2009

Nigam H. Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang and Mark A. Musen
Comparison of Concept Recognizers for building the Open Biomedical Annotator
BMC Bioinformatics 2009, 10(Suppl 9):S14
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Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA
BioPortal: ontologies and integrated data resources at the click of a mouse.
Nucleic Acids Res. 2009 May 29;
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Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen and Mark A. Musen
Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
BMC Bioinformatics 2009, 10(Suppl 2):S1
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Kotecha N, Bruck K, Lu W and Shah N.H.
Pathway Knowledge Base: An Integrated pathway resource using BioPAX
Applied Ontology, Vol 3:4, pg 235-245, December 2008
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Rubin D.L., Shah N.H. and Noy N.F.
Biomedical Ontologies: a functional perspective
Briefings in Bioinformatics, 2008 Jan;9(1):75-90.
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Marinelli R.J., Montgomery K., Liu C. L., Shah N. H., Nitzberg M., Zachariah Z. K., SherlockG., Natkunam Y., West R. B., Van de Rijn M., Brown P.O., and Ball C.A.
The Stanford Tissue Microarray Database
Nucleic Acid Research, 2008 Jan;36(Database issue):D871-7
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Shah NH, Marinelli R, Rubin DL, Espinosa I, Montgomery K, and Musen MA
Annotation and Query of Tissue Microarray Data Using the NCI Thesaurus
BMC Bioinformatics, July 2007 (8):296
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Srinivasan B.S., Shah N.H., Flannick J.A., Abeliuk E., Novak A.F. and Batzoglou S.
Current progress in network research: toward reference networks for key model organisms
Briefings in Bioinformatics, 2007, doi: 10.1093/bib/bbm038
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Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Nature Biotechnology, Nov 2007, doi:10.1038/nbt1346
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Racunas SA*, Shah NH* and Fedoroff NV
A case study in pathway knowledgebase verification
BMC Bioinformatics 2006, 7:196 (*= equal authors)
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Mahalingam R, Shah NH, Scrymgeour A and Fedoroff NV
Temporal evolution of the Arabidopsis oxidative stress response
Plant Molecular Biology, March 2005;57(5):709-730.
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Racunas SA*, Shah NH*, Albert I and Fedoroff NV
HyBrow: A prototype system for computer aided hypothesis evaluation
Bioinformatics 2004 Supplement; 20: i257-i264 (*= equal authors)
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Shah NH and Fedoroff NV
CLENCH: A Program for Calculating Cluster Enrichment using the Gene Ontology
Bioinformatics. 2004 May 1;20(7):1196-7.
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Shah NH, King DC, Shah PN and Fedoroff NV
A Tool-kit for cDNA microarray and promoter analysis
Bioinformatics. 2003 Sep 22;19(14):1846-8.
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Mahalingam R, Gomez-Buitrago A, Eckardt N, Shah N, Guevara-Garcia A, Day P, Raina R and Fedoroff NV
Characterizing the stress/defense transcriptome of Arabidopsis
Genome Biology 2003, 4:R20.
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Jelinek DF, Tschumper RC, Stolovitzky GA, Iturria SJ, Tu Y, Lepre J, Shah N and Kay NE
Identification of a global gene expression signature of B-chronic lymphocytic leukemia.
Mol Cancer Res. 2003 Mar;1(5):346-61.
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Mitra M, Shah NH, Mueller L, Pin S and Fedoroff NV
StressDB: A locally installable web-based relational microarray database designed for small user communities.
Comparative and Functional Genomics, 2002, 3(2): 91-96
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2009

Shah NH, Noy NF, Jonquet CM, Coulet A, Whetzel P, Griffith NB, Youn C, Dai B, Dorf M and Musen MA
Ontology Services for Semantic Applications in Healthcare and Life Sciences
AMIA Annual Symposium, Nov 14-18, San Francisco, CA.

Ghazvinian A, Noy NF, Jonquet CM, Shah NH, Musen MA
What Four Million Mappings Can Tell You About Two Hundred Ontologies
ISWC 2009, 25-29 October 2009, Washington DC.

Jonquet CM, Shah NH and Musen MA.
Prototyping a Biomedical Ontology Recommender Service
Bio-Ontologies SIG at ISMB 2009, Stockholm, Sweden

Jonquet CM, Shah NH and Musen MA.
The Open Biomedical Annotator
AMIA Summit on Translational Bioinformatics, March 2009, p. 56-60.

Theobald M, Shah NH and Shrager J.
Extraction of Conditional Probabilities of the Relationships between Drugs, Diseases, and Genes from PubMed guided by relationships in PharmGKB.
AMIA Summit on Translational Bioinformatics, March 2009, p. 124-128.

Bhatia, N, Shah NH and Musen MA.
Comparing Concept Recognizers for Ontology-Based Indexing: MGREP vs. MetaMap
AMIA Summit on Translational Bioinformatics, March 2009, p. 12-16.

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Nigam H. Shah and Mark A. Musen
UMLS-Query: A Perl Module for Querying the UMLS
AMIA Annual Symposium 2008 pg 652-656, Washington DC.
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Wei-Nchih Lee, Nigam Shah, Karanjot Sundlass, Mark Musen
Comparison of Ontology-based Semantic-Similarity Measures
AMIA Annual Symposium 2008 pg 384–388, Washington DC.
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Shah NH, Chiang AP, Butte AJ, Chen R and Musen MA.
Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
AMIA Summit on Translational Bioinformatics 2008 pg 100-104, San Francisco, CA, 2008
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Jonquet C, Musen MA, Shah NH
A System for Ontology-Based Annotation of Biomedical Data
Accepted at DILS 2008
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Moreira D, Shah NH and Musen MA
Interpretation Errors related to the GO Annotation File Format
AMIA Annual Symposium Proceedings pg, 759-764, 2007
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Alani, H., Noy, N.F., Shah, N.H., Shadbolt, N and Musen, M.A.
Searching Ontologies Based on Content: Experiments in the Biomedical Domain
Proceedings of The Fourth International Conference on Knowledge Capture (KCAP07), pg 55-62 (ISBN:978-1-59593-643-1)
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W.-J. Lee, L. Raschid, P. Srinivasan, N. Shah, D. Rubin, N. Noy
Using annotations from controlled vocabularies to find meaning associations
Lecture Notes in Bioinformatics, Vol.4544, pp.247-263, June 2007
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Shah NH, Rubin DL, Supekar KS and Musen MA
Ontology-based Annotation and Query of Tissue Microarray Data
AMIA Annual Symposium Proceedings pg 709-713, 2006
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Nikesh Kotecha, Kyle Bruck, William Lu and Nigam Shah
Pathway Knowledge Base: Integrating BioPAX compliant pathways
using Oracle RDF Store (W3C HCLS Workshop @ ISWC 2006)
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Racunas SA, Griffin C and Shah NH
A Finite Model Theory for Biological Hypotheses
IEEE Computer Society CSB Conference, Aug 2004, Proc pg 585-589
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Shah NH, Lepre J, Tu Y and Stolovitzky G
Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data?
IEEE Computer Society CSB Conference, Aug 2003, Proc pg 94 - 103
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Racunas SA, Shah NH and Fedoroff NV
A Contradiction-Based Framework for Testing Gene Regulation Hypotheses
IEEE Computer Society CSB Conference, Aug 2003, Proc pg 634 - 638
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Ontologies in support of formal representations of biological systems
Nigam Shah and Mark Musen
in The Handbook on Ontologies, (second edition)
Editors: Stephen Staab and Rudi Studer

Biomedical Data/Content Acquisition, Curation.
Nigam Shah
in the Encyclopedia of Database Systems, (Springer Verlag)
Area Editor: Vipul Kashyap

Shah NH, and Mark A. Musen
Which Annotation did you mean?
Stanford Medical Informatics Technical Report, SMI-2007-1247, May 2007
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Shah NH, and Mark A. Musen
UMLS-Query: A Perl Module for Querying the UMLS
Stanford Medical Informatics Technical Report, SMI-2007-1242, March 2007
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Shah NH, Mark A. Musen and Nina V. Fedoroff
Clench2.0: Cluster enrichment analysis and visualization of expression, annotation and transcription factor binding site data
Stanford Medical Informatics Technical Report, SMI-2006-1248, Aug 2006
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