Michel J. Dumontier, Ph.D. - Publications

Affiliations: 
2004 University of Toronto, Toronto, ON, Canada 
Area:
Biochemistry

51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, ... ... Dumontier M, et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications. 7: 12460. PMID 27549343 DOI: 10.1038/Ncomms12460  0.52
2016 Leung TI, Dumontier M. Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications. Journal of Biomedical Semantics. 7: 37. PMID 27277160 DOI: 10.1186/S13326-016-0081-1  0.52
2016 Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, et al. The Ontology for Biomedical Investigations. Plos One. 11: e0154556. PMID 27128319 DOI: 10.1371/Journal.Pone.0154556  0.52
2016 Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, et al. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 3: 160018. PMID 26978244 DOI: 10.1038/Sdata.2016.18  0.52
2016 Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Van Auken K, Dumontier M, Musen MA. Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. Journal of Biomedical Informatics. PMID 26873781 DOI: 10.1016/J.Jbi.2016.02.005  0.52
2015 Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH. Special issue on bio-ontologies and phenotypes. Journal of Biomedical Semantics. 6: 40. PMID 26682035 DOI: 10.1186/S13326-015-0040-2  0.52
2015 McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC. Analysis of In Vitro Aptamer Selection Parameters. Journal of Molecular Evolution. PMID 26530075 DOI: 10.1007/S00239-015-9708-6  0.52
2015 Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O'Connor MJ, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA. The center for expanded data annotation and retrieval. Journal of the American Medical Informatics Association : Jamia. PMID 26112029 DOI: 10.1093/Jamia/Ocv048  0.52
2015 Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M. GFVO: the Genomic Feature and Variation Ontology. Peerj. 3: e933. PMID 26019997 DOI: 10.7717/Peerj.933  0.52
2015 Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD. Toward a complete dataset of drug-drug interaction information from publicly available sources. Journal of Biomedical Informatics. 55: 206-17. PMID 25917055 DOI: 10.1016/J.Jbi.2015.04.006  0.52
2015 Samwald M, Miñarro Giménez JA, Boyce RD, Freimuth RR, Adlassnig KP, Dumontier M. Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies. Bmc Medical Informatics and Decision Making. 15: 12. PMID 25880555 DOI: 10.1186/S12911-015-0130-1  0.52
2015 Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. SPARQL-enabled identifier conversion with Identifiers.org. Bioinformatics (Oxford, England). 31: 1875-7. PMID 25638809 DOI: 10.1093/Bioinformatics/Btv064  0.52
2015 Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, ... ... Dumontier M, et al. Finding our way through phenotypes. Plos Biology. 13: e1002033. PMID 25562316 DOI: 10.1371/Journal.Pbio.1002033  0.52
2015 Gottlieb A, Hoehndorf R, Dumontier M, Altman RB. Ranking adverse drug reactions with crowdsourcing Journal of Medical Internet Research. 17. DOI: 10.2196/jmir.3962  0.52
2014 Boyce RD, Ryan PB, Norén GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifirò G, Harpaz R, Overhage JM, Hartzema AG, Khayter M, Voss EA, Lambert CG, Huser V, ... Dumontier M, et al. Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. Drug Safety. 37: 557-67. PMID 24985530 DOI: 10.1007/S40264-014-0189-0  0.52
2014 Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, et al. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. Journal of Biomedical Semantics. 5: 14. PMID 24602174 DOI: 10.1186/2041-1480-5-14  0.52
2014 Soldatova LN, Rocca-Serra P, Dumontier M, Shah NH. Selected papers from the 16th annual Bio-Ontologies Special Interest Group Meeting Journal of Biomedical Semantics. 5. DOI: 10.1186/2041-1480-5-S1-I1  0.52
2013 Samwald M, Freimuth R, Luciano JS, Lin S, Powers RL, Marshall MS, Adlassnig KP, Dumontier M, Boyce RD. An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. Studies in Health Technology and Informatics. 192: 539-42. PMID 23920613 DOI: 10.3233/978-1-61499-289-9-539  0.52
2012 Cruz-Toledo J, McKeague M, Zhang X, Giamberardino A, McConnell E, Francis T, DeRosa MC, Dumontier M. Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database : the Journal of Biological Databases and Curation. 2012: bas006. PMID 22434840 DOI: 10.1093/Database/Bas006  0.52
2012 Samwald M, Coulet A, Huerga I, Powers RL, Luciano JS, Freimuth RR, Whipple F, Pichler E, Prud'hommeaux E, Dumontier M, Marshall MS. Semantically enabling pharmacogenomic data for the realization of personalized medicine. Pharmacogenomics. 13: 201-12. PMID 22256869 DOI: 10.2217/Pgs.11.179  0.52
2012 Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M. Self-organizing ontology of biochemically relevant small molecules. Bmc Bioinformatics. 13: 3. PMID 22221313 DOI: 10.1186/1471-2105-13-3  0.52
2012 Callahan A, Dumontier M. Evaluating scientific hypotheses using the SPARQL inferencing notation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7295: 647-658. DOI: 10.1007/978-3-642-30284-8_50  0.52
2011 Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, et al. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 7: 543. PMID 22027554 DOI: 10.1038/Msb.2011.77  0.52
2011 Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. Plos One. 6: e25513. PMID 21991315 DOI: 10.1371/Journal.Pone.0025513  0.52
2011 Samwald M, Stenzhorn H, Dumontier M, Marshall MS, Luciano J, Adlassnig KP. Towards an interoperable information infrastructure providing decision support for genomic medicine. Studies in Health Technology and Informatics. 169: 165-9. PMID 21893735 DOI: 10.3233/978-1-60750-806-9-165  0.52
2011 Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV. Integrating systems biology models and biomedical ontologies. Bmc Systems Biology. 5: 124. PMID 21835028 DOI: 10.1186/1752-0509-5-124  0.52
2011 Hoehndorf R, Dumontier M, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. Plos One. 6: e22006. PMID 21789201 DOI: 10.1371/Journal.Pone.0022006  0.52
2011 Callahan A, Dumontier M, Shah NH. HyQue: evaluating hypotheses using Semantic Web technologies. Journal of Biomedical Semantics. 2: S3. PMID 21624158 DOI: 10.1186/2041-1480-2-S2-S3  0.52
2011 Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, ... ... Dumontier M, et al. The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. Journal of Biomedical Semantics. 2: S1. PMID 21624155 DOI: 10.1186/2041-1480-2-S2-S1  0.52
2011 Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV. A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (Oxford, England). 27: 1001-8. PMID 21343142 DOI: 10.1093/Bioinformatics/Btr058  0.52
2011 Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, Zirbel CL, Leontis NB. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data Applied Ontology. 6: 53-89. DOI: 10.1038/Npre.2009.3561.1  0.52
2010 Samwald M, Dumontier M, Zhao J, Luciano JS, Marshall MS, Cheung K. Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data. Chinese Medicine. 5: 43. PMID 21167050 DOI: 10.1186/1749-8546-5-43  0.52
2010 Luo X, McKeague M, Pitre S, Dumontier M, Green J, Golshani A, Derosa MC, Dehne F. Computational approaches toward the design of pools for the in vitro selection of complex aptamers. Rna (New York, N.Y.). 16: 2252-62. PMID 20870801 DOI: 10.1261/Rna.2102210  0.52
2010 Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H. Relations as patterns: bridging the gap between OBO and OWL. Bmc Bioinformatics. 11: 441. PMID 20807438 DOI: 10.1186/1471-2105-11-441  0.52
2010 Cruz-Toledo J, Dumontier M, Parisien M, Major F. RKB: a Semantic Web knowledge base for RNA. Journal of Biomedical Semantics. 1: S2. PMID 20626922 DOI: 10.1186/2041-1480-1-S1-S2  0.52
2010 Mir-Rashed N, Cruz I, Jessulat M, Dumontier M, Chesnais C, Ng J, Amiguet VT, Golshani A, Arnason JT, Smith ML. Disruption of fungal cell wall by antifungal Echinacea extracts. Medical Mycology. 48: 949-58. PMID 20429770 DOI: 10.3109/13693781003767584  0.52
2010 Dumontier M, Ferres L, Villanueva-Rosales N. Modeling and querying graphical representations of statistical data Journal of Web Semantics. 8: 241-254. DOI: 10.1016/J.Websem.2009.12.002  0.52
2009 Dumontier M, Villanueva-Rosales N. Towards pharmacogenomics knowledge discovery with the semantic web Briefings in Bioinformatics. 10: 153-163. PMID 19240125 DOI: 10.1093/Bib/Bbn056  0.52
2009 Chepelev LL, Chepelev NL, Shadnia H, Willmore WG, Wright JS, Dumontier M. Development of Small-Molecule Ligands and Inhibitors Protein Targeting With Small Molecules: Chemical Biology Techniques and Applications. 115-147. DOI: 10.1002/9780470495018.ch7  0.52
2008 Pitre S, North C, Alamgir M, Jessulat M, Chan A, Luo X, Green JR, Dumontier M, Dehne F, Golshani A. Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic Acids Research. 36: 4286-94. PMID 18586826 DOI: 10.1093/Nar/Gkn390  0.52
2008 Villanueva-Rosales N, Dumontier M. yOWL: An ontology-driven knowledge base for yeast biologists Journal of Biomedical Informatics. 41: 779-789. PMID 18562252 DOI: 10.1016/J.Jbi.2008.05.001  0.52
2008 Pitre S, Alamgir M, Green JR, Dumontier M, Dehne F, Golshani A. Computational methods for predicting protein-protein interactions. Advances in Biochemical Engineering/Biotechnology. 110: 247-67. PMID 18202838 DOI: 10.1007/10_2007_089  0.52
2007 Ferres L, Dumontier M, Villanueva-Rosales N. Semantic query answering with time-series graphs Proceedings - Ieee International Enterprise Distributed Object Computing Workshop, Edoc. DOI: 10.1109/EDOCW.2007.28  0.52
2006 Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW. Domain-based small molecule binding site annotation. Bmc Bioinformatics. 7: 152. PMID 16545112 DOI: 10.1186/1471-2105-7-152  0.52
2005 Feldman HJ, Dumontier M, Ling S, Haider N, Hogue CW. CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. Febs Letters. 579: 4685-91. PMID 16098521 DOI: 10.1016/J.Febslet.2005.07.039  0.6
2005 Dumontier M, Yao R, Feldman HJ, Hogue CW. Armadillo: domain boundary prediction by amino acid composition. Journal of Molecular Biology. 350: 1061-73. PMID 15978619 DOI: 10.1016/J.Jmb.2005.05.037  0.6
2005 Alex AT, Dumontier M, Rose JS, Hogue CW. Hardware-accelerated protein identification for mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 19: 833-7. PMID 15723443 DOI: 10.1002/Rcm.1853  0.52
2005 Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, ... Dumontier MJ, ... ... Dumontier MR, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Research. 33: D418-24. PMID 15608229 DOI: 10.1093/Nar/Gki051  0.52
2002 Dumontier M, Michalickova K, Hogue CW. Species-specific protein sequence and fold optimizations. Bmc Bioinformatics. 3: 39. PMID 12487631 DOI: 10.1186/1471-2105-3-39  0.6
2002 Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW. SeqHound: biological sequence and structure database as a platform for bioinformatics research. Bmc Bioinformatics. 3: 32. PMID 12401134 DOI: 10.1186/1471-2105-3-32  0.6
2002 Dumontier M, Hogue CW. NBLAST: a cluster variant of BLAST for NxN comparisons. Bmc Bioinformatics. 3: 13. PMID 12019022 DOI: 10.1186/1471-2105-3-13  0.6
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