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Research Output

2020

Adoption of the Citation Typing Ontology by the Journal of Cheminformatics

Willighagen, E., 28 Jul 2020, In : Journal of Cheminformatics. 12, 1, 3 p., 47.

Research output: Contribution to journalEditorialAcademic

Open Access

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-resendiz, A., Messina, F., Valencia, A. & 5 others, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., 5 May 2020, In : Scientific data. 7, 1, 4 p., 136.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Learning cheminformatics

Guha, R. & Willighagen, E., 20 Jan 2020, In : Journal of Cheminformatics. 12, 1, 2 p., 4.

Research output: Contribution to journalEditorialAcademic

Open Access

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment

Afantitis, A., Melagraki, G., Isigonis, P., Tsoumanis, A., Varsou, D. D., Valsami-jones, E., Papadiamantis, A., Ellis, L. A., Sarimveis, H., Doganis, P., Karatzas, P., Tsiros, P., Liampa, I., Lobaskin, V., Greco, D., Serra, A., Kinaret, P. A. S., Saarimäki, L. A., Grafström, R., Kohonen, P. & 33 others, Nymark, P., Willighagen, E., Puzyn, T., Rybinska-fryca, A., Lyubartsev, A., Alstrup Jensen, K., Brandenburg, J. G., Lofts, S., Svendsen, C., Harrison, S., Maier, D., Tamm, K., Jänes, J., Sikk, L., Dusinska, M., Longhin, E., Rundén-pran, E., Mariussen, E., El Yamani, N., Unger, W., Radnik, J., Tropsha, A., Cohen, Y., Leszczynski, J., Ogilvie Hendren, C., Wiesner, M., Winkler, D., Suzuki, N., Yoon, T. H., Choi, J., Sanabria, N., Gulumian, M. & Lynch, I., 7 Mar 2020, In : Computational and Structural Biotechnology Journal. 18, p. 583-602 20 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

SCIENCE FORUM Wikidata as a knowledge graph for the life sciences

Waagmeester, A., Stupp, G., Burgstaller-muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-rosinach, N., Schriml, L. M. & 10 others, Shafee, T., Slenter, D., Stephan, R., Thornton, K., Tsueng, G., Tu, R., Ul-hasan, S., Willighagen, E., Wu, C. & Su, A. I., 17 Mar 2020, In : Elife. 9, 15 p., 52614.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2019

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

Miller, R. A., Ehrhart, F., Eijssen, L. M. T., Slenter, D. N., Curfs, L. M. G., Evelo, C. T., Willighagen, E. L. & Kutmon, M., 21 Feb 2019, In : Frontiers in Genetics. 10, 10 p., 59.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combinatio, 17 Jun 2019, In : Nature Communications. 10, 17 p., 2674.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

CyTargetLinker app update: A flexible solution for network extension in Cytoscape

Kutmon, M., Ehrhart, F., Willighagen, E. L., Evelo, C. T. & Coort, S. L., 13 Aug 2019, In : F1000Research. 7, p. 743

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
57 Downloads (Pure)

Journal of Cheminformatics, ORCID, and GitHub

Willighagen, E., Jeliazkova, N. & Guha, R., 8 Jul 2019, In : Journal of Cheminformatics. 11, 2 p., 44.

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access

The metaRbolomics Toolbox in Bioconductor and beyond

Stanstrup, J., Broeckling, C. D., Helmus, R., Hoffmann, N., Mathe, E., Naake, T., Nicolotti, L., Peters, K., Rainer, J., Salek, R. M., Schulze, T., Schymanski, E. L., Stravs, M. A., Thevenot, E. A., Treutler, H., Weber, R. J. M., Willighagen, E., Witting, M. & Neumann, S., Oct 2019, In : Metabolites. 9, 10, 55 p., 200.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access
2018

A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions

Nymark, P., Rieswijk, L., Ehrhart, F., Jeliazkova, N., Tsiliki, G., Sarimveis, H., Evelo, C. T., Hongisto, V., Kohonen, P., Willighagen, E. & Grafstrom, R. C., Mar 2018, In : Toxicological Sciences. 162, 1, p. 264-275 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
117 Downloads (Pure)

Geospatial data and Scholia

Nielsen, F. Å., Mietchen, D. & Willighagen, E., Jun 2018, GeoLD-QuWeDa 2018 ESWC 2018 Workshops: GeoLD 2018 and QuWeDa 2018. CEUR Workshop Proceedings, Vol. 2110. p. 34-40 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademic

Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service

Willighagen, E., 2018, Semantic Web Applications and Tools for Health Care and Life Sciences. CEUR Workshop Proceedings, Vol. 2275. p. 1-6 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademic

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Karcher, S., Willighagen, E. L., Rumble, J., Ehrhart, F., Evelo, C. T., Fritts, M., Gaheen, S., Harper, S. L., Hoover, M. D., Jeliazkova, N., Lewinski, N., Robinson, R. L. M., Mills, K. C., Mustad, A. P., Thomas, D. G., Tsiliki, G. & Hendren, C. O., 1 Jan 2018, In : NanoImpact. 9, p. 85-101 17 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

Martens, M., Verbruggen, T., Nymark, P., Grafstrom, R., Burgoon, L. D., Aladjov, H., Andon, F. T., Evelo, C. T. & Willighagen, E. L., 21 Dec 2018, In : Frontiers in Genetics. 9, 9 p., 661.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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. & Curfs, L. M. G., Jul 2018, In : Human Mutation. 39, 7, p. 914-924 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Kuhn, T., Meroño-Peñuela, A., Malic, A., Poelen, J. H., Hurlbert, A. H., Ortiz, E. C., Furlong, L. I., Queralt-Rosinach, N., Chichester, C., Banda, J. M., Willighagen, E., Ehrhart, F., Evelo, C., Malas, T. B. & Dumontier, M., 18 Sep 2018, 2018 IEEE 14th International Conference on e-Science (e-Science). p. 83-92 10 p. (Proceedings of IEEE e-Science).

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademic

The EU NanoSafety Cluster as Linked Data visualized with Scholia

Willighagen, E., Jahn, N. & Nielsen, F. Å., Jul 2018, In : NanoSafety Cluster Newsletter. p. 6

Research output: Contribution to journalArticleAcademic

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Slenter, D. N., Kutmon, M., Hanspers, K., Riutta, A., Windsor, J., Nunes, N., Mélius, J., Cirillo, E., Coort, S. L., Digles, D., Ehrhart, F., Giesbertz, P., Kalafati, M., Martens, M., Miller, R., Nishida, K., Rieswijk, L., Waagmeester, A., Eijssen, L. M. T., Evelo, C. T. & 2 others, Pico, A. R. & Willighagen, E. L., 4 Jan 2018, In : Nucleic Acids Research. 46, D1, p. D661-D667 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2017

Adverse outcome pathways: opportunities, limitations and open questions

Leist, M., Ghallab, A., Graepel, R., Marchan, R., Hassan, R., Bennekou, S. H., Limonciel, A., Vinken, M., Schildknecht, S., Waldmann, T., Danen, E., van Ravenzwaay, B., Kamp, H., Gardner, I., Godoy, P., Bois, F. Y., Braeuning, A., Reif, R., Oesch, F., Drasdo, D. & 33 others, Hoehme, S., Schwarz, M., Hartung, T., Braunbeck, T., Beltman, J., Vrieling, H., Sanz, F., Forsby, A., Gadaleta, D., Fisher, C., Kelm, J., Fluri, D., Ecker, G., Zdrazil, B., Terron, A., Jennings, P., van der Burg, B., Dooley, S., Meijer, A. H., Willighagen, E., Martens, M., Evelo, C., Mombelli, E., Taboureau, O., Mantovani, A., Hardy, B., Koch, B., Escher, S., van Thriel, C., Cadenas, C., Kroese, D., van de Water, B. & Hengstler, J. G., Nov 2017, In : Archives of Toxicology. 91, 11, p. 3477-3505 29 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
473 Downloads (Pure)

A SCIENCE OPEN COLLECTION OF NANOSAFETY CLUSTER PUBLICATIONS

Willighagen, E., Lynch, I. & Dawson, S., 2017, In : NSC WORKING GROUP NEWS. 9, p. 7-8 2 p.

Research output: Contribution to journalEditorialProfessional

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

Kohonen, P., Parkkinen, J. A., Willighagen, E. L., Ceder, R., Wennerberg, K., Kaski, S. & Grafstrom, R. C., 3 Jul 2017, In : Nature Communications. 8, 15 p., 15932.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Cherto, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R. & Steinbeck, C., 20 Sep 2017, In : Journal of Cheminformatics. 9, 1 p.

Research output: Contribution to journalErratum / corrigendumAcademic

Open Access

Helping to improve the practice of cheminformatics

Guha, R. & Willighagen, E., 14 Jun 2017, In : Journal of Cheminformatics. 9, 2 p., 40.

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

Lampa, S., Willighagen, E., Kohonen, P., King, A., Vrandecic, D., Grafstrom, R. & Spjuth, O., 4 Sep 2017, In : Journal of biomedical semantics. 8, 13 p., 35.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Reliable Granular References to Changing Linked Data

Kuhn, T., Willighagen, E., Evelo, C., Queralt-rosinach, N., Centeno, E. & Furlong, L. I., 4 Oct 2017, The Semantic Web – ISWC 2017: 16th International Semantic Web Conference, Vienna, Austria, October 21–25, 2017, Proceedings, Part I. d'Amato, C., Fernandez, M. & Tamma, V. (eds.). 1 ed. Vol. 10587. p. 436-451 16 p. (Lecture Notes in Computer Science, Vol. 10587).

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

Scholia, Scientometrics and Wikidata

Nielsen, F. Å., Mietchen, D. & Willighagen, E., 8 Nov 2017, The Semantic Web: ESWC 2017 Satellite Events. Blomqvist, E., Hose, K. & Paulheim, H. (eds.). 1 ed. p. 237-259 23 p. (Lecture Notes in Computer Science, Vol. 10577).

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

Open Access

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Cherto, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R. & Steinbeck, C., 6 Jun 2017, In : Journal of Cheminformatics. 9, 19 p., 33.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The future of metabolomics in ELIXIR

Van Rijswijk, M., Beirnaert, C., Caron, C., Cascante, M., Dominguez, V., Dunn, W. B., Ebbels, T. M. D., Giacomoni, F., Gonzalez-beltran, A., Hankemeier, T., Haug, K., Izquierdo-garcia, J. L., Jimenez, R. C., Jourdan, F., Kale, N., Klapa, M. I., Kohlbacher, O., Koort, K., Kultima, K., Le Corguillé, G. & 20 others, Moreno, P., Moschonas, N. K., Neumann, S., O’donovan, C., Reczko, M., Rocca-serra, P., Rosato, A., Salek, R. M., Sansone, S., Satagopam, V., Schober, D., Shimmo, R., Spicer, R. A., Spjuth, O., Thévenot, E. A., Viant, M. R., Weber, R. J. M., Willighagen, E. L., Zanetti, G. & Steinbeck, C., 30 Oct 2017, In : F1000Research. 6, 16 p., 1649.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2016

eNanoMapper Updates and its Collaborations with the Community #2

Willighagen, E., Tsiliki, G., Kohonen, P., Nymark, P., Chang, J., Owen, G., Rieswijk, L., Ehrhart, F., Helma, C., Rautenberg, M., Kilic, G., Jeliazkova, N., Doganis, P. & Sarimveis, H., 2016, In : NanoSafety Cluster Newsletter. Spring 2016, 7, p. 20-25

Research output: Contribution to journalArticleProfessional

SPLASH, a hashed identifier for mass spectra

Wohlgemuth, G., Mehta, S. S., Mejia, R. F., Neumann, S., Pedrosa, D., Pluskal, T., Schymanski, E. L., Willighagen, E. L., Wilson, M., Wishart, D. S., Arita, M., Dorrestein, P. C., Bandeira, N., Wang, M., Schulze, T., Salek, R. M., Steinbeck, C., Nainala, V. C., Mistrik, R., Nishioka, T. & 1 others, Fiehn, O., Nov 2016, In : Nature Biotechnology. 34, 11, p. 1099-1101

Research output: Contribution to journalComment/Letter to the editorAcademicpeer-review

Open Access
File
3 Citations (Scopus)
92 Downloads (Pure)

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Waagmeester, A., Kutmon, M., Riutta, A., Miller, R., Willighagen, E. L., Evelo, C. T. & Pico, A. R., Jun 2016, In : PLoS Computational Biology. 12, 6, 11 p., e1004989.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

WikiPathways: capturing the full diversity of pathway knowledge

Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E. L., Bohler, A., Melius, J., Waagmeester, A., Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T. & Pico, A. R., 4 Jan 2016, In : Nucleic Acids Research. 44, D1, p. D488-D494 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
37 Citations (Scopus)

XMetDB: an open access database for xenobiotic metabolism

Spjuth, O., Rydberg, P., Willighagen, E. L., Evelo, C. T. & Jeliazkova, N., 15 Sep 2016, In : Journal of Cheminformatics. 8, 47.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2015

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Bohler, A., Eijssen, L. M., van Iersel, M. P., Leemans, C., Willighagen, E. L., Kutmon, M., Jaillard, M. & Evelo, C. T., 1 Jan 2015, In : BMC Bioinformatics. 16, 267.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Current systems biology approaches in hazard assessment of nanoparticles

Ehrhart, F., Evelo, C. T. A. & Willighagen, E., 1 Jan 2015, bioRxiv. (bioRxiv).

Research output: Book/ReportReportProfessional

Enabling open science: Wikidata for research (Wiki4R)

Mietchen, D., Hagedorn, G., Willighagen, E., Rico, M., Gómez-Pérez, A., Aibar, E., Rafes, K., Germain, C., Dunning, A., Pintscher, L. & Kinzler, D., 1 Jan 2015, In : Research Ideas and Outcomes. 1, e7573.

Research output: Contribution to journalArticleProfessional

Open Access

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment

Hastings, J., Jeliazkova, N., Owen, G., Tsiliki, G., Munteanu, C. R., Steinbeck, C. & Willighagen, E., 1 Jan 2015, In : Journal of biomedical semantics. 6, 10.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

eNanoMapper updates and its collaborations with the community

Willighagen, E., Ehrhart, F., Rieswijk, L., Jeliazkova, N., Evelo, C. T. A., Farcal, L., Hardy, B. & Sarimveis, H., 1 Jan 2015, In : NanoSafety Cluster Newsletter. 6, p. 14-17

Research output: Contribution to journalArticleProfessional

Metabolite BridgeDb ID Mapping Database (20150717)

Willighagen, E., 1 Jan 2015, In : FigShare. July 2015

Research output: Contribution to journalArticleProfessional

NanoWiki (release 1),

Willighagen, E., 1 Jan 2015, In : FigShare. March 2015

Research output: Contribution to journalArticleProfessional

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Willighagen, E. & Bolton, E., 1 Jan 2015, In : Journal of Cheminformatics. 7, p. 34

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

RRegrs: an R package for computer-aided model selection with multiple regression models

Tsiliki, G., Munteanu, C. R., Seoane, J. A., Fernandez-Lozano, C., Sarimveis, H. & Willighagen, E. L., 1 Jan 2015, In : Journal of Cheminformatics. 7, 46.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

The eNanoMapper database for nanomaterial safety information

Jeliazkova, N., Chomenidis, C., Doganis, P., Fadeel, B., Grafstrom, R., Hardy, B., Hastings, J., Hegi, M., Jeliazkov, V., Kochev, N., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Sopasakis, P., Tsiliki, G., Vorgrimmler, D. & Willighagen, E., 1 Jan 2015, In : Beilstein Journal of Nanotechnology. 6, p. 1609-1634

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures.

Grafstrom, R. C., Nymark, P., Hongisto, V., Spjuth, O., Ceder, R., Willighagen, E., Hardy, B., Kaski, S. & Kohonen, P., Nov 2015, In : ATLA-Alternatives to laboratory animals. 43, 5, p. 325-332

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Using the RRegrs r package for automating predictive modelling

Tsiliki, G., Munteanu, C., Seoane, J., Fernandez-Lozano, C., Sarimveis, H. & Willighagen, E., 1 Jan 2015, Proceedings of MOL2NET. F009

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademic

WikiPathways SD file (v.1)

Willighagen, E., 1 Jan 2015, In : FigShare. March 2015

Research output: Contribution to journalArticleProfessional

2014

eNanoMapper: Opportunities and challenges in using ontologies to enable data integration for nanomaterial risk assessment

Hastings, J., Willighagen, E., Owen, G., Jeliazkova, N. & Steinbeck, C., 2014, Proceedings of the 17th Annual Bio-Ontologies Meeting . p. 18-21

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Scientific Lenses to Support Multiple Views over Linked Chemistry Data

Batchelor, C., Brenninkmeijer, C. A., Chichester, C., Davies, M., Digles, D., Dunlop, I., Evelo, C., Gaulton, A., Goble, C., Gray, A. G., Groth, P., Harland, L., Karapetyan, K., Loizou, A., Overington, J., Pettifer, S., Steele, J., Stevens, R., Tkachenko, V., Waagmeester, A. & 2 others, Williams, A. & Willighagen, E., 1 Jan 2014, The Semantic Web - ISWC 2014. Mika, P., Tudorache, T., Bernstein, A., Welty, C., Knoblock, C., Vrandečić, D., Groth, P., Noy, N., Janowicz, K. & Goble, C. (eds.). Italy: Springer, p. 98-113 (Lecture Notes in Computer Science).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

4 Citations (Scopus)

Summary of the Spring 2014 NSC Database Survey, figshare

Mustad, A. P., Smeets, B., Jeliazkova, N., Jeliazkov, V. & Willighagen, E., 2014, Creative Commons SABY 4.0.

Research output: Book/ReportReportProfessional

Open Access