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Article
2020

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

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)
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)

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

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 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

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

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

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)

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)

WikiPathways SD file (v.1)

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

Research output: Contribution to journalArticleProfessional

2013

Applications of the InChI in cheminformatics with the CDK and Bioclipse.

Spjuth, O., von Berg, A., Adams, S. & Willighagen, E. L., 13 Mar 2013, In : Journal of Cheminformatics. 5, 1, p. 14 7 p., 14.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Bioclipse-R: integrating management and visualization of life science data with statistical analysis

Spjuth, O., Georgiev, V., Carlsson, L., Alvarsson, J., Berg, A., Willighagen, E., Wikberg, J. E. & Eklund, M., 1 Jan 2013, In : Bioinformatics. 29, 2, p. 286-289

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

The ChEMBL database as linked open data

Willighagen, E. L., Waagmeester, A. S., Spjuth, O., Ansell, P., Williams, A. J., Tkachenko, V., Hastings, J., Chen, B. & Wild, D. J., 8 May 2013, In : Journal of Cheminformatics. 5, 1, 12 p., 23.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
32 Citations (Scopus)

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R. C., Healy, L., Helma, C., Jeliazkova, N., Jeliazkova, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, S., Willighagen, E., Wiseman, J. & Hardy, B., 1 Jan 2013, In : Molecular Informatics. 32, 1, p. 47-63 17 p.

Research output: Contribution to journalArticleAcademicpeer-review

19 Citations (Scopus)
2012

A survey of quantitative descriptions of molecular structure

Guha, R. & Willighagen, E., Sep 2012, In : Current Topics in Medicinal Chemistry. 12, 18, p. 1946-1956 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Changing computational research. The challenges ahead

Neylon, C., Aerts, J., Brown, C. T., Coles, S. J., Hatton, L., Lemire, D., Millman, K. J., Murray-Rust, P., Perez, F., Saunders, N., Shah, N., Smith, A., Varoquaux, G. & Willighagen, E., 1 Jan 2012, In : Source code for biology and medicine. 7, 1, p. 2

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Cheminformatics

Wegner, J. K., Sterling, A., Guha, R., Bender, A., Faulon, J. L., Hastings, J., O'Boyle, N., Overington, J., Van Vlijmen, H. & Willighagen, E., 1 Jan 2012, In : Communications of the Acm. 55, 11, p. 65-75

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

Emerging practices for mapping and linking life sciences data using RDF - A case series

Marshall, M. S., Boyce, R., Deus, H. F., Zhao, J., Willighagen, E. L., Samwald, M., Pichler, E., Hajagos, J., Prud'hommeaux, E. & Stephens, S., Jul 2012, In : Journal of Web Semantics. 14, p. 2-13 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

30 Citations (Scopus)

Open PHACTS: semantic interoperability for drug discovery

Williams, A. J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E. L., Evelo, C. T., Blomberg, N., Ecker, G., Goble, C. & Mons, B., Nov 2012, In : Drug Discovery Today. 17, 21-22, p. 1188-1198 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

146 Citations (Scopus)

Open source drug discovery with bioclipse.

Spjuth, O., Carlsson, L., Alvarsson, J., Georgiev, V., Willighagen, E. & Eklund, M., 1 Jan 2012, In : Current Topics in Medicinal Chemistry. 12, 18, p. 1980-6

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)
2011

Computational toxicology using the OpenTox application programming interface and Bioclipse

Willighagen, E. L., Jeliazkova, N., Hardy, B., Grafstrom, R. C. & Spjuth, O., 1 Jan 2011, In : BMC Research Notes. 4, p. 487

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Hastings, J., Chepelev, L., Willighagen, E., Adams, N., Steinbeck, C. & Dumontier, M., 3 Oct 2011, In : PLOS ONE. 6, 10, e25513.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access