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FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research.
Published in:
Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01265-x
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
Publication type:
Article
Therapeutic Prospects of Exon Skipping for Epidermolysis Bullosa.
Published in:
International Journal of Molecular Sciences, 2021, v. 22, n. 22, p. 12222, doi. 10.3390/ijms222212222
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.
Publication type:
Article
A Resource for Guiding Data Stewards to Make European Rare Disease Patient Registries FAIR.
Published in:
Data Science Journal, 2023, v. 22, p. 1, doi. 10.5334/dsj-2023-012
By:
- van Damme, Philip;
- Moreno, Pablo Alarcón;
- Bernabé, César H.;
- Ballesteros, Alberto Cámara;
- Le Cornec, Clémence M. A.;
- Dos Santos Vieira, Bruna;
- van der Velde, K. Joeri;
- Zhang, Shuxin;
- Carta, Claudio;
- Cornet, Ronald;
- 't Hoen, Peter A.C.;
- Jacobsen, Annika;
- Swertz, Morris A.;
- Roos, Marco;
- Benis, Nirupama
Publication type:
Article
WormQTLHD—a web database for linking human disease to natural variation data in C. elegans.
Published in:
Nucleic Acids Research, 2014, v. 42, n. D1, p. D794, doi. 10.1093/nar/gkt1044
By:
- van der Velde, K. Joeri;
- de Haan, Mark;
- Zych, Konrad;
- Arends, Danny;
- Snoek, L. Basten;
- Kammenga, Jan E.;
- Jansen, Ritsert C.;
- Swertz, Morris A.;
- Li, Yang
Publication type:
Article
WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp.
Published in:
Nucleic Acids Research, 2013, v. 41, p. D738, doi. 10.1093/nar/gks1124
By:
- Snoek, L. Basten;
- Van der Velde, K. Joeri;
- Arends, Danny;
- Yang Li;
- Beyer, Antje;
- Elvin, Mark;
- Fisher, Jasmin;
- Hajnal, Alex;
- Hengartner, Michael O.;
- Poulin, Gino B.;
- Rodriguez, Miriam;
- Schmid, Tobias;
- Schrimpf, Sabine;
- Feng Xue;
- Jansen, Ritsert C.;
- Kammenga, Jan E.;
- Swertz, Morris A.
Publication type:
Article
Bioinformatics tools and database resources for systems genetics analysis in mice—a short review and an evaluation of future needs.
Published in:
Briefings in Bioinformatics, 2012, v. 13, n. 2, p. 135, doi. 10.1093/bib/bbr026
By:
- Durrant, Caroline;
- Swertz, Morris A.;
- Alberts, Rudi;
- Arends, Danny;
- Möller, Steffen;
- Mott, Richard;
- Prins, Pjotr;
- van der Velde, K. Joeri;
- Jansen, Ritsert C.;
- Schughart, Klaus
Publication type:
Article
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data.
Published in:
Journal of Biomedical Semantics, 2022, v. 13, n. 1, p. 1, doi. 10.1186/s13326-022-00264-6
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
Publication type:
Article
Novel Rare Genetic Variants Associated with Airflow Obstruction in the General Population.
Published in:
2020
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.
Publication type:
Letter
Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10649-4
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.
Publication type:
Article
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.
Published in:
Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav089
By:
- Chao Pang;
- Sollie, Annet;
- Sijtsma, Anna;
- Hendriksen, Dennis;
- Charbon, Bart;
- de Haan, Mark;
- de Boer, Tommy;
- Kelpin, Fleur;
- Jetten, Jonathan;
- van der Velde, Joeri K.;
- Smidt, Nynke;
- Sijmons, Rolf;
- Hillege, Hans;
- Swertz, Morris A.
Publication type:
Article
Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.
Published in:
BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0475-6
By:
- Zych, Konrad;
- Yang Li;
- van der Velde, Joeri K.;
- Joosen, Ronny V. L.;
- Ligterink, Wilco;
- Jansen, Ritsert C.;
- Arends, Danny
Publication type:
Article
Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.
Published in:
BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0475-6
By:
- Zych, Konrad;
- Yang Li;
- van der Velde, Joeri K.;
- Joosen, Ronny V. L.;
- Ligterink, Wilco;
- Jansen, Ritsert C.;
- Arends, Danny
Publication type:
Article
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript.
Published in:
2011
By:
- Adamusiak, Tomasz;
- Burdett, Tony;
- Kurbatova, Natalja;
- van der Velde, K. Joeri;
- Abeygunawardena, Niran;
- Antonakaki, Despoina;
- Kapushesky, Misha;
- Parkinson, Helen;
- Swertz, Morris A.
Publication type:
Product Review
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-S12-S12
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
Publication type:
Article
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing.
Published in:
2015
By:
- Pang, Chao;
- Hendriksen, Dennis;
- Dijkstra, Martijn;
- van der Velde, K. Joeri;
- Kuiper, Joel;
- Hillege, Hans L.;
- Swertz, Morris A.
Publication type:
Product Review
Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.
Published in:
BMC Research Notes, 2014, v. 7, n. 1, p. 477, doi. 10.1186/1756-0500-7-901
By:
- Deelen, Patrick;
- Bonder, Marc Jan;
- van der Velde, K. Joeri;
- Westra, Harm-Jan;
- Winder, Erwin;
- Hendriksen, Dennis;
- Franke, Lude;
- Swertz, Morris A.
Publication type:
Article
Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries.
Published in:
Orphanet Journal of Rare Diseases, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s13023-022-02558-5
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
Publication type:
Article
Feasibility of predicting allele specific expression from DNA sequencing using machine learning.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-89904-y
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
Publication type:
Article
reGenotyper: Detecting mislabeled samples in genetic data.
Published in:
PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0171324
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
Publication type:
Article
Ten quick tips for building FAIR workflows.
Published in:
PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011369
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
Publication type:
Article
Validation of New Gene Variant Classification Methods: a Field-Test in Diagnostic Cardiogenetics.
Published in:
Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.824510
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.
Publication type:
Article
GAVIN: Gene-Aware Variant INterpretation for medical sequencing.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-016-1141-7
By:
- van der Velde, K. Joeri;
- de Boer, Eddy N.;
- van Diemen, Cleo C.;
- Sikkema-Raddatz, Birgit;
- Knopperts, Alain;
- Franke, Lude;
- Sijmons, Rolf H.;
- de Koning, Tom J.;
- Wijmenga, Cisca;
- Sinke, Richard J.;
- Swertz, Morris A.
Publication type:
Article
<italic>MYO5B</italic>, <italic>STX3</italic>, and <italic>STXBP2</italic> mutations reveal a common disease mechanism that unifies a subset of congenital diarrheal disorders: A mutation update.
Published in:
Human Mutation, 2018, v. 39, n. 3, p. 333, doi. 10.1002/humu.23386
By:
- Dhekne, Herschel S.;
- Pylypenko, Olena;
- Overeem, Arend W.;
- Ferreira, Rosaria J.;
- van der Velde, K. Joeri;
- Rings, Edmond H. H. M.;
- Posovszky, Carsten;
- Swertz, Morris A.;
- Houdusse, Anne;
- van IJzendoorn, Sven C. D.
Publication type:
Article
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels.
Published in:
Genome Medicine, 2015, v. 7, n. 1, p. 1, doi. 10.1186/s13073-015-0152-4
By:
- Deelen, Patrick;
- Zhernakova, Daria V.;
- de Haan, Mark;
- van der Sijde, Marijke;
- Bonder, Marc Jan;
- Karjalainen, Juha;
- van der Velde, K. Joeri;
- Abbott, Kristin M.;
- Jingyuan Fu;
- Wijmenga, Cisca;
- Sinke, Richard J.;
- Swertz, Morris A.;
- Franke, Lude
Publication type:
Article
No major role for rare plectin variants in arrhythmogenic right ventricular cardiomyopathy.
Published in:
PLoS ONE, 2018, v. 13, n. 8, p. 1, doi. 10.1371/journal.pone.0203078
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.
Publication type:
Article
MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.
Published in:
Bioinformatics, 2019, v. 35, n. 6, p. 1076, doi. 10.1093/bioinformatics/bty742
By:
- Velde, K Joeri van der;
- Imhann, Floris;
- Charbon, Bart;
- Pang, Chao;
- Enckevort, David van;
- Slofstra, Mariska;
- Barbieri, Ruggero;
- Alberts, Rudi;
- Hendriksen, Dennis;
- Kelpin, Fleur;
- Haan, Mark de;
- Boer, Tommy de;
- Haakma, Sido;
- Stroomberg, Connor;
- Scholtens, Salome;
- van de Geijn, Gert-Jan;
- Festen, Eleonora A M;
- Weersma, Rinse K;
- Swertz, Morris A
Publication type:
Article
MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.
Published in:
Bioinformatics, 2016, v. 32, n. 14, p. 2176, doi. 10.1093/bioinformatics/btw155
By:
- Chao Pang;
- van Enckevort, David;
- de Haan, Mark;
- Kelpin, Fleur;
- Jetten, Jonathan;
- Hendriksen, Dennis;
- de Boer, Tommy;
- Charbon, Bart;
- Winder, Erwin;
- van der Velde, K. Joeri;
- Doiron, Dany;
- Fortier, Isabel;
- Hillege, Hans;
- Swertz, Morris A.
Publication type:
Article
xQTL workbench: a scalable web environment for multi-level QTL analysis.
Published in:
Bioinformatics, 2012, v. 28, n. 7, p. 1042, doi. 10.1093/bioinformatics/bts049
By:
- Arends, Danny;
- van der Velde, K. Joeri;
- Prins, Pjotr;
- Broman, Karl W.;
- Möller, Steffen;
- Jansen, Ritsert C.;
- Swertz, Morris A.
Publication type:
Article
CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations.
Published in:
Genome Medicine, 2020, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13073-020-00775-w
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.
Publication type:
Article

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