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Research Output

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Article
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

2008

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

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

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

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

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

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

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

Chepelev, L. L., Riazanov, A., Kouznetsov, A., Low, H. S., Dumontier, M. & Baker, C. J. O., 26 Jul 2011, In : BMC Bioinformatics. 12, 303.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Semantic Web integration of Cheminformatics resources with the SADI framework

Chepelev, L. L. & Dumontier, M., 16 May 2011, In : Journal of Cheminformatics. 3, 16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Taking flight with OWL2

Dumontier, M., 2011, In : Semantic web. 2, 2, p. 67-70

Research output: Contribution to journalArticleAcademicpeer-review

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

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Hoehndorf, R., Batchelor, C., Bittner, T., Dumontier, M., Eilbeck, K., Knight, R., Mungall, C. J., Richardson, J. S., Stombaugh, J., Westhof, E., Zirbel, C. L. & Leontis, N. B., 2011, In : Applied Ontology. 6, 1, p. 53-89

Research output: Contribution to journalArticleAcademicpeer-review

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

Luciano, J. S., Andersson, B., Batchelor, C., Bodenreider, O., Clark, T., Denney, C. K., Domarew, C., Gambet, T., Harland, L., Jentzsch, A., Kashyap, V., Kos, P., Kozlovsky, J., Lebo, T., Marshall, M. S., McCusker, J. P., McGuinness, D. L., Ogbuji, C., Pichler, E., Powers, R. L. & 8 others, Prud'hommeaux, E., Samwald, M., Schriml, L., Tonellato, P. J., Whetzel, P. L., Zhao, J., Stephens, S. & Dumontier, M., 17 May 2011, In : Journal of biomedical semantics. 2 Suppl 2, p. S1

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Towards an interoperable information infrastructure providing decision support for genomic medicine

Samwald, M., Stenzhorn, H., Dumontier, M., Marshall, M. S., Luciano, J. S. & Adlassnig, K-P., 2011, In : Studies in Health Technology and Informatics. 169, p. 165-9 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

2012

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments

Cruz-Toledo, J., McKeague, M., Zhang, X., Giamberardino, A., McConnell, E., Francis, T., DeRosa, M. C. & Dumontier, M., 20 Mar 2012, In : Database-The Journal of Biological Databases and Curation. bas006.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Building an HIV data mashup using Bio2RDF

Nolin, M-A., Dumontier, M., Belleau, F. & Corbeil, J., Jan 2012, In : Briefings in Bioinformatics. 13, 1, p. 98-106

Research output: Contribution to journalArticleAcademicpeer-review

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics

Hoehndorf, R., Dumontier, M. & Gkoutos, G. V., 15 Aug 2012, In : Bioinformatics. 28, 16, p. 2169-2175

Research output: Contribution to journalArticleAcademicpeer-review

Linked Data in Drug Discovery

Dumontier, M. & Wild, D. J., 2012, In : Ieee Internet Computing. 16, 6, p. 68-71

Research output: Contribution to journalArticleAcademicpeer-review

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Soldatova, L. N., Sansone, S-A., Dumontier, M. & Shah, N. H., 24 Apr 2012, In : Journal of biomedical semantics. 3 Suppl 1, p. I1

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Self-organizing ontology of biochemically relevant small molecules

Chepelev, L. L., Hastings, J., Ennis, M., Steinbeck, C. & Dumontier, M., 6 Jan 2012, In : BMC Bioinformatics. 13, 3.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Semantically enabling pharmacogenomic data for the realization of personalized medicine

Samwald, M., Coulet, A., Huerga, I., Powers, R. L., Luciano, J. S., Freimuth, R. R., Whipple, F., Pichler, E., Prud'hommeaux, E., Dumontier, M. & Marshall, M. S., Jan 2012, In : Pharmacogenomics. 13, 2, p. 201-212

Research output: Contribution to journalArticleAcademicpeer-review

2013

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics

Samwald, M., Freimuth, R. R., Luciano, J. S., Lin, S. M., Powers, R. L., Marshall, M. S., Adlassnig, K-P., Dumontier, M. & Boyce, R. D., 2013, In : Studies in Health Technology and Informatics. 192, p. 539-542 4 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Evaluation of research in biomedical ontologies

Hoehndorf, R., Dumontier, M. & Gkoutos, G. V., Nov 2013, In : Briefings in Bioinformatics. 14, 6, p. 696-712

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Evaluation of the OQuaRE framework for ontology quality

Duque-Ramos, A., Tomas Fernandez-Breis, J., Iniesta, M., Dumontier, M., Egana Aranguren, M., Schulz, S., Aussenac-Gilles, N. & Stevens, R., 1 Jun 2013, In : Expert Systems with Applications. 40, 7, p. 2696-2703

Research output: Contribution to journalArticleAcademicpeer-review

Ontology-Based Querying with Bio2RDF's Linked Open Data

Callahan, A., Cruz-Toledo, J. & Dumontier, M., 15 Apr 2013, In : Journal of biomedical semantics. 4 Suppl 1, p. S1

Research output: Contribution to journalArticleAcademicpeer-review

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

Soldatova, L. N., Sansone, S-A., Dumontier, M. & Shah, N. H., 15 Apr 2013, In : Journal of biomedical semantics. 4 Suppl 1, p. I1

Research output: Contribution to journalArticleAcademicpeer-review

State of the art and open challenges in community-driven knowledge curation

Groza, T., Tudorache, T. & Dumontier, M., Feb 2013, In : Journal of Biomedical Informatics. 46, 1, p. 1-4

Research output: Contribution to journalArticleAcademicpeer-review

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions

Vandervalk, B., McCarthy, E. L., Cruz-Toledo, J., Klein, A., Baker, C. J. O., Dumontier, M. & Wilkinson, M. D., 5 Apr 2013, In : JMIR Research Protocols. 2, 1, p. e14

Research output: Contribution to journalArticleAcademicpeer-review