Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. - Morris A. Swertz; Engbert O. de Brock; Sacha A. F. T. van Hijum; Anne de Jong; Girbe Buist; Richard J. S. Baerends; Jan Kok; Oscar P. Kuipers; Ritsert C. Jansen (Bioinform., 2004)

Combining microarrays and genetic analysis. - Rudi Alberts; Jingyuan Fu; Morris A. Swertz; L. Alrik Lubbers; Casper J. Albers; Ritsert C. Jansen (Briefings Bioinform., 2005)

Towards dynamic database infrastructures for mouse genetics. - Morris A. Swertz; Damian Smedley; Katy Wolstencroft; Rudi Alberts; Michael Zouberakis; Vassilis Aidinis; Klaus Schughart; Paul N. Schofield; Ritsert C. Jansen (BIBE, 2008)

Solutions for data integration in functional genomics: a critical assessment and case study. - Damian Smedley; Morris A. Swertz; Katy Wolstencroft; Glenn Proctor; Michael Zouberakis; Jonathan B. L. Bard; John M. Hancock; Paul N. Schofield (Briefings Bioinform., 2008)

designGG: an R-package and web tool for the optimal design of genetical genomics experiments. - Yang Li 036; Morris A. Swertz; Gonzalo Vera; Jingyuan Fu; Rainer Breitling; Ritsert C. Jansen (BMC Bioinform., 2009)

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. - Damian Smedley; Paul N. Schofield; Chao-Kung Chen; Vassilis Aidinis; Crysanthi Ainali; Jonathan B. L. Bard; Rudi Balling; Ewan Birney; Andrew Blake 003; Erik Bongcam-Rudloff; Anthony J. Brookes; Gianni Cesareni; et al. (Database J. Biol. Databases Curation, 2010)

Mouse Resource Browser - a database of mouse databases. - Michael Zouberakis; Christina Chandras; Morris A. Swertz; Damian Smedley; Michael Gruenberger; Jonathan B. L. Bard; Klaus Schughart; Nadia A. Rosenthal; John M. Hancock; Paul N. Schofield; George Kollias; Vassilis Aidinis (Database J. Biol. Databases Curation, 2010)

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. - Morris A. Swertz; Martijn Dijkstra; Tomasz Adamusiak; K. Joeri van der Velde; Alexandros Kanterakis; Erik T. Roos; Joris Lops; Gudmundur A. Thorisson; Danny Arends; George Byelas; Juha Muilu; Anthony J. Brookes; et al. (BMC Bioinform., 2010)

Towards a MOLGENIS Based Computational Framework. - Heorhiy Byelas; Alexandros Kanterakis; Morris A. Swertz (PDP, 2011)

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. - Isthiaq Ahmad; Frank Suits; Berend Hoekman; Morris A. Swertz; Heorhiy Byelas; Martijn Dijkstra; Rob W. W. Hooft; Dmitry Katsubo; Bas van Breukelen; Rainer Bischoff 003; Peter Horvatovich (Bioinform., 2011)

ontoCAT: an R package for ontology traversal and search. - Natalja Kurbatova; Tomasz Adamusiak; Pavel Kurnosov; Morris A. Swertz; Misha Kapushesky (Bioinform., 2011)

OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. - Tomasz Adamusiak; Tony Burdett; Natalja Kurbatova; K. Joeri van der Velde; Niran Abeygunawardena; Despoina Antonakaki; Misha Kapushesky; Helen E. Parkinson; Morris A. Swertz (BMC Bioinform., 2011)

Introducing Data Provenance and Error Handling for NGS Workflows within the MOLGENIS Computational Framework. - Heorhiy Byelas; Martijn Dijkstra; Morris A. Swertz (BIOINFORMATICS, 2012)

Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs. - Caroline Durrant; Morris A. Swertz; Rudi Alberts; Danny Arends; Steffen Möller; Richard Mott; Pjotr Prins; K. Joeri van der Velde; Ritsert C. Jansen; Klaus Schughart (Briefings Bioinform., 2012)

xQTL workbench: a scalable web environment for multi-level QTL analysis. - Danny Arends; K. Joeri van der Velde; Pjotr Prins; Karl W. Broman; Steffen Möller; Ritsert C. Jansen; Morris A. Swertz (Bioinform., 2012)

VarioML framework for comprehensive variation data representation and exchange. - Myles Byrne; Ivo F. A. C. Fokkema; Owen Lancaster; Tomasz Adamusiak; Anni Ahonen-Bishopp; David Atlan; Christophe Béroud; Michael Cornell; Raymond Dalgleish; Andrew Devereau; George P. Patrinos; Morris A. Swertz; et al. (BMC Bioinform., 2012)

Visualization of Bioinformatics Workflows for Ease of Understanding and Design Activities. - Heorhiy Byelas; Morris A. Swertz (BIOINFORMATICS, 2013)

Scaling Bio-Analyses from Computational Clusters to Grids. - Heorhiy Byelas; Martijn Dijkstra; Pieter B. T. Neerincx; Freerk van Dijk; Alexandros Kanterakis; Patrick Deelen; Morris A. Swertz (IWSG, 2013)

Consensus and conflict cards for metabolic pathway databases. - Miranda D. Stobbe; Morris A. Swertz; Ines Thiele; Trebor Rengaw; Antoine H. C. van Kampen; Perry D. Moerland (BMC Syst. Biol., 2013)

WormQTL - public archive and analysis web portal for natural variation data in Caenorhabditis spp. - L. Basten Snoek; K. Joeri van der Velde; Danny Arends; Yang Li 036; Antje Beyer; Mark Elvin; Jasmin Fisher; Alex Hajnal; Michael O. Hengartner; Gino B. Poulin; Miriam Rodriguez; Tobias Schmid; et al. (Nucleic Acids Res., 2013)

Spá: A Web-Based Viewer for Text Mining in Evidence Based Medicine. - Joël Kuiper; Iain James Marshall; Byron C. Wallace; Morris A. Swertz (ECML/PKDD (3), 2014)

WormQTLHD - a web database for linking human disease to natural variation data in C. elegans. - K. Joeri van der Velde; Mark de Haan; Konrad Zych; Danny Arends; L. Basten Snoek; Jan E. Kammenga; Ritsert C. Jansen; Morris A. Swertz; Yang Li 036 (Nucleic Acids Res., 2014)

SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data. - Chao Pang; Annet Sollie; Anna Sijtsma; Dennis Hendriksen; Bart Charbon; Mark de Haan; Tommy de Boer; Fleur D. L. Kelpin; Jonathan Jetten; K. Joeri van der Velde; Nynke Smidt; Rolf Sijmons; et al. (Database J. Biol. Databases Curation, 2015)

BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. - Chao Pang; Dennis Hendriksen; Martijn Dijkstra; K. Joeri van der Velde; Joël Kuiper; Hans L. Hillege; Morris A. Swertz (J. Am. Medical Informatics Assoc., 2015)

MOLGENIS catalogue. - Morris A. Swertz; David van Enckevort; Chao Pang (J. Clin. Bioinform., 2015)

MOLGENIS/OMX for multi-omics and personalized medicine. - Morris A. Swertz; K. Joeri van der Velde (J. Clin. Bioinform., 2015)

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols. - Alexandros Kanterakis; Joël Kuiper; George Potamias; Morris A. Swertz (Source Code Biol. Medicine, 2015)

State-of-the-Art and Future Challenges in the Integration of Biobank Catalogues. - Heimo Müller; Robert Reihs; Kurt Zatloukal; Fleur Jeanquartier; Roxana Merino-Martinez; David van Enckevort; Morris A. Swertz; Andreas Holzinger (Smart Health, 2015)

Target and (Astro-)WISE technologies Data federations and its applications. - Edwin Valentijn; K. G. Begeman; Andrey N. Belikov; Danny Boxhoorn; Jarle Brinchmann; John McFarland; H. Holties; K. H. Kuijken; Gijs A. Verdoes Kleijn; Willem-Jan Vriend; O. Rees Williams; Jos B. T. M. Roerdink; et al. (Astroinformatics, 2016)

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks. - Chao Pang; David van Enckevort; Mark de Haan; Fleur D. L. Kelpin; Jonathan Jetten; Dennis Hendriksen; Tommy de Boer; Bart Charbon; Erwin Winder; K. Joeri van der Velde; Dany Doiron; Isabel Fortier; et al. (Bioinform., 2016)

Interoperability and FAIRness through a novel combination of Web technologies. - Mark D. Wilkinson; Ruben Verborgh; Luiz Olavo Bonino da Silva Santos; Tim Clark; Morris A. Swertz; Fleur D. L. Kelpin; Alasdair J. G. Gray; Erik A. Schultes; Erik M. van Mulligen; Paolo Ciccarese; Mark Thompson 002; Rajaram Kaliyaperumal; et al. (PeerJ Prepr., 2016)

BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. - Chao Pang; Fleur D. L. Kelpin; David van Enckevort; Niina Eklund; Kaisa Silander; Dennis Hendriksen; Mark de Haan; Jonathan Jetten; Tommy de Boer; Bart Charbon; Petr Holub; Hans L. Hillege; et al. (Bioinform., 2017)

Interoperability and FAIRness through a novel combination of Web technologies. - Mark D. Wilkinson; Ruben Verborgh; Luiz Olavo Bonino da Silva Santos; Tim Clark; Morris A. Swertz; Fleur D. L. Kelpin; Alasdair J. G. Gray; Erik A. Schultes; Erik M. van Mulligen; Paolo Ciccarese; Arnold Kuzniar; Anand K. Gavai; et al. (PeerJ Prepr., 2017)

Machine Learning for Multi-Omics Data Integration and Variant Pathogenicity Estimation. - Shuang Li; K. Joeri van der Velde; Morris A. Swertz (eScience, 2018)

NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing. - Lennart F. Johansson; Hendrik A. de Weerd; Eddy N. de Boer; Freerk van Dijk; Gerard J. te Meerman; Rolf Sijmons; Birgit Sikkema-Raddatz; Morris A. Swertz (BMC Bioinform., 2018)

MOLGENIS Catalogue - towards a Unified Application for Data and Sample Catalogues. - Alexander Kellmann; David van Enckevort; Marije van der Geest; Aneas Hodselmans; Morris A. Swertz (SWAT4HCLS, 2019)

MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians. - K. Joeri van der Velde; Floris Imhann; Bart Charbon; Chao Pang; David van Enckevort; Mariska Slofstra; Ruggero Barbieri; Rudi Alberts; Dennis Hendriksen; Fleur D. L. Kelpin; Mark de Haan; Tommy de Boer; et al. (Bioinform., 2019)

Deconvolution of bulk blood eQTL effects into immune cell subpopulations. - Raúl Aguirre-Gamboa; Niek de Klein; Jennifer di Tommaso; Annique Claringbould; Monique G. P. van der Wijst; Dylan de Vries; Harm Brugge; Roy Oelen; Urmo Võsa; Maria M. Zorro; Xiaojin Chu; Olivier B. Bakker; et al. (BMC Bioinform., 2020)

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. - David Salgado; Irina M. Armean; Michael Baudis; Sergi Beltran; Salvador Capella-Gutiérrez; Denise Carvalho-Silva; Victoria Dominguez Del Angel; Joaquín Dopazo; Laura I. Furlong; Bo Gao; Leyla Jael García Castro; Dietlind Gerloff; et al. (F1000Research, 2020)

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. - Rajaram Kaliyaperumal; Mark D. Wilkinson; Pablo Alarcón Moreno; Nirupama Benis; Ronald Cornet; Bruna dos Santos Vieira; Michel Dumontier; César Henrique Bernabé; Annika Jacobsen; Clémence M. A. Le Cornec; Mario Prieto Godoy; Núria Queralt-Rosinach; et al. (J. Biomed. Semant., 2022)

Surveyed common data access policies preferences amongst European Reference Networks. - Alberto Cámara Ballesteros; Nirupama Benis; César Henrique Bernabé; Inés de Oliveira Coelho; Clémence M. A. Le Cornec; Aylin Demir; Bruna dos Santos Vieira; Jose Antonio Ramírez; K. Joeri van der Velde; Shuxin Zhang; Ronald Cornet; Annika Jacobsen; et al. (SWAT4HCLS, 2023)

Visualisation and Exploration of Linked Data Using Virtual Reality - a preview of Graph2VR. - Alexander Kellmann; Max Postema; Joris de Keijser; Pjotr Svetachov; Becca Wilson; Esther van Enckevort; Morris A. Swertz (SWAT4HCLS, 2023)

Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes. - Alexander Kellmann; Pauline Lanting; Lude Franke; David van Enckevort; Morris A. Swertz (Database J. Biol. Databases Curation, 2023)

Ten quick tips for building FAIR workflows. - Casper de Visser; Lennart F. Johansson; Purva Kulkarni; Hailiang Mei; Pieter B. T. Neerincx; K. Joeri van der Velde; Peter Horvatovich; Alain J. van Gool; Morris A. Swertz; Peter A. C. 't Hoen; Anna Niehues (PLoS Comput. Biol., 2023)

A Resource for Guiding Data Stewards to Make European Rare Disease Patient Registries FAIR. - Philip van Damme; Pablo Alarcón Moreno; César Henrique Bernabé; Alberto Cámara Ballesteros; Clémence M. A. Le Cornec; Bruna dos Santos Vieira; K. Joeri van der Velde; Shuxin Zhang; Claudio Carta; Ronald Cornet; Peter A. C. 't Hoen; Annika Jacobsen; et al. (Data Sci. J., 2023)

Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. - Luc Mottin; Nona Naderi; Anaïs Mottaz; Pierre-André Michel; Lennart F. Johansson; Morris A. Swertz; Andrew Stubbs; Emilie Pasche; Julien Gobeill; Patrick Ruch (MIE, 2024)

FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis. - Xiaofeng Liao; Yuliia Orlova; Cenna Doornbos; Anna Niehues; Casper de Visser; Junda Huang; Thomas H. A. Ederveen; Purva Kulkarni; K. Joeri van der Velde; Morris A. Swertz; Martin Brandt; Alain J. van Gool; et al. (SWAT4HCLS, 2024)

Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content. - Yanni Li; Eline H. van den Berg; Alexander Kurilshikov; Dasha V. Zhernakova; Ranko Gacesa; Shixian Hu; Esteban A. Lopera-Maya; Alexandra Zhernakova; Raúl Aguirre-Gamboa; Patrick Deelen; Lude Franke; Jan A. Kuivenhoven; et al. (Genom. Proteom. Bioinform., 2024)

Visualization and exploration of linked data using virtual reality. - Alexander Kellmann; Max Postema; Joris de Keijser; Pjotr Svetachov; Rebecca C. Wilson; Esther van Enckevort; Morris A. Swertz (Database J. Biol. Databases Curation, 2024)

FAIR Data Cube, a FAIR data infrastructure for integrated multi-omics data analysis. - Xiaofeng Liao; Thomas H. A. Ederveen; Anna Niehues; Casper de Visser; Junda Huang; Firdaws Badmus; Cenna Doornbos; Yuliia Orlova; Purva Kulkarni; K. Joeri van der Velde; Morris A. Swertz; Martin Brandt; et al. (J. Biomed. Semant., 2024)

An exploratory study combining Virtual Reality and Semantic Web for life science research using Graph2VR. - Alexander Kellmann; Sander van den Hoek; Max Postema; W. T. Kars Maassen; Brenda S. Hijmans; Marije van der Geest; K. Joeri van der Velde; Esther van Enckevort; Morris A. Swertz (Database J. Biol. Databases Curation, 2025)