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  2020 (6)
BioHackathon 2015: Semantics of data for life sciences and reproducible research. Vos, R., A.; Katayama, T.; Mishima, H.; Kawano, S.; Kawashima, S.; Kim, J.; Moriya, Y.; Tokimatsu, T.; Yamaguchi, A.; Yamamoto, Y.; Wu, H.; Amstutz, P.; Antezana, E.; Aoki, N., P.; Arakawa, K.; Bolleman, J., T.; Bolton, E.; Bonnal, R., J., P.; Bono, H.; Burger, K.; Chiba, H.; Cohen, K., B.; Deutsch, E., W.; Fernández-Breis, J., T.; Fu, G.; Fujisawa, T.; Fukushima, A.; García, A.; Goto, N.; Groza, T.; Hercus, C.; Hoehndorf, R.; Itaya, K.; Juty, N.; Kawashima, T.; Kim, J.; Kinjo, A., R.; Kotera, M.; Kozaki, K.; Kumagai, S.; Kushida, T.; Lütteke, T.; Matsubara, M.; Miyamoto, J.; Mohsen, A.; Mori, H.; Naito, Y.; Nakazato, T.; Nguyen-Xuan, J.; Nishida, K.; Nishida, N.; Nishide, H.; Ogishima, S.; Ohta, T.; Okuda, S.; Paten, B.; Perret, J.; Prathipati, P.; Prins, P.; Queralt-Rosinach, N.; Shinmachi, D.; Suzuki, S.; Tabata, T.; Takatsuki, T.; Taylor, K.; Thompson, M.; Uchiyama, I.; Vieira, B.; Wei, C.; Wilkinson, M.; Yamada, I.; Yamanaka, R.; Yoshitake, K.; Yoshizawa, A., C.; Dumontier, M.; Kosaki, K.; and Takagi, T. F1000Research, 9: 136. 2 2020.
BioHackathon 2015: Semantics of data for life sciences and reproducible research [link]Website   bibtex   abstract
Data-driven classification of the certainty of scholarly assertions. Prieto, M.; Deus, H.; de Waard, A.; Schultes, E.; García-Jiménez, B.; and Wilkinson, M., D. PeerJ, 8: e8871. 4 2020.
Data-driven classification of the certainty of scholarly assertions [link]Website   bibtex   abstract   1 download
FAIR Principles: Interpretations and Implementation Considerations. Jacobsen, A.; de Miranda Azevedo, R.; Juty, N.; Batista, D.; Coles, S.; Cornet, R.; Courtot, M.; Crosas, M.; Dumontier, M.; Evelo, C., T.; Goble, C.; Guizzardi, G.; Hansen, K., K.; Hasnain, A.; Hettne, K.; Heringa, J.; Hooft, R., W.; Imming, M.; Jeffery, K., G.; Kaliyaperumal, R.; Kersloot, M., G.; Kirkpatrick, C., R.; Kuhn, T.; Labastida, I.; Magagna, B.; McQuilton, P.; Meyers, N.; Montesanti, A.; van Reisen, M.; Rocca-Serra, P.; Pergl, R.; Sansone, S.; da Silva Santos, L., O., B.; Schneider, J.; Strawn, G.; Thompson, M.; Waagmeester, A.; Weigel, T.; Wilkinson, M., D.; Willighagen, E., L.; Wittenburg, P.; Roos, M.; Mons, B.; and Schultes, E. Data Intelligence, 2(1-2): 10-29. 1 2020.
FAIR Principles: Interpretations and Implementation Considerations [link]Website   bibtex   abstract
Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and ABA, and trigger plant stress responses in Arabidopsis thaliana. Pérez-Alonso, M.; Ortiz-García, P.; Moya-Cuevas, J.; Lehmann, T.; Sánchez-Parra, B.; Björk, R., G.; Karim, S.; Amirjani, M., R.; Aronsson, H.; Wilkinson, M., D.; and Pollmann, S. Journal of Experimental Botany. 10 2020.
Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and ABA, and trigger plant stress responses in Arabidopsis thaliana [link]Website   bibtex   abstract
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering. García-Jiménez, B.; Carrasco, J.; Medina, J.; and Wilkinson, M., D. Research Square Preprints. 2020.
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering [link]Website   bibtex   2 downloads
Predicting microbiomes through a deep latent space. García-Jiménez, B.; Muñoz, J.; Cabello, S.; Medina, J.; and Wilkinson, M., D. Bioinformatics. 11 2020.
Predicting microbiomes through a deep latent space [link]Website   bibtex
  2019 (9)
Robust and automatic definition of microbiome states. García-Jiménez, B.; and Wilkinson, M., D. PeerJ, 7: e6657. 3 2019.
Robust and automatic definition of microbiome states [link]Website   bibtex   abstract   1 download
Data-driven classification of the certainty of scholarly assertions. Prieto, M.; Deus, H.; De Waard, A.; Schultes, E.; García-Jiménez, B.; and Wilkinson, M., D. PeerJ Preprints, 7: e27829v1. 6 2019.
Data-driven classification of the certainty of scholarly assertions [link]Website   bibtex   abstract
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data. Wittenburg, P.; Sustkova, H., P.; Montesanti, A.; Bloemers, S., M.; de Waard, S., H.; Musen, M., A.; Graybeal, J., B.; Hettne, K., M.; Jacobsen, A.; Pergl, R.; Hooft, R., W., W.; Staiger, C.; van Gelder, C., W., G.; Knijnenburg, S., L.; van Arkel, A., C.; Meerman, B.; Wilkinson, M., D.; Sansone, S.; Rocca-Serra, P.; McQuilton, P.; Gonzalez-Beltran, A., N.; Aben, G., J., C.; Henning, P.; Alencar, S.; Ribeiro, C.; Silva, C., R., L.; Sayao, L.; Sales, L.; Veiga, V.; Lima, J.; Dib, S.; Xavier, P.; Murtinho, R.; Tendel, J.; Schaap, B., F.; Brouwer, P., M.; Gavai, A., K.; Bouzembrak, Y.; Marvin, H., J., P.; Mons, A.; Kuhn, T.; Gambardella, A., A.; Azevedo, R., d., M.; Muhonen, V.; van der Naald, M.; Smit, N., W.; Buys, M., J.; de Bruin, T., F.; Schoots, F.; Goodson, H., J., E.; Rzepa, H., S.; Jeffery, K., G.; Shanahan, H., P.; Axton, M.; Tkachenko, V.; Maya, A., D.; Meyers, N., K.; Conlon, M.; Haak, L., L.; and Schultes, E., A. arXiv, arXiv:1902. 2 2019.
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data [link]Website   bibtex   abstract
Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework. Wilkinson, M., D.; Dumontier, M.; Sansone, S.; da Silva Santos, L., O., B.; Prieto, M.; Batista, D.; McQuilton, P.; Kuhn, T.; Rocca-Serra, P.; Crosas, M.; and Schultes, E. bioRxiv. 2019.
Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework [link]Website   bibtex   abstract
Evaluating FAIR maturity through a scalable, automated, community-governed framework. Wilkinson, M., D.; Dumontier, M.; Sansone, S.; Bonino da Silva Santos, L., O.; Prieto, M.; Batista, D.; McQuilton, P.; Kuhn, T.; Rocca-Serra, P.; Crosas, M.; and Schultes, E. Scientific Data, 6(1): 174. 12 2019.
Evaluating FAIR maturity through a scalable, automated, community-governed framework [link]Website   bibtex
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. Katayama, T.; Kawashima, S.; Micklem, G.; Kawano, S.; Kim, J.; Kocbek, S.; Okamoto, S.; Wang, Y.; Wu, H.; Yamaguchi, A.; Yamamoto, Y.; Antezana, E.; Aoki-Kinoshita, K., F.; Arakawa, K.; Banno, M.; Baran, J.; Bolleman, J., T.; Bonnal, R., J.; Bono, H.; Fernández-Breis, J., T.; Buels, R.; Campbell, M., P.; Chiba, H.; Cock, P., J., A.; Cohen, K., B.; Dumontier, M.; Fujisawa, T.; Fujiwara, T.; Garcia, L.; Gaudet, P.; Hattori, E.; Hoehndorf, R.; Itaya, K.; Ito, M.; Jamieson, D.; Jupp, S.; Juty, N.; Kalderimis, A.; Kato, F.; Kawaji, H.; Kawashima, T.; Kinjo, A., R.; Komiyama, Y.; Kotera, M.; Kushida, T.; Malone, J.; Matsubara, M.; Mizuno, S.; Mizutani, S.; Mori, H.; Moriya, Y.; Murakami, K.; Nakazato, T.; Nishide, H.; Nishimura, Y.; Ogishima, S.; Ohta, T.; Okuda, S.; Ono, H.; Perez-Riverol, Y.; Shinmachi, D.; Splendiani, A.; Strozzi, F.; Suzuki, S.; Takehara, J.; Thompson, M.; Tokimatsu, T.; Uchiyama, I.; Verspoor, K.; Wilkinson, M., D.; Wimalaratne, S.; Yamada, I.; Yamamoto, N.; Yarimizu, M.; Kawamoto, S.; and Takagi, T. F1000Research, 8: 1677. 9 2019.
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services [link]Website   bibtex   abstract
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. Payá-Milans, M.; Poza-Viejo, L.; Martín-Uriz, P., S.; Lara-Astiaso, D.; Wilkinson, M., D.; and Crevillén, P. GigaScience, 8(12). 12 2019.
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa [link]Website   bibtex   abstract
Conserved Roles of the H3K27ME3 Epigenome on Plant Development. Crevillén, P.; Poza-Viejo, L.; Payá-Milans, M.; Del Olmo, I.; and Wilkinson​, M., D. IMPACT OF CHROMATIN DOMAINS ON PLANT PHENOTYPES,28. 2019.
Conserved Roles of the H3K27ME3 Epigenome on Plant Development [pdf]Website   bibtex   abstract
Erratum: Addendum: The FAIR Guiding Principles for scientific data management and stewardship (Scientific data (2016) 3 (160018)). Wilkinson, M.; Dumontier, M.; Jan Aalbersberg, I.; Appleton, G.; Axton, M.; Baak, A.; Blomberg, N.; Boiten, J.; da Silva Santos, L.; Bourne, P.; Bouwman, J.; Brookes, A.; Clark, T.; Crosas, M.; Dillo, I.; Dumon, O.; Edmunds, S.; Evelo, C.; Finkers, R.; Gonzalez-Beltran, A.; Gray, A.; Groth, P.; Goble, C.; Grethe, J.; Heringa, J.; Hoen, P.; Hooft, R.; Kuhn, T.; Kok, R.; Kok, J.; Lusher, S.; Martone, M.; Mons, A.; Packer, A.; Persson, B.; Rocca-Serra, P.; Roos, M.; van Schaik, R.; Sansone, S.; Schultes, E.; Sengstag, T.; Slater, T.; Strawn, G.; Swertz, M.; Thompson, M.; van der Lei, J.; van Mulligen, E.; Jan Velterop; Waagmeester, A.; Wittenburg, P.; Wolstencroft, K.; Zhao, J.; and Mons, B. Scientific data, 6(1). 2019.
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  2018 (10)
Enrichment of rare disease patient registries by FAIRification. Jacobsen, A.; Thompson, M.; Schultes, E., A.; Cornet, R.; Wilkinson, M.; Thompson, R.; Mordenti, M.; Sangiorgi, L.; Carta, C.; Groenen, K.; Kersloot, M.; Schultze Kool, L.; van Enckevort, D.; and Roos, M. In ECRD 2018, pages POSTER, 2018.
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FAIRification of rare disease patient registries. Jacobsen, A.; Thompson, M.; Sernadela, P.; Ehrhart, F.; Carta, C.; Groenen, K.; Kersloot, M.; Kool, L., S.; Mordenti, M.; Locatelli, M.; Sangiorgi, L.; Schultes, E., A.; Cornet, R.; Wilkinson, M., D.; Taruscio, D.; Thompson, R.; van Enckevort, D.; Evelo, C.; and Roos, M. In Proceedings of the 2018 Annual Partner Meeting of RD Connect, 2018.
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A design framework and exemplar metrics for FAIRness. Wilkinson, M., D.; Sansone, S.; Schultes, E.; Doorn, P.; Bonino da Silva Santos, L., O.; and Dumontier, M. Scientific Data, 5: 180118. 6 2018.
A design framework and exemplar metrics for FAIRness [link]Website   bibtex
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. Townend, G., S.; Ehrhart, F.; van Kranen, H., J.; Wilkinson, M.; Jacobsen, A.; Roos, M.; Willighagen, E., L.; van Enckevort, D.; Evelo, C., T.; and Curfs, L., M., G. Human Mutation, 39(7): 914-924. 7 2018.
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases [link]Website   bibtex
Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus. Rodríguez-Romero, J.; Marconi, M.; Ortega-Campayo, V.; Demuez, M.; Wilkinson, M., D.; and Sesma, A. New Phytologist. 8 2018.
Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus [link]Website   bibtex
MDPbiome: microbiome engineering through prescriptive perturbations. García-Jiménez, B.; de la Rosa, T.; and Wilkinson, M., D. Bioinformatics, 34(17): i838-i847. 9 2018.
MDPbiome: microbiome engineering through prescriptive perturbations [link]Website   bibtex
Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework. Wilkinson, M., D.; Dumontier, M.; Sansone, S.; Bonino da Silva Santos, L., O.; Prieto, M.; Gautier, J.; McQuilton, P.; Murphy, D.; Crosas, M.; and Schultes, E. bioRxiv. 1 2018.
Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework [link]Website   bibtex   abstract
Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae. Marconi, M.; Sesma, A.; Rodríguez-Romero, J., L.; González, M., L., R.; and Wilkinson, M., D. Scientific Data, 5: 180271. 11 2018.
Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae [link]Website   bibtex
Automatic definition of robust microbiome sub-states in longitudinal data. García-Jiménez, B.; and Wilkinson, M., D. PeerJ Preprints, 6: e26657v1. 3 2018.
Automatic definition of robust microbiome sub-states in longitudinal data [link]Website   bibtex   abstract
FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies. Sansone, S.; McQuilton, P.; Rocca-Serra, P.; Gonzalez-Beltran, A.; Izzo, M.; Lister, A.; Thurston, M.; Batista, D.; Granell, R.; Adekale, M.; Dauga, D.; Ganley, E.; Hodson, S.; Lawrence, R.; Khodiyar, V.; Tenenbaum, J.; Axton, J., M.; Ball, M.; Besson, S.; Bloom, T.; Bonazzi, V.; Jimenez, R.; Carr, D.; Chan, W., M.; Chung, C.; Clement-Stoneham, G.; Cousijn, H.; Dayalan, S.; Dumontier, M.; Dzale Yeumo, E.; Edmunds, S.; Everitt, N.; Fripp, D.; Goble, C.; Golebiewski, M.; Hall, N.; Hanisch, R.; Hucka, M.; Huerta, M.; Kenall, A.; Kiley, R.; Klenk, J.; Koureas, D.; Larkin, J.; Lemberger, T.; Lynch, N.; Schriml, L.; Ma\textquoterightayan, A.; MacCallum, C.; Mons, B.; Moore, J.; Muller, W.; Murray, H.; Nobusada, T.; Noesgaard, D.; Paxton-Boyd, J.; Orchard, S.; Rustici, G.; Schurer, S.; Sharples, K.; e Silva, M.; Stanford, N., J.; Subirats-Coll, I.; Swedlow, J.; Tong, W.; Wilkinson, M.; Wise, J.; and Yilmaz, P. bioRxiv. 2018.
FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies [link]Website   bibtex   abstract
  2017 (16)
Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae. Illana, A.; Marconi, M.; Rodríguez-Romero, J.; Xu, P.; Dalmay, T.; Wilkinson, M., D.; Ayllón, M., Á.; and Sesma, A. Archives of Virology, 162(3): 891-895. 3 2017.
Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae [link]Website   bibtex
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud. Mons, B.; Neylon, C.; Velterop, J.; Dumontier, M.; da Silva Santos, L., O., B.; and Wilkinson, M., D. Information Services & Use, 37(1): 49-56. 3 2017.
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud [link]Website   bibtex
Identifying Bioinformatics Subworkflows with SCOFF: Semantic Clustering Of Functional Fragments. García-Jiménez, B.; and Wilkinson​, M., D. SUBMITTED. 2017.
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Boosting health care and life science research on rare diseases by creating a robust infrastructure of independently Findable, Accessible, Interoperable, and Reusable (FAIR) biobanks, registries, and molecular data resources. Enckevort, D., v.; Thompson, R.; Carta, C.; Wilkinson, M.; and Roos, M. In IRDiRC 2017, 2017.
Boosting health care and life science research on rare diseases by creating a robust infrastructure of independently Findable, Accessible, Interoperable, and Reusable (FAIR) biobanks, registries, and molecular data resources [pdf]Website   bibtex
Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies. Enckevort, D., v.; Carta, C.; Thompson, R.; Thompson, M.; Ehrhart, F.; Kaliyaperumal, R.; Sernadela, P.; Reihs, R.; Jacobsen, A.; da Silva Santos, L., O., B.; Wilkinson, M., D.; Muller, H.; Oliviera, J., L.; Evelo, C., T.; Taruscio, D.; ‘t Hoen, P., A.; and Roos, M. In ESHG 2017, 2017.
Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies [link]Website   bibtex
Findable, Accessible, Interoperable and Reusable data resources to speed up research on rare diseases. Carta, C.; Roos, M.; Jansen, M.; Enckevort, D., v.; Wilkinson, M., D.; Kaliyaperumal, R.; Thompson, M.; Torreri, P.; da Silva Santos, L., O., B.; Cornet, R.; Kodra, Y.; and Taruscio, D. Technical Report 2017.
Findable, Accessible, Interoperable and Reusable data resources to speed up research on rare diseases. [link]Website   bibtex   abstract
Preparing Data at the Source to Foster Interoperability across Rare Disease Resources. Roos, M.; López Martin, E.; and Wilkinson, M., D. Rare Diseases Epidemiology: Update and overview 2nd Edition, pages 165-179. Posada, M.; and Groft, S., editor(s). Springer International Publishing AG, 2017.
Rare Diseases Epidemiology: Update and overview 2nd Edition [link]Website   bibtex
Boosting genotype-phenotype and translational research on rare diseases by establishing Findable, Accessible, Interoperable and Reusable data resources through data linking technologies. Enckevort, D., v.; Claudio, C.; Thompson, R.; Thompson, M.; Ehrhart, F.; Kaliyaperumal, R.; Sernadela, P.; Da Silva Santos, L., O., B.; Jacobsen, A.; Wilkinson, M.; Müller, H.; Reihs, R.; Oliviera, J., L.; Evelo, C.; Taruscio, D.; 'T Hoen, P.; and Roos, M. In BioSB2017, 2017.
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Interoperability and FAIRness through a novel combination of Web technologies. Wilkinson, M., D.; van Mulligen, E., M.; Ciccarese, P.; Schultes, E., A.; Verborgh, R.; Kaliyaperumal, R.; Clark, T.; Bolleman, J., T.; Thompson, M.; Kelpin, F., D.; Swertz, M., A.; Dumontier, M.; Bonino da Silva Santos, L., O.; Gray, A., J.; Kuzniar, A.; and Gavai, A. PeerJ Computer Science, 3: e110. 4 2017.
Interoperability and FAIRness through a novel combination of Web technologies [link]Website   bibtex   abstract
Overview of a suite of tools and training material for implementing FAIR data principles. Thompson, M.; Wilkinson, M.; Kaliyaperumal, R.; Burger, K.; Leeuwen, S., v.; Jacobsen, A.; Carta, C.; Schultes, E.; Finkers, R.; Enckevort, D., v.; Jansen, M.; Roos, M.; Mons, B.; and Bonino, L. In ELIXIR Webinar, 2017.
Overview of a suite of tools and training material for implementing FAIR data principles [link]Website   bibtex
Implementing ELSI 2.0 for international collaborative research: improving access to clinical and genetics data by connecting ELSI policies, FAIR data software solutions, and ELIXIR-AAI. Gainotti, S.; Petrini, C.; Mascalzoni, D.; Floridia, G.; Riva, L.; Wilkinson, M.; and Roos, M. In SWAT4HCLS 2017, pages POSTER, 2017.
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The FAIRification of data and the potentialities of FAIR resources showed, in practice, at the Rome “Bring Your Own Data” workshop. Carta, C.; Roos, M.; Jacobsen, A.; Kaliyaperumal, R.; Thompson, M.; Wilkinson, M.; Cornet, R.; Waagmeester, A.; van Enckevort, D.; Jansen, M.; Licata, L.; Via, A.; and Taruscio, D. In Proceedings of SWAT4HCLS 2017, 2017.
The FAIRification of data and the potentialities of FAIR resources showed, in practice, at the Rome “Bring Your Own Data” workshop [pdf]Website   bibtex
FAIRMetrics/Metrics: Initial set of proposed FAIR Metrics for community discussion. Wilkinson, M.; Sansone, S.; Bonino, L., O.; Schultes, E.; Doorn, P.; and Dumontier, M. Technical Report 11 2017.
FAIRMetrics/Metrics: Initial set of proposed FAIR Metrics for community discussion [link]Website   bibtex
A design framework and exemplar metrics for FAIRness. Wilkinson, M., D.; Sansone, S.; Schultes, E.; Doorn, P.; da Silva Santos, L., O., B.; and Dumontier, M. bioRxiv. 2017.
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Overview of a suite of middle-ware services for implementing FAIR data principles. Thompson, M.; Bonino, L.; Wilkinson, M.; Kaliyaperumal, R.; Burger, K.; Van Leeuwen, S.; Jacobsen, A.; Carta, C.; Schultes, E.; Van Enckevort, D.; Finkers, R.; Jansen, M.; Mons, B.; and Roos, M. In CEUR Workshop Proceedings, volume 2042, 2017.
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Bring Your Own Data workshop is an excellent tool to promote the establishment of Findable, Accessible, Interoperable, and Reusable rare disease registries. Carta, C.; Roos, M.; Jansen, M.; Wilkinson, M., D.; Bonino da Silva Santos, L.; van Enckevort, D.; and Taruscio, D. In Procedigs of the European Human Genetics Conference 2017, 2017.
Bring Your Own Data workshop is an excellent tool to promote the establishment of Findable, Accessible, Interoperable, and Reusable rare disease registries [link]Website   bibtex
  2016 (8)
The FAIR Guiding Principles for scientific data management and stewardship. Wilkinson, M., D.; Dumontier, M.; Aalbersberg, I., J.; Appleton, G.; Axton, M.; Baak, A.; Blomberg, N.; Boiten, J.; da Silva Santos, L., B.; Bourne, P., E.; Bouwman, J.; Brookes, A., J.; Clark, T.; Crosas, M.; Dillo, I.; Dumon, O.; Edmunds, S.; Evelo, C., T.; Finkers, R.; Gonzalez-Beltran, A.; Gray, A., J.; Groth, P.; Goble, C.; Grethe, J., S.; Heringa, J.; ’t Hoen, P., A.; Hooft, R.; Kuhn, T.; Kok, R.; Kok, J.; Lusher, S., J.; Martone, M., E.; Mons, A.; Packer, A., L.; Persson, B.; Rocca-Serra, P.; Roos, M.; van Schaik, R.; Sansone, S.; Schultes, E.; Sengstag, T.; Slater, T.; Strawn, G.; Swertz, M., A.; Thompson, M.; van der Lei, J.; van Mulligen, E.; Velterop, J.; Waagmeester, A.; Wittenburg, P.; Wolstencroft, K.; Zhao, J.; and Mons, B. Scientific Data, 3: 160018. 3 2016.
The FAIR Guiding Principles for scientific data management and stewardship [link]Website   bibtex
Temporal microbiome road-maps guided by perturbations. García-Jiménez, B.; and Wilkinson, M. bioRxiv,049510. 4 2016.
Temporal microbiome road-maps guided by perturbations [link]Website   bibtex   abstract
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. Rodríguez-Iglesias, A.; Rodríguez-González, A.; Irvine, A., G.; Sesma, A.; Urban, M.; Hammond-Kosack, K., E.; and Wilkinson, M., D. Frontiers in Plant Science, 7. 5 2016.
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base [link]Website   bibtex
MDPbiome: Predicting temporal microbiome dynamics influenced by external perturbations. García-Jiménez, B.; and Wilkinson, M. In XIII Symposium on Bioinformatics, 2016.
MDPbiome: Predicting temporal microbiome dynamics influenced by external perturbations [pdf]Website   bibtex
From hypothesis construction, through experimental execution, to result publication and citation. Wilkinson, M., D. In Francisco de Asis, A., H.; Gutiérrez-Cortines, M., E.; Fernández Hernández, J., A.; Baille, A., D.; and Calatrava Leyva, J., editor(s), Proceedings of the 4th Workshop on agri-food research, pages 14, 2016.
From hypothesis construction, through experimental execution, to result publication and citation [link]Website   bibtex
Interoperability and FAIRness through a novel combination of Web technologies. Wilkinson​, M., D.; Verborgh, R.; da Silva Santos, L., O., B.; Clark, T.; Swertz, M., A.; Kelpin, F., D.; Gray, A., J., G.; Schultes, E., A.; Mulligen, E., M., v.; Ciccarese, P.; Thompson, M.; Kaliyaperumal, R.; Bolleman, J., T.; and Dumontier, M. PeerJ Preprints, 4(e2522v1). 2016.
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FAIR Data Points Supporting Big Data Interoperability. Bonino Da Silva Santos, L.; Wilkinson, M., D.; Kuzniar, A.; Kaliyaperumal, R.; Thompson, M.; Dumontier, M.; and Burger, K. Enterprise Interoperability in the Digitized and Networked Factory of the Future, pages 270-279. Zelm, M.; Doumeingts, G.; and Mendonça, J., P., editor(s). iSTE Press, 2016.
Enterprise Interoperability in the Digitized and Networked Factory of the Future [link]Website   bibtex
Registries of domain-relevant semantic reference models help bootstrap interoperability in domains with fragmented data resources. Roos, M.; Wilkinson, M., D.; Kaliyaperumal, R.; Thompson, M.; Carta, C.; Cornet, R.; van Enckevort, D.; and Bonino, L. In Paschke, A.; Burger, A.; Splendiani, A.; Marshall, M., S.; and Romano, P., editor(s), Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016. CEUR Workshop Proceedings
Registries of domain-relevant semantic reference models help bootstrap interoperability in domains with fragmented data resources [pdf]Website   bibtex
  2015 (6)
VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock. Nakada, T.; Boyd, J., H.; Russell, J., A.; Aguirre-Hern�ndez, R.; Wilkinson, M., D.; Thair, S., A.; Nakada, E.; McConechy, M., K.; Fjell, C., D.; and Walley, K., R. Journal of Innate Immunity, 7(5): 545-553. 4 2015.
<b><i>VPS13D</i></b> Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock [link]Website   bibtex
Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. Rodríguez-González, A.; Martínez-Romero, M.; Costumero, R.; Wilkinson, M., D.; and Menasalvas-Ruiz, E. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, pages 79-87. Overbeek, R.; Rocha, M., P.; Fdez-Riverola, F.; and Paz, J., F., D., editor(s). Springer International Publishing, 2015.
9th International Conference on Practical Applications of Computational Biology and Bioinformatics [link]Website   bibtex   abstract
DataFairPort: The Perl libraries version 0.231. Wilkinson, M.; Dumontier, M.; and Durbin, P. 11 2015.
DataFairPort: The Perl libraries version 0.231 [link]Website   bibtex
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. Aranguren, M., E.; and Wilkinson, M., D. GigaScience, 4(1): 59. 12 2015.
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker [link]Website   bibtex
Erratum to: Diagnostic knowledge extraction from MedlinePlus: An application for infectious diseases (9th International Conference on Practical Applications of Computational Biology and Bioinformatics, Advances in Intelligent Systems and Computing 375, 10. Rodríguez-González, A.; Martínez-Romero, M.; Costumero, R.; Wilkinson, M.; and Menasalvas-Ruiz, E. Volume 375 2015.
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  2014 (13)
Executing SADI services in Galaxy. Egaña Aranguren, M.; Rodríguez González, A.; and Wilkinson, M., D. Journal of Biomedical Semantics, 5(1): 42. 2014.
Executing SADI services in Galaxy [link]Website   bibtex
Nanopublishing clinical diagnoses: tracking diagnostic knowledge base content and utilization. Rodríguez-González, A.; Martinez-Romero, M.; Aranguren, M., E.; and Wilkinson, M., D. In CBMS '14 Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical Systems, pages 335-340, 2014.
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Bioinformatics Tools for Next-Generation RNA Sequencing Analysis. Marconi, M.; Rodriguez-Romero, J.; Sesma, A.; and Wilkinson, M., D. Fungal RNA biology, pages 371-391. Sesma, A.; and von der Haar, T., editor(s). Springer International Publishing, 2014.
Fungal RNA biology [link]Website   bibtex   abstract
The Crop Ontology, a resource for enabling access to breeders'data. Arnaud, E.; Matteis, L.; Laporte, M., A.; Espinosa, H.; Hyman, G.; Shrestha, R.; Portugal, A.; Chibon, P., Y.; Devare, M.; Akintunde, A.; White, J., W.; Wilkinson, M.; Caracciolo, C.; Celli, F.; and Mclaren, G. In In proceeding of: Plant and Animal Genome XXII, pages W352, 2014.
The Crop Ontology, a resource for enabling access to breeders'data [link]Website   bibtex   abstract
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. Dumontier, M.; Baker, C., J.; Baran, J.; Callahan, A.; Chepelev, L.; Cruz-Toledo, J.; Del Rio, N., R.; Duck, G.; Furlong, L., I.; Keath, N.; Klassen, D.; McCusker, J., P.; Queralt-Rosinach, N.; Samwald, M.; Villanueva-Rosales, N.; Wilkinson, M., D.; and Hoehndorf, R. Journal of biomedical semantics, 5(1): 14. 3 2014.
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. [link]Website   bibtex   abstract
Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies. García-Jiménez, B.; and Wilkinson, M., D. In Margaria, T.; and Steffen, B., editor(s), Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications - 6th International Symposium, ISoLA 2014, Imperial, Corfu, Greece, October 8-11, 2014, Proceedings, Part II, volume 8803, of Lecture Notes in Computer Science, pages 464-478, 2014. Springer Berlin Heidelberg
Automatic Annotation of Bioinformatics Workflows with Biomedical Ontologies [link]Website   bibtex
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Katayama, T.; Wilkinson, M.; Aoki-Kinoshita, K.; Kawashima, S.; Yamamoto, Y.; Yamaguchi, A.; Okamoto, S.; Kawano, S.; Kim, J.; Wang, Y.; Wu, H.; Kano, Y.; Ono, H.; Bono, H.; Kocbek, S.; Aerts, J.; Akune, Y.; Antezana, E.; Arakawa, K.; Aranda, B.; Baran, J.; Bolleman, J.; Bonnal, R.; Buttigieg, P.; Campbell, M.; Chen, Y.; Chiba, H.; Cock, P.; Cohen, K.; and Constantin, A. Journal of Biomedical Semantics, 5(1): 5. 2014.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains [pdf]Paper   BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains [link]Website   bibtex   abstract
Automatic detection and resolution of measurement-unit conflicts in aggregated data. Samadian, S.; McManus, B.; and Wilkinson, M. BMC Medical Genomics, 7(Suppl 1): S12. 2014.
Automatic detection and resolution of measurement-unit conflicts in aggregated data [link]Website   bibtex   abstract
Automatically exposing OpenLifeData via SADI semantic Web Services. González, A., R.; Callahan, A.; Cruz-Toledo, J.; Garcia, A.; Egaña Aranguren, M.; Dumontier, M.; and Wilkinson, M., D. Journal of Biomedical Semantics, 5(1): 46. 2014.
Automatically exposing OpenLifeData via SADI semantic Web Services [link]Website   bibtex   abstract
The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus. Hily, J., M.; García, A.; Moreno, A.; Plaza, M.; Wilkinson, M., D.; Fereres, A.; Fraile, A.; and García-Arenal, F. PLoS pathogens, 10(11): e1004492. 11 2014.
The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus. [link]Website   bibtex   abstract
Health Web Science. Luciano, J., S.; Cumming, G., P.; Kahana, E.; Wilkinson, M., D.; Brooks, E., H.; Jarman, H.; McGuinness, D., L.; and Levine, M., S. Foundations and Trends® in Web Science, 4(4): 269-419. 2014.
Health Web Science [link]Website   bibtex
Bring Your Own Data workshops: a mechanism to aid data owners to comply with Linked Data best practices. Roos, M.; Gray, A., J., G.; Waagmeester, A.; Thompson, M.; Kaliyaperumal, R.; Horst, E., v., d.; Mons, B.; and Wilkinson, M., D. Proceedings of Semantic Web Applications and Tools for Life Sciences 2014. Paschke, A.; Burger, A.; Romano, P.; Marshall, M., S.; and Andrea, S., editor(s). CEUR Workshop Proceedings, Volume 132 edition, 2014.
Proceedings of Semantic Web Applications and Tools for Life Sciences 2014 [pdf]Website   bibtex
Automatic annotation of bioinformatics workflows with biomedical ontologies. García-Jiménez, B.; and Wilkinson, M. Volume 8803 2014.
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  2013 (8)
Plant Pathogen Interactions Ontology (PPIO). Iglesias, A., R.; Aranguren, M., E.; Gonzalez, A., R.; and Wilkinson, M., D. Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering,695-702. 2013.
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The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions. Vandervalk, B.; McCarthy, E., L.; Cruz-Toledo, J.; Klein, A.; Baker, C., J., O.; Dumontier, M.; and Wilkinson, M., D. JMIR Research Protocols, 2(1): e14. 4 2013.
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions [link]Website   bibtex   abstract
Plant Pathogen Interactions Ontology (PPIO). Iglesias, A., R.; Aranguren, M., E.; Gonzalez, A., R.; and Wilkinson, M., D. In Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering, pages 695-702, 2013.
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The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions. Vandervalk, B.; McCarthy, E., L.; Cruz-Toledo, J.; Klein, A.; Baker, C., J., O.; Dumontier, M.; and Wilkinson, M., D. JMIR Research Protocols, 2(1): e14. 4 2013.
The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions [link]Website   bibtex
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Egaña Aranguren, M.; Fernández-Breis, J., T.; Antezana, E.; Mungall, C.; Rodríguez González, A.; and Wilkinson, M., D. Journal of biomedical semantics, 4(1): 2. 1 2013.
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. [link]Website   bibtex   abstract
The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Katayama, T.; Wilkinson, M., D.; Micklem, G.; Kawashima, S.; Yamaguchi, A.; Nakao, M.; Yamamoto, Y.; Okamoto, S.; Oouchida, K.; Chun, H.; Aerts, J.; Afzal, H.; Antezana, E.; Arakawa, K.; Aranda, B.; Belleau, F.; Bolleman, J.; Bonnal, R., J.; Chapman, B.; Cock, P.; Eriksson, T.; Gordon, P.; Goto, N.; Hayashi, K.; Horn, H.; Ishiwata, R.; Kaminuma, E.; Kasprzyk, A.; Kawaji, H.; Kido, N.; Kim, Y., J.; Kinjo, A., R.; Konishi, F.; Kwon, K.; Labarga, A.; Lamprecht, A.; Lin, Y.; Lindenbaum, P.; McCarthy, L.; Morita, H.; Murakami, K.; Nagao, K.; Nishida, K.; Nishimura, K.; Nishizawa, T.; Ogishima, S.; Ono, K.; Oshita, K.; Park, K.; Prins, P.; Saito, T., L.; Samwald, M.; Satagopam, V., P.; Shigemoto, Y.; Smith, R.; Splendiani, A.; Sugawara, H.; Taylor, J.; Vos, R.; Withers, D.; Yamasaki, C.; Zmasek, C., M.; Kawamoto, S.; Okubo, K.; Asai, K.; and Takagi, T. Journal of Biomedical Semantics, 4(1): 6. 2013.
The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies [link]Website   bibtex
Web Science Studies into Semantic Web Service-Based Research Environments (Awarded "Best Paper"). Wilkinson, M., D. The Fifth International Conferences on Advanced Service Computing, SERVICE COMPUTATION 2013, pages 71-74. Copyright (c) IARIA, 2013, 2013.
The Fifth International Conferences on Advanced Service Computing, SERVICE COMPUTATION 2013 [link]Website   bibtex   abstract
The emergent discipline of health web science. Luciano, J., S.; Cumming, G., P.; Wilkinson, M., D.; and Kahana, E. Journal of medical Internet research, 15(8): e166. 1 2013.
The emergent discipline of health web science. [link]Website   bibtex   abstract
  2012 (11)
Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web. Samadian, S.; McManus, B.; and Wilkinson, M., D. Journal of biomedical semantics, 3(1): 6. 7 2012.
Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web. [link]Website   bibtex   abstract
SPARQL Assist language-neutral query composer. McCarthy, L.; Vandervalk, B.; and Wilkinson, M. BMC bioinformatics, 13 Suppl 1(Suppl 1): S2. 1 2012.
SPARQL Assist language-neutral query composer. [pdf]Paper   SPARQL Assist language-neutral query composer. [link]Website   bibtex   abstract
Genomics data resources: frameworks and standards. Wilkinson, M., D. Volume 856 . Methods in molecular biology (Clifton, N.J.), pages 489-511. 1 2012.
Methods in molecular biology (Clifton, N.J.) [link]Website   bibtex   abstract
OWL-DL Domain-Models as Abstract Workflows. Wood, I.; Vandervalk, B.; McCarthy, L.; and Wilkinson, M., D. Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies, pages 56-66. Margaria, T.; and Steffen, B., editor(s). Springer Berlin/Heidelberg, 2012.
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Bioscientific Data Processing and Modeling. Kok, J.; Lamprecht, A., L.; Verbeek, F.; and Wilkinson, M. Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies,7-11. 2012.
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Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study. Rodríguez-González, A.; Torres-Niño, J.; Mayer, M., A.; Alor-Hernandez, G.; and Wilkinson, M., D. Computational and Mathematical Methods in Medicine, 2012: 1-9. 2012.
Analysis of a Multilevel Diagnosis Decision Support System and Its Implications: A Case Study [link]Website   bibtex