternal blood, the reliability of tests depends on the fraction of DNA that originates from the fetus. Existing methods to determine this fetal fraction require additional work or are limited to male fetuses. We aimed to create a sex...journal article 2016
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Pelkmans, Jordi F. (author), Vos, A.M. (author), Scholtmeijer, Karin (author), Hendrix, Ed (author), Baars, Johan J.P. (author), Gehrmann, T. (author), Reinders, M.J.T. (author), Lugones, Luis G. (author), Wösten, Han A.B. (author)The Cys2His2 zinc finger protein gene c2h2 of Schizophyllum commune is involved in mushroom formation. Its inactivation results in a strain that is arrested at the stage of aggregate formation. In this study, the c2h2 orthologue of Agaricus bisporus was over-expressed in this white button mushroom forming basidiomycete using Agrobacterium...journal article 2016
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Sontrop, HMJ (author), Reinders, M.J.T. (author), Moerland, Perry D. (author)Background: At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-stage approach consisting of clustering and subtype predictor construction based on the cluster labels of individual cases. SSPs...journal article 2016
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Van Dyk, H.O. (author), Hoogstraat, M (author), ten Hoeve, J (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)The frequent recurrence of copy number aberrations across tumour samples is a reliable hallmark of certain cancer driver genes. However, state-of-the-art algorithms for detecting recurrent aberrations fail to detect several known drivers. In this study, we propose RUBIC, an approach that detects recurrent copy number breaks, rather than...journal article 2016
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Reinders, S.N. (author)Innovation offers opportunities for modernization and development. In recent years it has become a buzzword in the world of NGO’s, IGO’s and governments in developing countries and is featured in the proposed UN Sustainable Development Goals. Different types of innovation are increasingly recognized, complicating the classic notion of innovation...conference paper 2015
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Reinders, K.J. (author), Schoenmaker, B. (author), Nohl, W.A. (author)New vertical steel storage tanks founded on a shallow foundation of a crushed rock ring are planned at the same location of former storage tanks. The dimensions, loads and foundation of the new tanks are identical to the old tanks which were erected 40 years ago and demolished a few years ago. Despite the fact that the new tanks are identical to...conference paper 2015
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Mahfouz, A. (author), Ziats, M.N. (author), Rennert, O.M. (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)Autism spectrum disorder (ASD) is a neurodevelopmental syndrome known to have a significant but complex genetic etiology. Hundreds of diverse genes have been implicated in ASD; yet understanding how many genes, each with disparate function, can all be linked to a single clinical phenotype remains unclear. We hypothesized that understanding...journal article 2015
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Gehrmann, T. (author), Reinders, M.J.T. (author)Background: With more and more genomes being sequenced, detecting synteny between genomes becomes more and more important. However, for microorganisms the genomic divergence quickly becomes large, resulting in different codon usage and shuffling of gene order and gene elements such as exons. Results: We present Proteny, a methodology to detect...journal article 2015
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Gritsenko, A.A. (author), Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of...journal article 2015
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Babaei, S. (author), Mahfouz, A.M.E.T.A. (author), Hulsman, M. (author), Lelieveldt, B.P.F. (author), De Ridder, J. (author), Reinders, M.J.T. (author)The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains...journal article 2015
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Van den Berg, B.A. (author), Reinders, M.J.T. (author), De Ridder, D. (author), De Beer, T.A.P. (author)A variety of methods that predict human nonsynonymous single nucleotide polymorphisms (SNPs) to be neutral or disease-associated have been developed over the last decade. These methods are used for pinpointing disease-associated variants in the many variants obtained with next-generation sequencing technologies. The high performances of current...journal article 2015
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Bleichrodt, R.J. (author), Hulsman, M. (author), Wösten, H.A.B. (author), Reinders, A.J.T. (author)Pores in fungal septa enable cytoplasmic streaming between hyphae and their compartments. Consequently, the mycelium can be considered unicellular. However, we show here that Woronin bodies close ~50% of the three most apical septa of growing hyphae of Aspergillus niger. The incidence of closure of the 9th and 10th septa was even ?94%....journal article 2015
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Babaei, S. (author), Akhtar, W. (author), De Jong, J. (author), Reinders, M.J.T. (author), De Ridder, J. (author)Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D...journal article 2015
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Taskesen, E. (author), Babaei, S. (author), Reinders, M.J.M. (author), De Ridder, J. (author)Background Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and the gene signatures derived from GEP, can be used...journal article 2015
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Taskesen, E. (author), Staal, F.J.T. (author), Reinders, M.J.T. (author)Background The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart of HSC, currently only a selective number of genes of the WNT pathway are analyzed by using either gene expression or DNA-methylation profiles for the identification of...journal article 2015
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- Reinders, G.M.A. (author) master thesis 2015