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Researcher

Dumontier, M.J.

Professor

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  1. 2019
  2. Published
    Celebi, R., Walk, O. B. D., Movva, R., Alpsoy, S., & Dumontier, M. (2019). 3In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. Scientific Reports, 9, [8949]. https://doi.org/10.1038/s41598-019-45236-6
  3. Published
    AstraZeneca-Sanger Drug Combinatio (2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications, 10, [2674]. https://doi.org/10.1038/s41467-019-09799-2
  4. Published
    Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., ... Mons, B. (2019). The FAIR Guiding Principles for scientific data management and stewardship (vol 15, 160018, 2016). Scientific data, 6, [6]. https://doi.org/10.1038/s41597-019-0009-6
  5. Published
    Biomed Data Translator Consortium (2019). The Biomedical Data Translator Program: Conception, Culture, and Community. Cts-Clinical and Translational Science, 12(2), 91-94. https://doi.org/10.1111/cts.12592
  6. Published
    Biomed Data Translator Consortium (2019). Toward A Universal Biomedical Data Translator. Cts-Clinical and Translational Science, 12(2), 86-90. https://doi.org/10.1111/cts.12591
  7. Published
    Sang, S., Yang, Z., Liu, X., Wang, L., Lin, H., Wang, J., & Dumontier, M. (2019). GrEDeL: A Knowledge Graph Embedding Based Method for Drug Discovery From Biomedical Literatures. IEEE Access, 7, 8404-8415. https://doi.org/10.1109/ACCESS.2018.2886311
  8. 2018
  9. Published
    Celebi, R., Yasar, E., Uyar, H., Gumus, O., Dikenelli, O., & Dumontier, M. (2018). Evaluation of Knowledge Graph Embedding Approaches for Drug-Drug Interaction Prediction using Linked Open Data.
  10. Published
    Sun, C., Ippel, L., Wouters, B., Soest, J. V., Malic, A., Adekunle, O., ... Dumontier, M. (2018). Analyzing Partitioned FAIR Health Data Responsibly. arXiv , 1-6.
  11. Published
    Emonet, V., Zaveri, A., Malic, A., Grigoriu, A., & Dumontier, M. (2018). Data2Services: enabling automated conversion of data to services. In SWAT4LS
  12. Published
    Ta, C. N., Dumontier, M., Hripcsak, G., Tatonetti, N. P., & Weng, C. (2018). Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records. Scientific data, 5, [180273]. https://doi.org/10.1038/sdata.2018.273
  13. Published
    Coulet, A., Shah, N. H., Wack, M., Chawki, M. B., Jay, N., & Dumontier, M. (2018). Predicting the need for a reduced drug dose, at first prescription. Scientific Reports, 8, [15558]. https://doi.org/10.1038/s41598-018-33980-0
  14. Published
    Kuhn, T., Meroño-Peñuela, A., Malic, A., Poelen, J. H., Hurlbert, A. H., Ortiz, E. C., ... Dumontier, M. (2018). Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. In 2018 IEEE 14th International Conference on e-Science (e-Science) (pp. 83-92). (Proceedings of IEEE e-Science).
  15. Published
    Moodley, K., Hardi, J., Graybeal, J., Musen, M. A., & Dumontier, M. (2018). Assessing Schema.org's Coverage of Terms from Key Biomedical Datasets. Paper presented at Bio-Ontologies, Prague, Czech Republic.
  16. Published
    Wilkinson, M. D., Sansone, S-A., Schultes, E., Doorn, P., Santos, L. O. B. D. S., & Dumontier, M. (2018). A design framework and exemplar metrics for FAIRness: A design framework and exemplar metrics for FAIRness. Scientific data, 5, [180118]. https://doi.org/10.1038/sdata.2018.118
  17. Published
    Zhang, Y., Zheng, W., Lin, H., Wang, J., Yang, Z., & Dumontier, M. (2018). Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths. Bioinformatics, 34(5), 828-835. https://doi.org/10.1093/bioinformatics/btx659
  18. Published
    Garcia, A., Lopez, F., Garcia, L., Giraldo, O., Bucheli, V., & Dumontier, M. (2018). Biotea: semantics for Pubmed Central. PEERJ, 6, [e4201]. https://doi.org/10.7717/peerj.4201
  19. Published
    Moodley, K., Zaveri, A., Wu, C., & Dumontier, M. (2018). A model for capturing provenance of assertions about chemical substances. In C. J. O. Baker, A. Waagmeester, A. Splendiani, O. D. Beyan, & M. S. Marshall (Eds.), Semantic Web Applications and Tools for Health Care and Life Sciences (Vol. 2275). Antwerp, Belgium: CEUR-WS.org.
  20. Published
    Verborgh, R., & Dumontier, M. (2018). A Web API Ecosystem through Feature Based Reuse. Ieee Internet Computing, 22(3), 29-37. https://doi.org/10.1109/MIC.2018.032501515
  21. Published
    Zaveri, A., Serrano, P. H., Desai, M., & Dumontier, M. (2018). CrowdED: Guideline for Optimal Crowdsourcing Experimental Design. In Companion Proceedings of the The Web Conference 2018 (pp. 1109-1116). (WWW '18). Republic and Canton of Geneva, Switzerland: International World Wide Web Conferences Steering Committee. https://doi.org/10.1145/3184558.3191543
  22. Published
    Zaveri, A., Dumontier, M., & Nayak, S. (2018). Quality Assessment of Biomedical Metadata Using Topic Modeling. In Quality Assessment of Biomedical Metadata Using Topic Modeling.
  23. Published
    van Soest, J., Sun, C., Mussmann, O., Puts, M., van den Berg, B., Malic, A., ... Dumontier, M. (2018). Using the Personal Health Train for Automated and Privacy-Preserving Analytics on Vertically Partitioned Data. 581-585.
  24. 2017
  25. Published
    Nelson, S. J., Oprea, T. I., Ursu, O., Bologa, C. G., Zaveri, A., Holmes, J., ... Dumontier, M. (2017). Formalizing drug indications on the road to therapeutic intent. Journal of the American Medical Informatics Association, 24(6), 1169-1172. https://doi.org/10.1093/jamia/ocx064
  26. Published
    Hu, W., Zaveri, A., Qiu, H., & Dumontier, M. (2017). Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. BMC Bioinformatics, 18. https://doi.org/10.1186/s12859-017-1832-4
  27. Published
    Personeni, G., Bresso, E., Devignes, M-D., Dumontier, M., Smail-Tabbone, M., & Coulet, A. (2017). Discovering associations between adverse drug events using pattern structures and ontologies. Journal of biomedical semantics, 8. https://doi.org/10.1186/s13326-017-0137-x
  28. Published
    Hu, W., Qiu, H., Huang, J., & Dumontier, M. (2017). BioSearch: a semantic search engine for Bio2RDF. Database-The Journal of Biological Databases and Curation, 1-13. https://doi.org/10.1093/database/bax059
  29. Published
    Panahiazar, M., Dumontier, M., & Gevaert, O. (2017). Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO). Journal of Biomedical Informatics, 72, 132-139. https://doi.org/10.1016/j.jbi.2017.06.017
  30. Published
    Moodley, K., Rieswijk, L., Oprea, T. I., & Dumontier, M. (2017). Assessing the quality of manually curated drug indication and usage information via ontology term mappings. Paper presented at Bio-Ontologies, Prague, Czech Republic.
  31. Published
    Jagodnik, K. M., Koplev, S., Jenkins, S., Ohno-Machado, L., Paten, B., Schurer, S. C., ... Ma'ayan, A. (2017). Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Informatics, 71, 49-57. https://doi.org/10.1016/j.jbi.2017.05.006
  32. Published
    McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., ... Parkinson, H. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biology , 15(6), [ e2001414]. https://doi.org/10.1371/journal.pbio.2001414
  33. Published
    Fajardo-Ortiz, D., Lopez-Cervantes, M., Duran, L., Dumontier, M., Lara, M., Ochoa, H., & Castano, V. M. (2017). The emergence and evolution of the research fronts in HIV/AIDS research. PLOS ONE, 12(5), e0178293. [0178293]. https://doi.org/10.1371/journal.pone.0178293
  34. Noor, A., Assiri, A., Ayvaz, S., Clark, C., & Dumontier, M. (2017). Drug-drug interaction discovery and demystification using Semantic Web technologies. Journal of the American Medical Informatics Association, 24(3), 556-564. https://doi.org/10.1093/jamia/ocw128
  35. Published
    Zaveri, A., Dastgheib, S., Whetzel, T., Verborgh, R., Avillach, P., Korodi, G., ... Dumontier, M. (2017). smartAPI: Towards a more intelligent network of Web APIs. In E. Blomqvist, D. Maynard, A. Gangemi, R. Hoekstra, P. Hitzler, & O. Hartig (Eds.), Proceedings of the 14th ESWC (Vol. 10250, pp. 154-169). (Lecture Notes in Computer Science). Springer. https://doi.org/10.1007/978-3-319-58451-5_11
  36. Published
    Wilkinson, M. D., Verborgh, R., Santos, L. O. B. D. S., Clark, T., Swertz, M. A., Kelpin, F. D. L., ... Dumontier, M. (2017). Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Computer Science. https://doi.org/10.7717/peerj-cs.110
  37. Boyce, R. D., Voss, E. A., Huser, V., Evans, L., Reich, C., Duke, J. D., ... Ryan, P. B. (2017). Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. Journal of biomedical semantics, 8. https://doi.org/10.1186/s13326-017-0115-3
  38. McCusker, J. P., Dumontier, M., Yan, R., He, S., Dordick, J. S., & McGuinness, D. L. (2017). Finding melanoma drugs through a probabilistic knowledge graph. PeerJ Computer Science, 3, e106. [106]. https://doi.org/10.7717/peerj-cs.106
  39. Published
    Mons, B., Neylon, C., Velterop, J., Dumontier, M., Da Silva Santos, L. O. B., & Wilkinson, M. D. (2017). Cloudy, increasingly FAIR; Revisiting the FAIR Data guiding principles for the European Open Science Cloud. Information Services and Use, 37(1), 49-56. https://doi.org/10.3233/ISU-170824
  40. McMurry, J., Juty, N., Blomberg, N., Burdett, A., Conlin, T., Conte, N., ... Parkinson, H. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. bioRxiv. https://doi.org/10.1101/117812
  41. Published
    Celebi, R., Erten, O., & Dumontier, M. (2017). Machine Learning based Drug Indication Prediction using Linked Open Data. In 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences
  42. Published
    Zaveri, A., & Dumontier, M. (2017). MetaCrowd: Crowdsourcing Biomedical Metadata Quality Assessment.. Paper presented at Bio-Ontologies, Prague, Czech Republic.
  43. Published
    He, Z., Tao, C., Bian, J., Dumontier, M., & Hogan, W. R. (2017). Semantics-Powered Healthcare Engineering and Data Analytics. Journal of Healthcare Engineering. https://doi.org/10.1155/2017/7983473
  44. Published
    Dastgheib, S., Whetzel, T., Zaveri, A., Afrasiabe, C., Assis, P., Availlach, P., ... Dumontier, M. (2017). The smartAPI ecosystem for making Web APIs FAIR. In The smartAPI ecosystem for making web APIs FAIR (Vol. 1931, pp. 1-4)
  45. 2016
  46. Verspoor, K., Oellrich, A., Collier, N., Groza, T., Rocca-Serra, P., Soldatova, L., ... Shah, N. (2016). Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. Journal of biomedical semantics, 7, [66]. https://doi.org/10.1186/s13326-016-0108-7
  47. Sieberts, S. K., Zhu, F., García-García, J., Stahl, E. A., Pratap, A., Pandey, G., ... Members of the Rheumatoid Arthritis Challenge Consortium (2016). Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7, 13205. [13205]. https://doi.org/10.1038/ncomms13205
  48. Published
    Verborgh, R., & Dumontier, M. (2016). A Web API ecosystem through feature-based reuse. arXiv , (1609.07108).
  49. Oellrich, A., Collier, N., Groza, T., Rebholz-Schuhmann, D., Shah, N., Bodenreider, O., ... Dumontier, M. (2016). The digital revolution in phenotyping. Briefings in Bioinformatics, 17(5), 819-830. https://doi.org/10.1093/bib/bbv083
  50. Sieberts, S. K., Zhu, F., García-García, J., Stahl, E. A., Pratap, A., Pandey, G., ... Mangravite, L. M. (2016). Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7, 12460. [12460]. https://doi.org/10.1038/ncomms12460
  51. Published
    Dumontier, M., Gray, A. J. G., Marshall, M. S., Alexiev, V., Ansell, P., Bader, G., ... Yamaguchi, A. (2016). The health care and life sciences community profile for dataset descriptions. PEERJ, 4, [2331]. https://doi.org/10.7717/peerj.2331
  52. Bolleman, J. T., Mungall, C. J., Strozzi, F., Baran, J., Dumontier, M., Bonnal, R. J. P., ... Cock, P. J. A. (2016). FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. Journal of biomedical semantics, 7, [39]. https://doi.org/10.1186/s13326-016-0067-z
  53. Posch, L., Panahiazar, M., Dumontier, M., & Gevaert, O. (2016). Predicting structured metadata from unstructured metadata. Database-The Journal of Biological Databases and Curation, [baw097]. https://doi.org/10.1093/database/baw097
  54. Leung, T. I., & Dumontier, M. (2016). Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications. Journal of biomedical semantics, 7, [37]. https://doi.org/10.1186/s13326-016-0081-1
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