Search Results - "Van der Velde, Joeri"

GAVIN: Gene-Aware Variant INterpretation for medical sequencing by van der Velde, K Joeri, de Boer, Eddy N, van Diemen, Cleo C, Sikkema-Raddatz, Birgit, Abbott, Kristin M, Knopperts, Alain, Franke, Lude, Sijmons, Rolf H, de Koning, Tom J, Wijmenga, Cisca, Sinke, Richard J, Swertz, Morris A

“…We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are…”
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The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button by Swertz, Morris A, Dijkstra, Martijn, Adamusiak, Tomasz, van der Velde, Joeri K, Kanterakis, Alexandros, Roos, Erik T, Lops, Joris, Thorisson, Gudmundur A, Arends, Danny, Byelas, George, Muilu, Juha, Brookes, Anthony J, de Brock, Engbert O, Jansen, Ritsert C, Parkinson, Helen

“…There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and…”
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Therapeutic Prospects of Exon Skipping for Epidermolysis Bullosa by Vermeer, Franciscus C, Bremer, Jeroen, Sietsma, Robert J, Sandilands, Aileen, Hickerson, Robyn P, Bolling, Marieke C, Pasmooij, Anna M G, Lemmink, Henny H, Swertz, Morris A, Knoers, Nine V A M, van der Velde, K Joeri, van den Akker, Peter C

“…Epidermolysis bullosa is a group of genetic skin conditions characterized by abnormal skin (and mucosal) fragility caused by pathogenic variants in various…”
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Feasibility of predicting allele specific expression from DNA sequencing using machine learning by Zhang, Zhenhua, van Dijk, Freerk, de Klein, Niek, van Gijn, Mariëlle E, Franke, Lude H, Sinke, Richard J, Swertz, Morris A, van der Velde, K Joeri

“…Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that…”
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OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript by Adamusiak, Tomasz, Burdett, Tony, Kurbatova, Natalja, Joeri van der Velde, K, Abeygunawardena, Niran, Antonakaki, Despoina, Kapushesky, Misha, Parkinson, Helen, Swertz, Morris A

“…Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI…”
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Rapid Targeted Genomics in Critically Ill Newborns by van Diemen, Cleo C, Kerstjens-Frederikse, Wilhelmina S, Bergman, Klasien A, de Koning, Tom J, Sikkema-Raddatz, Birgit, van der Velde, Joeri K, Abbott, Kristin M, Herkert, Johanna C, Löhner, Katharina, Rump, Patrick, Meems-Veldhuis, Martine T, Neerincx, Pieter B T, Jongbloed, Jan D H, van Ravenswaaij-Arts, Conny M, Swertz, Morris A, Sinke, Richard J, van Langen, Irene M, Wijmenga, Cisca

“…Rapid diagnostic whole-genome sequencing has been explored in critically ill newborns, hoping to improve their clinical care and replace time-consuming and/or…”
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Ten quick tips for building FAIR workflows by de Visser, Casper, Johansson, Lennart F, Kulkarni, Purva, Mei, Hailiang, Neerincx, Pieter, Joeri van der Velde, K, Horvatovich, Péter, van Gool, Alain J, Swertz, Morris A, Hoen, Peter A. C. 't, Niehues, Anna

“…Research data is accumulating rapidly and with it the challenge of fully reproducible science. As a consequence, implementation of high-quality management of…”
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Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis by Deelen, Patrick, van Dam, Sipko, Herkert, Johanna C., Karjalainen, Juha M., Brugge, Harm, Abbott, Kristin M., van Diemen, Cleo C., van der Zwaag, Paul A., Gerkes, Erica H., Zonneveld-Huijssoon, Evelien, Boer-Bergsma, Jelkje J., Folkertsma, Pytrik, Gillett, Tessa, van der Velde, K. Joeri, Kanninga, Roan, van den Akker, Peter C., Jan, Sabrina Z., Hoorntje, Edgar T., te Rijdt, Wouter P., Vos, Yvonne J., Jongbloed, Jan D. H., van Ravenswaaij-Arts, Conny M. A., Sinke, Richard, Sikkema-Raddatz, Birgit, Kerstjens-Frederikse, Wilhelmina S., Swertz, Morris A., Franke, Lude

“…The diagnostic yield of exome and genome sequencing remains low (8–70%), due to incomplete knowledge on the genes that cause disease. To improve this, we use…”
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Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries by Dos Santos Vieira, Bruna, Bernabé, César H, Zhang, Shuxin, Abaza, Haitham, Benis, Nirupama, Cámara, Alberto, Cornet, Ronald, Le Cornec, Clémence M A, 't Hoen, Peter A C, Schaefer, Franz, van der Velde, K Joeri, Swertz, Morris A, Wilkinson, Mark D, Jacobsen, Annika, Roos, Marco

“…Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data…”
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Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains by Zych, Konrad, Li, Yang, van der Velde, Joeri K, Joosen, Ronny V L, Ligterink, Wilco, Jansen, Ritsert C, Arends, Danny

“…Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on…”
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Novel Rare Genetic Variants Associated with Airflow Obstruction in the General Population by de Vries, Maaike, van der Plaat, Diana A, Nedeljkovic, Ivana, van der Velde, K Joeri, Amin, Najaf, van Duijn, Cornelia M, Vonk, Judith M, Boezen, H Marike, van Diemen, Cleo C

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CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations by Li, Shuang, van der Velde, K. Joeri, de Ridder, Dick, van Dijk, Aalt D. J, Soudis, Dimitrios, Zwerwer, Leslie R, Deelen, Patrick, Hendriksen, Dennis, Charbon, Bart, van Gijn, Marielle E, Abbott, Kristin, Sikkema-Raddatz, Birgit, van Diemen, Cleo C, Kerstjens-Frederikse, Wilhelmina S, Sinke, Richard J, Swertz, Morris A

“…Abstract Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part,…”
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BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing by Pang, Chao, Hendriksen, Dennis, Dijkstra, Martijn, van der Velde, K Joeri, Kuiper, Joel, Hillege, Hans L, Swertz, Morris A

“…Pooling data across biobanks is necessary to increase statistical power, reveal more subtle associations, and synergize the value of data sources. However,…”
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Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data by Kaliyaperumal, Rajaram, Wilkinson, Mark D, Moreno, Pablo Alarcón, Benis, Nirupama, Cornet, Ronald, Dos Santos Vieira, Bruna, Dumontier, Michel, Bernabé, César Henrique, Jacobsen, Annika, Le Cornec, Clémence M A, Godoy, Mario Prieto, Queralt-Rosinach, Núria, Schultze Kool, Leo J, Swertz, Morris A, van Damme, Philip, van der Velde, K Joeri, Lalout, Nawel, Zhang, Shuxin, Roos, Marco

“…The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered…”
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Validation of New Gene Variant Classification Methods: a Field-Test in Diagnostic Cardiogenetics by Alimohamed, Mohamed Z, Westers, Helga, Vos, Yvonne J, Van der Velde, K Joeri, Sijmons, Rolf H, Van der Zwaag, Paul A, Sikkema-Raddatz, Birgit, Jongbloed, Jan D H

“…In the molecular genetic diagnostics of Mendelian disorders, solutions are needed for the major challenge of dealing with the large number of variants of…”
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reGenotyper: Detecting mislabeled samples in genetic data by Zych, Konrad, Snoek, Basten L, Elvin, Mark, Rodriguez, Miriam, Van der Velde, K Joeri, Arends, Danny, Westra, Harm-Jan, Swertz, Morris A, Poulin, Gino, Kammenga, Jan E, Breitling, Rainer, Jansen, Ritsert C, Li, Yang

“…In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples…”
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FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research by van der Velde, K. Joeri, Singh, Gurnoor, Kaliyaperumal, Rajaram, Liao, XiaoFeng, de Ridder, Sander, Rebers, Susanne, Kerstens, Hindrik H. D., de Andrade, Fernanda, van Reeuwijk, Jeroen, De Gruyter, Fini E., Hiltemann, Saskia, Ligtvoet, Maarten, Weiss, Marjan M., van Deutekom, Hanneke W. M., Jansen, Anne M. L., Stubbs, Andrew P., Vissers, Lisenka E. L. M., Laros, Jeroen F. J., van Enckevort, Esther, Stemkens, Daphne, ‘t Hoen, Peter A. C., Beliën, Jeroen A. M., van Gijn, Mariëlle E., Swertz, Morris A.

“…The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical…”
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No major role for rare plectin variants in arrhythmogenic right ventricular cardiomyopathy by Hoorntje, Edgar T, Posafalvi, Anna, Syrris, Petros, van der Velde, K Joeri, Bolling, Marieke C, Protonotarios, Alexandros, Boven, Ludolf G, Amat-Codina, Nuria, Groeneweg, Judith A, Wilde, Arthur A, Sobreira, Nara, Calkins, Hugh, Hauer, Richard N W, Jonkman, Marcel F, McKenna, William J, Elliott, Perry M, Sinke, Richard J, van den Berg, Maarten P, Chelko, Stephen P, James, Cynthia A, van Tintelen, J Peter, Judge, Daniel P, Jongbloed, Jan D H

“…Likely pathogenic/pathogenic variants in genes encoding desmosomal proteins play an important role in the pathophysiology of arrhythmogenic right ventricular…”
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Strategies in Rapid Genetic Diagnostics of Critically Ill Children: Experiences From a Dutch University Hospital by Imafidon, Miriam E, Sikkema-Raddatz, Birgit, Abbott, Kristin M, Meems-Veldhuis, Martine T, Swertz, Morris A, van der Velde, K Joeri, Beunders, Gea, Bos, Dennis K, Knoers, Nine V A M, Kerstjens-Frederikse, Wilhelmina S, van Diemen, Cleo C

“…Genetic disorders are a substantial cause of infant morbidity and mortality and are frequently suspected in neonatal intensive care units. Non-specific…”
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A pipeline‐friendly software tool for genome diagnostics to prioritize genes by matching patient symptoms to literature by Velde, K. Joeri, Hoek, Sander, Dijk, Freerk, Hendriksen, Dennis, Diemen, Cleo C., Johansson, Lennart F., Abbott, Kristin M., Deelen, Patrick, Sikkema‐Raddatz, Birgit, Swertz, Morris A.

“…Despite an explosive growth of next‐generation sequencing data, genome diagnostics only provides a molecular diagnosis to a minority of patients. Software…”
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