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Research Output

1998

3D topography of noncompact zone Golgi tubules in rat spermatids: A computer-assisted serial section reconstruction study

Thorne-Tjomsland, G., Dumontier, M. & Jamieson, JC., Apr 1998, In : ANATOMICAL RECORD. 250, 4, p. 381-396

Research output: Contribution to journalArticleAcademicpeer-review

2000

Rac1 GTPases control filopodia formation, cell motility, endocytosis, cytokinesis and development in Dictyostelium

Dumontier, M., Hocht, P., Mintert, U. & Faix, J., Jun 2000, In : Journal of Cell Science. 113, 12, p. 2253-2265

Research output: Contribution to journalArticleAcademicpeer-review

2002

NBLAST: a cluster variant of BLAST for NxN comparisons

Dumontier, M. & Hogue, CWV., 2002, In : BMC Bioinformatics. 3, 13.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

SeqHound: biological sequence and structure database as a platform for bioinformatics research

Michalickova, K., Bader, G. D., Dumontier, M., Lieu, H., Betel, D., Isserlin, R. & Hogue, CWV., 2002, In : BMC Bioinformatics. 3, 32.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Species-specific protein sequence and fold optimizations

Dumontier, M., Michalickova, K. & Hogue, CWV., 2002, In : BMC Bioinformatics. 3, 39.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2005

Armadillo: Domain boundary prediction by amino acid composition

Dumontier, M., Yao, R., Feldman, HJ. & Hogue, CWV., 29 Jul 2005, In : Journal of Molecular Biology. 350, 5, p. 1061-1073

Research output: Contribution to journalArticleAcademicpeer-review

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules

Feldman, HJ., Dumontier, M., Sue-Ling, H. M., Haider, N. & Hogue, CWV., 29 Aug 2005, In : Febs Letters. 579, 21, p. 4685-4691

Research output: Contribution to journalArticleAcademicpeer-review

Hardware-accelerated protein identification for mass spectrometry

Alex, AT., Dumontier, M., Rose, JS. & Hogue, CWV., 2005, In : Rapid Communications in Mass Spectrometry. 19, 6, p. 833-837

Research output: Contribution to journalArticleAcademicpeer-review

The Biomolecular Interaction Network Database and related tools 2005 update

Alfarano, C., Andrade, CE., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., Betel, D., Bobechko, B., Boutilier, K., Burgess-Wilson, M. E., Buzadzija, K., Cavero, R., D'Abreo, C., Donaldson, I., Dorairajoo, D., Dumontier, MR., Dumontier, MR., Earles, V., Farrall, R., Feldman, H. H. & 55 others, Garderman, E., Gong, Y., Gonzaga, R., Grytsan, V., Gryz, E., Gu, V., Haldorsen, E., Halupa, A., Haw, R., Hrvojic, A., Hurrell, L., Isserlin, R., Jack, F., Juma, F., Khan, A., Tjon-Kon-Fat, R. I., Konopinsky, S., Van Le, L., Lee, E. H. M., Sue-Ling, H. M., Magidin, M., Moniakis, J., Montojo, J., Moore, C. S., Muskat, B., Ng, I., Paraiso, JP., Parker, B., Pintilie, G., Pirone, R., Salama, JJ., Sgro, S., Shan, T., Shu, S-Y., Siew, J., Skinner, D., Snyder, K., Stasiuk, R., Strumpf, D., Tuekam, B., Tao, S., Wang, Z., White, M., Willis, R., Wolting, C., Wong, S., Wrong, A., Xin, C., Yao, R., Yates, B., Zhang, S., Zheng, K., Pawson, T., Ouellette, BFF. & Hogue, CWV., 1 Jan 2005, In : Nucleic Acids Research. 33, p. D418-D424

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2006

Domain-based small molecule binding site annotation

Snyder, K. A., Feldman, H. J., Dumontier, M., Salama, J. J. & Hogue, C. W. V., 17 Mar 2006, In : BMC Bioinformatics. 7, p. 152

Research output: Contribution to journalArticleAcademicpeer-review

2007

A stochastic particle-based biological system simulator

Boulianne, L., Dumontier, M. & Gross, W. J., 2007, SCSC '07: Proceedings of the 2007 Summer Computer Simulation Conference. Society for Computer Simulation, p. 794-801 8 p.

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

Describing chemical functional groups in OWL-DL for the classification of chemical compounds

Villanueva-Rosales, N. & Dumontier, M., 2007, In : CEUR Workshop Proceedings. 258, 10 p., 22.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Semantic query answering with time-series graphs

Ferres, L., Dumontier, M. & Villanueva-Rosales, N., 2007, 2007 Eleventh International IEEE EDOC Conference Workshop. IEEE

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

SMART: A web-based, ontology-driven, semantic web query answering application

De Leon Battista, A., Villanueva-Rosales, N., Palenychka, M. & Dumontier, M., 2007, In : CEUR Workshop Proceedings. 295, 8 p., 17.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Three-layer OWL ontology design

Dumontier, M. & Villanueva-Rosales, N., 2007, In : CEUR Workshop Proceedings. 315, 6 p., 3.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access
2008

Chemical knowledge for the semantic web

Konyk, M., Leon, AS. & Dumontier, M., 2008, Data Integration in the Life Sciences: 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008. Proceedings. Springer, p. 169-176 8 p. (Lecture Notes in Computer Science, Vol. 5109).

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

Computational Methods For Predicting Protein-Protein Interactions

Pitre, S., Alamgir, M., Green, J. R., Dumontier, M., Dehne, F. & Golshani, A., 2008, PROTEIN - PROTEIN INTERACTION. Vol. 110. p. 247-267 (Advances in Biochemical Engineering-Biotechnology).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences

Pitre, S., North, C., Alamgir, M., Jessulat, M., Chan, A., Luo, X., Green, J. R., Dumontier, M., Dehne, F. & Golshani, A., Aug 2008, In : Nucleic Acids Research. 36, 13, p. 4286-4294

Research output: Contribution to journalArticleAcademicpeer-review

GridCell: a stochastic particle-based biological system simulator

Boulianne, L., Al Assaad, S., Dumontier, M. & Gross, W. J., 23 Jul 2008, In : BMC Systems Biology. 2

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Report on semantic web for health care and life sciences workshop

Chen, H., Cheung, K., Dumontier, M., Prud'hommeaux, E., Ruttenberg, A., Stephens, S. & Wang, Y., 2008, Proceedings of the 17th International Conference on World Wide Web 2008, WWW'08. Association for Computing Machinery (ACM), p. 1273-1274 2 p. (Proceeding of the 17th International Conference on World Wide Web 2008, WWW'08).

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

Semantic annotation and question answering of statistical graphs

Dumontier, M., Ferres, L. & Villanueva-Rosales, N., 2008, MICAI 2008: Advances in Artificial Intelligence: 7th Mexican International Conference on Artificial Intelligence, Atizapán de Zaragoza, Mexico, October 27-31, 2008 Proceedings. Springer, p. 100-110 11 p. (Lecture Notes in Computer Science, Vol. 5317).

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

yOWL: An ontology-driven knowledge base for yeast biologists

Villanueva-Rosales, N. & Dumontier, M., Oct 2008, In : Journal of Biomedical Informatics. 41, 5, p. 779-789

Research output: Contribution to journalArticleAcademicpeer-review

2009

A platform for distributing and reasoning with owl-el knowledge bases in a peer-to-peer environment

Leon, AS. & Dumontier, M., 2009, In : CEUR Workshop Proceedings. 529, 8 p., 24.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Conjunctive query answering in distributed ontology systems for ontologies with large OWL ABoxes

Chen, X. & Dumontier, M., 2009, In : CEUR Workshop Proceedings. 529, 4 p., 30.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Development of Small-Molecule Ligands and Inhibitors

Chepelev, L., Chepelev, N. L., Shadnia, H., Willmore, W. G., Wright, J. S. & Dumontier, M., 2009, Protein Targeting with Small Molecules: Chemical Biology Techniques and Applications. Osada, H. (ed.). John Wiley & Sons, p. 115-147 33 p.

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Modeling life science knowledge with OWL 1.1

Dumontier, M. & Villanueva-Rosales, N., 2009, In : CEUR Workshop Proceedings. 496, 10 p., 14.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Modeling tryptic digestion on the Cell BE processor

Green, J. R., Mahmoud, H. & Dumontier, M., 2009, 2009 Canadian Conference on Electrical and Computer Engineering: "From Electrons to Oceans: Innovation at Many Scales," May 3-6, 2009, Newfoundland & Labrador, Canada. IEEE, p. 701-705 5 p. (Canadian Conference on Electrical and Computer Engineering).

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

Publishing owl ontologies with Presto

DeLeon, A. & Dumontier, M., 2009, In : CEUR Workshop Proceedings. 496, 9 p., 13.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Situational modeling: Defining molecular roles in biochemical pathways and reactions

Dumontier, M., 2009, In : CEUR Workshop Proceedings. 432, 12 p., 13.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Target Profiling of Small Molecules

Chepelev, L. & Dumontier, M., 2009, Protein Targeting with Small Molecules: Chemical Biology Techniques and Applications. John Wiley & Sons, p. 11-38 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

Towards pharmacogenomics knowledge discovery with the semantic web

Dumontier, M. & Villanueva-Rosales, N., Mar 2009, In : Briefings in Bioinformatics. 10, 2, p. 153-163

Research output: Contribution to journalArticleAcademicpeer-review

2010

Building an effective Semantic Web for health care and the life sciences

Dumontier, M., 2010, In : Semantic web. 1, 1-2, p. 131-135 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

Luo, X., McKeague, M., Pitre, S., Dumontier, M., Green, J., Golshani, A., Derosa, M. C. & Dehne, F., Nov 2010, In : Rna-A Publication of the Rna Society. 16, 11, p. 2252-2262

Research output: Contribution to journalArticleAcademicpeer-review

Disruption of fungal cell wall by antifungal Echinacea extracts

Mir-Rashed, N., Cruz, I., Jessulat, M., Dumontier, M., Chesnais, C., Ng, J., Amiguet, V. T., Golshani, A., Arnason, J. T. & Smith, M. L., Nov 2010, In : Medical Mycology. 48, 7, p. 949-958

Research output: Contribution to journalArticleAcademicpeer-review

Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data

Samwald, M., Dumontier, M., Zhao, J., Luciano, J. S., Marshall, M. S. & Cheung, K., 17 Dec 2010, In : Chinese Medicine. 5, p. 43

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Modeling and querying graphical representations of statistical data

Dumontier, M., Ferres, L. & Villanueva-Rosales, N., Jul 2010, In : Journal of Web Semantics. 8, 2-3, p. 241-254

Research output: Contribution to journalArticleAcademicpeer-review

Realism for scientific ontologies

Dumontier, M. & Hoehndorf, R., 2010, Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS 2010) . Galton, A. & Mizoguchi, R. (eds.). ACM, p. 387-399 13 p. (Frontiers in Artificial Intelligence and Applications, Vol. 209).

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

Relational patterns in OWL and their application to OBO

Hoehndorf, R., Oellrich, A., Dumontier, M., Kelso, J., Herre, H. & Rebholz Schuhmann, D., 2010, In : CEUR Workshop Proceedings. 614, 10 p., 1.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

Relations as patterns: bridging the gap between OBO and OWL

Hoehndorf, R., Oellrich, A., Dumontier, M., Kelso, J., Rebholz-Schuhmann, D. & Herre, H., 31 Aug 2010, In : BMC Bioinformatics. 11

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Representing chemicals using OWL, description graphs and rules

Hastings, J., Dumontier, M., Hull, D., Horridge, M., Steinbeck, C., Sattler, U., Stevens, R., Hörne, T. & Britz, K., 2010, In : CEUR Workshop Proceedings. 614, 10 p., 2.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

RKB: a Semantic Web knowledge base for RNA

Cruz-Toledo, J., Dumontier, M., Parisien, M. & Major, F., 22 Jun 2010, In : Journal of biomedical semantics. 1 Suppl 1, p. S2

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2011

A common layer of interoperability for biomedical ontologies based on OWL EL

Hoehndorf, R., Dumontier, M., Oellrich, A., Wimalaratne, S., Rebholz-Schuhmann, D., Schofield, P. & Gkoutos, G. V., 1 Apr 2011, In : Bioinformatics. 27, 7, p. 1001-1008

Research output: Contribution to journalArticleAcademicpeer-review

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration

Chepelev, L. L. & Dumontier, M., 19 May 2011, In : Journal of Cheminformatics. 3, 20.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Controlled vocabularies and semantics in systems biology

Courtot, M., Juty, N., Knuepfer, C., Waltemath, D., Zhukova, A., Draeger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., Hoops, S., Keating, S., Kell, D. B., Kerrien, S., Lawson, J., Lister, A., Lu, J., Machne, R., Mendes, P., Pocock, M. & 7 others, Rodriguez, N., Villeger, A., Wilkinson, D. J., Wimalaratne, S., Laibe, C., Hucka, M. & Le Novere, N., Oct 2011, In : Molecular Systems Biology. 7

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Hazard estimation and method comparison with OWL-encoded toxicity decision trees

Chepelev, L., Klassen, D. & Dumontier, M., 2011, In : CEUR Workshop Proceedings. 796, 10 p., 1.

Research output: Contribution to journalConference article in journalAcademicpeer-review

Open Access

HyQue: evaluating hypotheses using Semantic Web technologies

Callahan, A., Dumontier, M. & Shah, N. H., 17 May 2011, In : Journal of biomedical semantics. 2 Suppl 2, p. S3

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Integrating systems biology models and biomedical ontologies

Hoehndorf, R., Dumontier, M., Gennari, J. H., Wimalaratne, S., de Bono, B., Cook, D. L. & Gkoutos, G. V., 11 Aug 2011, In : BMC Systems Biology. 5, 124.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Integration and publication of heterogeneous text-mined relationships on the Semantic Web

Coulet, A., Garten, Y., Dumontier, M., Altman, R. B., Musen, M. A. & Shah, N. H., 17 May 2011, In : Journal of biomedical semantics. 2 Suppl 2, p. S10

Research output: Contribution to journalArticleAcademicpeer-review

Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning

Hoehndorf, R., Dumontier, M., Oellrich, A., Rebholz-Schuhmann, D., Schofield, P. N. & Gkoutos, G. V., 18 Jul 2011, In : PLOS ONE. 6, 7, e22006.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets

Gawronski, A. & Dumontier, M., Aug 2011, In : Computers & Graphics. 35, 4, p. 823-830

Research output: Contribution to journalArticleAcademicpeer-review