Michel Dumontier

Michel Dumontier

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Michel Dumontier

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Putting FAIR Evidence into Practice.

J Gen Intern Med 2019 Aug;34(8):1369

Institute of Data Science, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1007/s11606-019-05021-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667602PMC
August 2019

FAIR Principles for Clinical Practice Guidelines in a Learning Health System.

Stud Health Technol Inform 2019 Aug;264:1690-1691

Institute of Data Science, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.3233/SHTI190599DOI Listing
August 2019

Semantics-Powered Healthcare Engineering and Data Analytics.

J Healthc Eng 2017 26;2017:7983473. Epub 2017 Oct 26.

Department of Health Outcomes and Policy, University of Florida, Gainesville, FL, USA.

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https://www.hindawi.com/journals/jhe/2017/7983473/
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http://dx.doi.org/10.1155/2017/7983473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5682067PMC
July 2019

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data.

Sci Rep 2019 Jun 20;9(1):8949. Epub 2019 Jun 20.

Maastricht University, Institute of Data Science, Maastricht, Netherlands.

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http://dx.doi.org/10.1038/s41598-019-45236-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586895PMC
June 2019

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records.

Sci Data 2018 11 27;5:180273. Epub 2018 Nov 27.

Department of Biomedical Informatics, Columbia University, NY, USA.

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http://dx.doi.org/10.1038/sdata.2018.273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6257042PMC
November 2018

Predicting the need for a reduced drug dose, at first prescription.

Sci Rep 2018 10 22;8(1):15558. Epub 2018 Oct 22.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA.

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http://www.nature.com/articles/s41598-018-33980-0
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http://dx.doi.org/10.1038/s41598-018-33980-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197198PMC
October 2018

Using the Personal Health Train for Automated and Privacy-Preserving Analytics on Vertically Partitioned Data.

Stud Health Technol Inform 2018 ;247:581-585

Institute of Data Science, Maastricht University, Maastricht, The Netherlands.

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June 2018

A design framework and exemplar metrics for FAIRness.

Sci Data 2018 06 26;5:180118. Epub 2018 Jun 26.

Institute of Data Science, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1038/sdata.2018.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018520PMC
June 2018

Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths.

Bioinformatics 2018 03;34(5):828-835

Institute of Data Science, Maastricht University, Maastricht, 6229 ER, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btx659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030919PMC
March 2018

Biotea: semantics for Pubmed Central.

PeerJ 2018 2;6:e4201. Epub 2018 Jan 2.

Maastricht University, Institute of Data Science, Maastricht, The Netherlands.

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http://dx.doi.org/10.7717/peerj.4201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755483PMC
January 2018

The emergence and evolution of the research fronts in HIV/AIDS research.

PLoS One 2017 25;12(5):e0178293. Epub 2017 May 25.

Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Queretaro, Mexico.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178293PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444800PMC
September 2017

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata.

BMC Bioinformatics 2017 Sep 18;18(1):415. Epub 2017 Sep 18.

Institute of Data Science, Maastricht University, Maastricht, 6200, MD, The Netherlands.

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http://dx.doi.org/10.1186/s12859-017-1832-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604298PMC
September 2017

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

J Biomed Inform 2017 08 16;72:132-139. Epub 2017 Jun 16.

Stanford Center for Biomedical Informatics Research, Center for Data Annotation and Retrieval, Department of Medicine, Stanford University, Stanford, 94305, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2017.06.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643580PMC
August 2017

Discovering associations between adverse drug events using pattern structures and ontologies.

J Biomed Semantics 2017 Aug 22;8(1):29. Epub 2017 Aug 22.

LORIA (CNRS, Inria NGE, Université de Lorraine), Campus Scientifique, Vandœuvre-lès-Nancy, F-54506, France.

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http://dx.doi.org/10.1186/s13326-017-0137-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567667PMC
August 2017

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

J Biomed Inform 2017 07 10;71:49-57. Epub 2017 May 10.

Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2017.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5545976PMC
July 2017

Drug-drug interaction discovery and demystification using Semantic Web technologies.

J Am Med Inform Assoc 2017 May;24(3):556-564

Stanford Center for Biomedical Informatics Research, Stanford, California.

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http://dx.doi.org/10.1093/jamia/ocw128DOI Listing
May 2017

BioSearch: a semantic search engine for Bio2RDF.

Database (Oxford) 2017 01;2017

Institute of Data Science, Maastricht University, The Netherlands.

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http://dx.doi.org/10.1093/database/bax059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569678PMC
January 2017

Comparing Drug-Disease Associations in Clinical Practice Guideline Recommendations and Drug Product Label Indications.

Stud Health Technol Inform 2015 ;216:1039

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA.

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December 2016

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

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http://dx.doi.org/10.1038/ncomms13205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062501PMC
October 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

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http://dx.doi.org/10.1038/ncomms12460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996969PMC
August 2016

Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy.

AMIA Jt Summits Transl Sci Proc 2016 20;2016:176-83. Epub 2016 Jul 20.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001752PMC
August 2016

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

J Biomed Semantics 2016 Jun 8;7:37. Epub 2016 Jun 8.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s13326-016-0081-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898307PMC
June 2016

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

J Biomed Inform 2016 Apr 10;60:199-209. Epub 2016 Feb 10.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305-5479, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836980PMC
April 2016

An Ebola virus-centered knowledge base.

Database (Oxford) 2015 8;2015:bav049. Epub 2015 Jun 8.

Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA

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http://dx.doi.org/10.1093/database/bav049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460400PMC
March 2016

Predicting structured metadata from unstructured metadata.

Database (Oxford) 2016 01;2016

Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/database/baw080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892825PMC
January 2016

Analysis of In Vitro Aptamer Selection Parameters.

J Mol Evol 2015 Dec 3;81(5-6):150-61. Epub 2015 Nov 3.

Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.

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http://dx.doi.org/10.1007/s00239-015-9708-6DOI Listing
December 2015

Mining Electronic Health Records using Linked Data.

AMIA Jt Summits Transl Sci Proc 2015 23;2015:217-21. Epub 2015 Mar 23.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525267PMC
August 2015

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines.

AMIA Jt Summits Transl Sci Proc 2015 25;2015:456-60. Epub 2015 Mar 25.

Department of Veterans Affairs, VA Palo Alto Health Care System, Palo Alto, CA ; Center for Primary Care and Outcomes Research, Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525235PMC
August 2015

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

J Cheminform 2015 14;7:34. Epub 2015 Jul 14.

National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD USA.

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http://dx.doi.org/10.1186/s13321-015-0084-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500850PMC
July 2015

SPARQL-enabled identifier conversion with Identifiers.org.

Bioinformatics 2015 Jun 31;31(11):1875-7. Epub 2015 Jan 31.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443684PMC
June 2015

Automatically exposing OpenLifeData via SADI semantic Web Services.

J Biomed Semantics 2014 19;5:46. Epub 2014 Nov 19.

Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain.

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http://dx.doi.org/10.1186/2041-1480-5-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417525PMC
May 2015

GFVO: the Genomic Feature and Variation Ontology.

PeerJ 2015 5;3:e933. Epub 2015 May 5.

Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University , Stanford, CA , USA.

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http://dx.doi.org/10.7717/peerj.933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435477PMC
May 2015

Ranking adverse drug reactions with crowdsourcing.

J Med Internet Res 2015 Mar 23;17(3):e80. Epub 2015 Mar 23.

Department of Genetics, Stanford University, Stanford, CA, United States.

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http://dx.doi.org/10.2196/jmir.3962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387295PMC
March 2015

Drug-drug interaction data source survey and linking.

AMIA Jt Summits Transl Sci Proc 2014 7;2014:16. Epub 2014 Apr 7.

University of Pittsburgh, Pittsburgh, PA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333686PMC
February 2015

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.

BMC Med Inform Decis Mak 2015 Feb 22;15:12. Epub 2015 Feb 22.

Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA, 94305-5479, USA.

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http://dx.doi.org/10.1186/s12911-015-0130-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340468PMC
February 2015

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans.

BMC Bioinformatics 2015 Feb 7;16:40. Epub 2015 Feb 7.

Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford California, AC, USA.

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http://dx.doi.org/10.1186/s12859-015-0469-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339751PMC
February 2015

Finding our way through phenotypes.

PLoS Biol 2015 Jan 6;13(1):e1002033. Epub 2015 Jan 6.

Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285398PMC
January 2015

Mouse model phenotypes provide information about human drug targets.

Bioinformatics 2014 Mar 24;30(5):719-25. Epub 2013 Oct 24.

Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth SY23 2AX, Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933875PMC
March 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Evaluation of research in biomedical ontologies.

Brief Bioinform 2013 Nov 8;14(6):696-712. Epub 2012 Sep 8.

Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, UK.

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http://bib.oxfordjournals.org/content/14/6/696.full.pdf
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http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbs053
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http://dx.doi.org/10.1093/bib/bbs053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888109PMC
November 2013

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

JMIR Res Protoc 2013 Apr 5;2(1):e14. Epub 2013 Apr 5.

James Hogg Research Centre, Heart & Lung Institute, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.2196/resprot.2315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628156PMC
April 2013

Ontology-Based Querying with Bio2RDF's Linked Open Data.

J Biomed Semantics 2013 Apr 15;4 Suppl 1:S1. Epub 2013 Apr 15.

Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada.

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http://dx.doi.org/10.1186/2041-1480-4-S1-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632999PMC
April 2013

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

J Biomed Inform 2013 Feb 3;46(1):1-4. Epub 2012 Dec 3.

School of ITEE, The University of Queensland, Queensland, Australia.

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http://dx.doi.org/10.1016/j.jbi.2012.11.007DOI Listing
February 2013

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.

Bioinformatics 2012 Aug 17;28(16):2169-75. Epub 2012 Jun 17.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493115PMC
August 2012

Self-organizing ontology of biochemically relevant small molecules.

BMC Bioinformatics 2012 Jan 6;13. Epub 2012 Jan 6.

Department of Biology, Carleton University, Ottawa, Canada.

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http://dx.doi.org/10.1186/1471-2105-13-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267649PMC
January 2012

Building an HIV data mashup using Bio2RDF.

Brief Bioinform 2012 Jan 24;13(1):98-106. Epub 2011 Mar 24.

Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6.

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http://dx.doi.org/10.1093/bib/bbr003DOI Listing
January 2012

Semantically enabling pharmacogenomic data for the realization of personalized medicine.

Pharmacogenomics 2012 Jan;13(2):201-12

Department of Medical Statistics & Bioinformatics, Leiden University Medical Center/Informatics Institute, University of Amsterdam, Einthovenweg 20, 2333 ZC Leiden, The Netherlands.

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http://dx.doi.org/10.2217/pgs.11.179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957334PMC
January 2012

Towards an interoperable information infrastructure providing decision support for genomic medicine.

Stud Health Technol Inform 2011 ;169:165-9

Section for Medical Expert and Knowledge-Based Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna.

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December 2011

Integrating systems biology models and biomedical ontologies.

BMC Syst Biol 2011 Aug 11;5:124. Epub 2011 Aug 11.

Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-5-124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170340PMC
August 2011

Semantic Web integration of Cheminformatics resources with the SADI framework.

J Cheminform 2011 May 16;3:16. Epub 2011 May 16.

Department of Biology, Carleton University, Ottawa, Canada.

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http://dx.doi.org/10.1186/1758-2946-3-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114010PMC
May 2011

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

J Biomed Semantics 2011 May 17;2 Suppl 2:S10. Epub 2011 May 17.

LORIA - INRIA Nancy - Grand-Est, Campus Scientifique - BP 239 - 54506 Vandoeuvre-lès-Nancy Cedex, France.

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http://dx.doi.org/10.1186/2041-1480-2-S2-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102890PMC
May 2011

HyQue: evaluating hypotheses using Semantic Web technologies.

J Biomed Semantics 2011 May 17;2 Suppl 2:S3. Epub 2011 May 17.

Department of Biology, Carleton University, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1186/2041-1480-2-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102892PMC
May 2011

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

Chin Med 2010 Dec 17;5:43. Epub 2010 Dec 17.

Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland.

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http://cmjournal.biomedcentral.com/articles/10.1186/1749-854
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http://dx.doi.org/10.1186/1749-8546-5-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017053PMC
December 2010

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

RNA 2010 Nov 24;16(11):2252-62. Epub 2010 Sep 24.

School of Computer Science, Carleton University, Ottawa, Ontario K1S5B6, Canada.

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http://dx.doi.org/10.1261/rna.2102210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957063PMC
November 2010

Relations as patterns: bridging the gap between OBO and OWL.

BMC Bioinformatics 2010 Aug 31;11:441. Epub 2010 Aug 31.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2105-11-441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2942855PMC
August 2010

RKB: a Semantic Web knowledge base for RNA.

J Biomed Semantics 2010 Jun 22;1 Suppl 1:S2. Epub 2010 Jun 22.

Department of Biology, Carleton University 1125 Colonel By Drive, K1S5B6, Ottawa, Canada .

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http://dx.doi.org/10.1186/2041-1480-1-S1-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903721PMC
June 2010

Towards pharmacogenomics knowledge discovery with the semantic web.

Brief Bioinform 2009 Mar 24;10(2):153-63. Epub 2009 Feb 24.

Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6.

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http://dx.doi.org/10.1093/bib/bbn056DOI Listing
March 2009

Computational methods for predicting protein-protein interactions.

Adv Biochem Eng Biotechnol 2008 ;110:247-67

School of Computer Science, Carleton University, 5304 Herzberg Building, 1125 Colonel By Drive, K1S 5B6, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1007/10_2007_089DOI Listing
October 2008

yOWL: an ontology-driven knowledge base for yeast biologists.

J Biomed Inform 2008 Oct 11;41(5):779-89. Epub 2008 May 11.

School of Computer Science, Carleton University, Ottawa, Ont., Canada K1S5B6.

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http://linkinghub.elsevier.com/retrieve/pii/S153204640800062
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http://dx.doi.org/10.1016/j.jbi.2008.05.001DOI Listing
October 2008

GridCell: a stochastic particle-based biological system simulator.

BMC Syst Biol 2008 Jul 23;2:66. Epub 2008 Jul 23.

Department of Electrical and Computer Engineering, McGill University, Montreal, QC, H3A 2A7, Canada.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-2-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2517591PMC
July 2008

Domain-based small molecule binding site annotation.

BMC Bioinformatics 2006 Mar 17;7:152. Epub 2006 Mar 17.

The Blueprint Initiative, Toronto ON, M5T 1K4, Canada.

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http://dx.doi.org/10.1186/1471-2105-7-152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435939PMC
March 2006

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

FEBS Lett 2005 Aug;579(21):4685-91

The Blueprint Initiative of the Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, ON, Canada.

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http://doi.wiley.com/10.1016/j.febslet.2005.07.039
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http://dx.doi.org/10.1016/j.febslet.2005.07.039DOI Listing
August 2005

Armadillo: domain boundary prediction by amino acid composition.

J Mol Biol 2005 Jul;350(5):1061-73

Department of Biochemistry, University of Toronto, Toronto, Ont., Canada M5S 1A8.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360500580
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http://dx.doi.org/10.1016/j.jmb.2005.05.037DOI Listing
July 2005

Hardware-accelerated protein identification for mass spectrometry.

Rapid Commun Mass Spectrom 2005 ;19(6):833-7

Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario, M5S 3G4 Canada.

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http://dx.doi.org/10.1002/rcm.1853DOI Listing
May 2005

Species-specific protein sequence and fold optimizations.

BMC Bioinformatics 2002 Dec 17;3:39. Epub 2002 Dec 17.

Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139977PMC
December 2002

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

BMC Bioinformatics 2002 Oct 25;3:32. Epub 2002 Oct 25.

Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138791PMC
October 2002

NBLAST: a cluster variant of BLAST for NxN comparisons.

BMC Bioinformatics 2002 May 8;3:13. Epub 2002 May 8.

Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.

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May 2002