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2020 – today
- 2024
[j33]Alexander Kellmann
, Max Postema, Joris de Keijser, Pjotr Svetachov, Rebecca C. Wilson, Esther van Enckevort, Morris A. Swertz:
Visualization and exploration of linked data using virtual reality. Database J. Biol. Databases Curation 2024 (2024)- [j32]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, Ilja M. Nolte, Serena Sanna, Harold Snieder, Morris A. Swertz, Peter M. Visscher, Judith M. Vonk, Cisca Wijmenga, Vincent E. de Meijer, Robin P. F. Dullaart, Hans Blokzijl, Eleonora A. M. Festen, Jingyuan Fu, Rinse K. Weersma:
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content. Genom. Proteom. Bioinform. 22(1) (2024) - [c12]Luc Mottin, Nona Naderi, Anaïs Mottaz, Pierre-André Michel, Lennart F. Johansson, Morris A. Swertz, Andrew Stubbs, Emilie Pasche, Julien Gobeill, Patrick Ruch:
Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. MIE 2024: 1684-1688 - 2023
- [j31]Alexander Kellmann, Pauline Lanting, Lude Franke, David van Enckevort, Morris A. Swertz:
Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes. Database J. Biol. Databases Curation 2023 (2023) - [j30]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, Morris A. Swertz, Marco Roos, Nirupama Benis:
A Resource for Guiding Data Stewards to Make European Rare Disease Patient Registries FAIR. Data Sci. J. 22 (2023) - [j29]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:
Ten quick tips for building FAIR workflows. PLoS Comput. Biol. 19(9) (2023) - [c11]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, Marco Roos, Franz Schaefer, Morris A. Swertz, Mark D. Wilkinson:
Surveyed common data access policies preferences amongst European Reference Networks. SWAT4HCLS 2023: 107-111 - [c10]Alexander Kellmann, Max Postema, Joris de Keijser, Pjotr Svetachov, Becca Wilson, Esther van Enckevort, Morris A. Swertz:
Visualisation and Exploration of Linked Data Using Virtual Reality - a preview of Graph2VR. SWAT4HCLS 2023: 153-154 - 2022
- [j28]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, Leo J. Schultze Kool, Morris A. Swertz, Philip van Damme, K. Joeri van der Velde, Nawel Lalout, Shuxin Zhang, Marco Roos:
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. J. Biomed. Semant. 13(1): 9 (2022) - 2020
- [j27]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, Zuzanna Borek, Isis Ricaño-Ponce, Patrick Deelen, Cheng-Jiang Xu, Morris A. Swertz, Iris Jonkers, Sebo Withoff, Irma Joosten, Serena Sanna, Vinod Kumar, Hans J. P. M. Koenen, Leo A. B. Joosten, Mihai G. Netea, Cisca Wijmenga, Lude Franke, Yang Li:
Deconvolution of bulk blood eQTL effects into immune cell subpopulations. BMC Bioinform. 21(1): 243 (2020) - [i3]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, Ivo Glynne Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskosek, David Lloyd, Tomàs Marquès-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, Christophe Béroud:
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research 9: 1229 (2020)
2010 – 2019
- 2019
- [j26]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, Sido Haakma, Connor Stroomberg, Salome Scholtens, Gert-Jan van de Geijn, Eleonora A. M. Festen, Rinse K. Weersma, Morris A. Swertz:
MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians. Bioinform. 35(6): 1076-1078 (2019) - [c9]Alexander Kellmann, David van Enckevort, Marije van der Geest, Aneas Hodselmans, Morris A. Swertz:
MOLGENIS Catalogue - towards a Unified Application for Data and Sample Catalogues. SWAT4HCLS 2019: 139-140 - 2018
- [j25]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:
NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing. BMC Bioinform. 19(1): 531:1-531:5 (2018) - [c8]Shuang Li, K. Joeri van der Velde, Morris A. Swertz:
Machine Learning for Multi-Omics Data Integration and Variant Pathogenicity Estimation. eScience 2018: 301 - 2017
- [j24]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, Morris A. Swertz:
BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. Bioinform. 33(22): 3627-3634 (2017) - [j23]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, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier:
Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Comput. Sci. 3: e110 (2017) - [i2]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, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier:
Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Prepr. 5: e2522 (2017) - 2016
- [j22]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, Hans L. Hillege, Morris A. Swertz:
MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks. Bioinform. 32(14): 2176-2183 (2016) - [c7]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, Lambert R. B. Schomaker, Morris A. Swertz, A. Tsyganov, G. J. W. van Dijk:
Target and (Astro-)WISE technologies Data federations and its applications. Astroinformatics 2016: 333-340 - [i1]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, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier:
Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Prepr. 4: e2522 (2016) - 2015
- [j21]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, Hans L. Hillege, Morris A. Swertz:
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data. Database J. Biol. Databases Curation 2015 (2015) - [j20]Chao Pang, Dennis Hendriksen, Martijn Dijkstra, K. Joeri van der Velde, Joël Kuiper, Hans L. Hillege, Morris A. Swertz:
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. J. Am. Medical Informatics Assoc. 22(1): 65-75 (2015) - [j19]Morris A. Swertz, K. Joeri van der Velde:
MOLGENIS/OMX for multi-omics and personalized medicine. J. Clin. Bioinform. 5(S-1): S5 (2015) - [j18]Morris A. Swertz, David van Enckevort, Chao Pang:
MOLGENIS catalogue. J. Clin. Bioinform. 5(S-1): S8 (2015) - [j17]Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz:
PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols. Source Code Biol. Medicine 10: 14 (2015) - [p1]Heimo Müller, Robert Reihs, Kurt Zatloukal, Fleur Jeanquartier, Roxana Merino-Martinez, David van Enckevort, Morris A. Swertz, Andreas Holzinger:
State-of-the-Art and Future Challenges in the Integration of Biobank Catalogues. Smart Health 2015: 261-273 - 2014
- [j16]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:
WormQTLHD - a web database for linking human disease to natural variation data in C. elegans. Nucleic Acids Res. 42(Database-Issue): 794-801 (2014) - [c6]Joël Kuiper, Iain James Marshall, Byron C. Wallace, Morris A. Swertz:
Spá: A Web-Based Viewer for Text Mining in Evidence Based Medicine. ECML/PKDD (3) 2014: 452-455 - 2013
- [j15]Miranda D. Stobbe, Morris A. Swertz, Ines Thiele, Trebor Rengaw, Antoine H. C. van Kampen, Perry D. Moerland:
Consensus and conflict cards for metabolic pathway databases. BMC Syst. Biol. 7: 50 (2013) - [j14]L. Basten Snoek, K. Joeri van der Velde, Danny Arends, Yang Li, Antje Beyer, Mark Elvin, Jasmin Fisher, Alex Hajnal, Michael O. Hengartner, Gino B. Poulin, Miriam Rodriguez, Tobias Schmid, Sabine Schrimpf, Feng Xue, Ritsert C. Jansen, Jan E. Kammenga, Morris A. Swertz:
WormQTL - public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Res. 41(Database-Issue): 738-743 (2013) - [c5]Heorhiy Byelas, Morris A. Swertz:
Visualization of Bioinformatics Workflows for Ease of Understanding and Design Activities. BIOINFORMATICS 2013: 116-121 - [c4]Heorhiy Byelas, Martijn Dijkstra, Pieter B. T. Neerincx, Freerk van Dijk, Alexandros Kanterakis, Patrick Deelen, Morris A. Swertz:
Scaling Bio-Analyses from Computational Clusters to Grids. IWSG 2013 - 2012
- [j13]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:
Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs. Briefings Bioinform. 13(2): 135-142 (2012) - [j12]Danny Arends, K. Joeri van der Velde, Pjotr Prins, Karl W. Broman, Steffen Möller, Ritsert C. Jansen, Morris A. Swertz:
xQTL workbench: a scalable web environment for multi-level QTL analysis. Bioinform. 28(7): 1042-1044 (2012) - [j11]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, Peter E. M. Taschner, Gudmundur A. Thorisson, Mauno Vihinen, Anthony J. Brookes, Juha Muilu:
VarioML framework for comprehensive variation data representation and exchange. BMC Bioinform. 13: 254 (2012) - [c3]Heorhiy Byelas, Martijn Dijkstra, Morris A. Swertz:
Introducing Data Provenance and Error Handling for NGS Workflows within the MOLGENIS Computational Framework. BIOINFORMATICS 2012: 42-50 - 2011
- [j10]Isthiaq Ahmad, Frank Suits, Berend Hoekman, Morris A. Swertz, Heorhiy Byelas, Martijn Dijkstra, Rob W. W. Hooft, Dmitry Katsubo, Bas van Breukelen, Rainer Bischoff, Peter Horvatovich:
A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. Bioinform. 27(8): 1176-1178 (2011) - [j9]Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris A. Swertz, Misha Kapushesky:
ontoCAT: an R package for ontology traversal and search. Bioinform. 27(17): 2468-2470 (2011) - [j8]Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen E. Parkinson, Morris A. Swertz:
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinform. 12: 218 (2011) - [c2]Heorhiy Byelas, Alexandros Kanterakis, Morris A. Swertz:
Towards a MOLGENIS Based Computational Framework. PDP 2011: 331-338 - 2010
- [j7]Damian Smedley, Paul N. Schofield, Chao-Kung Chen, Vassilis Aidinis, Crysanthi Ainali, Jonathan B. L. Bard, Rudi Balling, Ewan Birney, Andrew Blake, Erik Bongcam-Rudloff, Anthony J. Brookes, Gianni Cesareni, Christina Chandras, Janan T. Eppig, Paul Flicek, Georgios V. Gkoutos, Simon Greenaway, Michael Gruenberger, Jean-Karim Hériché, Andrew Lyall, Ann-Marie Mallon, Dawn Muddyman, Florian Reisinger, Martin Ringwald, Nadia A. Rosenthal, Klaus Schughart, Morris A. Swertz, Gudmundur A. Thorisson, Michael Zouberakis, John M. Hancock:
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database J. Biol. Databases Curation 2010 (2010) - [j6]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:
Mouse Resource Browser - a database of mouse databases. Database J. Biol. Databases Curation 2010 (2010) - [j5]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, Engbert O. de Brock, Ritsert C. Jansen, Helen E. Parkinson:
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinform. 11(S-12): S12 (2010)
2000 – 2009
- 2009
- [j4]Yang Li, Morris A. Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, Ritsert C. Jansen:
designGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinform. 10 (2009) - 2008
- [j3]Damian Smedley, Morris A. Swertz, Katy Wolstencroft, Glenn Proctor, Michael Zouberakis, Jonathan B. L. Bard, John M. Hancock, Paul N. Schofield:
Solutions for data integration in functional genomics: a critical assessment and case study. Briefings Bioinform. 9(6): 532-544 (2008) - [c1]Morris A. Swertz, Damian Smedley, Katy Wolstencroft, Rudi Alberts, Michael Zouberakis, Vassilis Aidinis, Klaus Schughart, Paul N. Schofield, Ritsert C. Jansen:
Towards dynamic database infrastructures for mouse genetics. BIBE 2008: 1-7 - 2005
- [j2]Rudi Alberts, Jingyuan Fu, Morris A. Swertz, L. Alrik Lubbers, Casper J. Albers, Ritsert C. Jansen:
Combining microarrays and genetic analysis. Briefings Bioinform. 6(2): 135-145 (2005) - 2004
- [j1]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:
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinform. 20(13): 2075-2083 (2004)
Coauthor Index
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