Nigam H Shah

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. ncbi request reprint Translational bioinformatics embraces big data
    N H Shah
    Stanford University School of Medicine, 1265 Welch Road, Room X 229, Stanford, CA 94305, USA E mail
    Yearb Med Inform 7:130-4. 2012
  2. pmc Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting
    Larisa N Soldatova
    Brunel University, London, UK
    J Biomed Semantics 4:I1. 2013
  3. pmc STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
    Tobias Wittkop
    Buck Institute for Research on Aging, Novato, CA, USA
    BMC Bioinformatics 14:53. 2013
  4. pmc Chapter 9: Analyses using disease ontologies
    Nigam H Shah
    Center for Biomedical Informatics Research, Stanford University, Stanford, California, United States of America
    PLoS Comput Biol 8:e1002827. 2012
  5. pmc Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting
    Larisa N Soldatova
    Aberystwyth University, Wales, UK
    J Biomed Semantics 3:I1. 2012
  6. pmc Mapping between the OBO and OWL ontology languages
    Syed Hamid Tirmizi
    Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA
    J Biomed Semantics 2:S3. 2011
  7. pmc HyQue: evaluating hypotheses using Semantic Web technologies
    Alison Callahan
    Department of Biology, Carleton University, Ottawa, Ontario, Canada
    J Biomed Semantics 2:S3. 2011
  8. pmc Integration and publication of heterogeneous text-mined relationships on the Semantic Web
    Adrien Coulet
    LORIA INRIA Nancy Grand Est, Campus Scientifique BP 239 54506 Vandoeuvre lès Nancy Cedex, France
    J Biomed Semantics 2:S10. 2011
  9. pmc Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting
    Larisa N Soldatova
    Aberystwyth University, Wales, UK
    J Biomed Semantics 2:I1. 2011
  10. pmc Ontology-driven indexing of public datasets for translational bioinformatics
    Nigam H Shah
    Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 10:S1. 2009

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Translational bioinformatics embraces big data
    N H Shah
    Stanford University School of Medicine, 1265 Welch Road, Room X 229, Stanford, CA 94305, USA E mail
    Yearb Med Inform 7:130-4. 2012
    ..Research that bridges the latest multimodal measurement technologies with large amounts of electronic healthcare data is increasing; and is where new breakthroughs will occur...
  2. pmc Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting
    Larisa N Soldatova
    Brunel University, London, UK
    J Biomed Semantics 4:I1. 2013
    ....
  3. pmc STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
    Tobias Wittkop
    Buck Institute for Research on Aging, Novato, CA, USA
    BMC Bioinformatics 14:53. 2013
    ..Here, we developed and evaluated a tool for hypothesis generation from gene or protein lists using ontological concepts present in manually curated text that describes those genes and proteins...
  4. pmc Chapter 9: Analyses using disease ontologies
    Nigam H Shah
    Center for Biomedical Informatics Research, Stanford University, Stanford, California, United States of America
    PLoS Comput Biol 8:e1002827. 2012
    ....
  5. pmc Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting
    Larisa N Soldatova
    Aberystwyth University, Wales, UK
    J Biomed Semantics 3:I1. 2012
    ....
  6. pmc Mapping between the OBO and OWL ontology languages
    Syed Hamid Tirmizi
    Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA
    J Biomed Semantics 2:S3. 2011
    ..In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner...
  7. pmc HyQue: evaluating hypotheses using Semantic Web technologies
    Alison Callahan
    Department of Biology, Carleton University, Ottawa, Ontario, Canada
    J Biomed Semantics 2:S3. 2011
    ..Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks...
  8. pmc Integration and publication of heterogeneous text-mined relationships on the Semantic Web
    Adrien Coulet
    LORIA INRIA Nancy Grand Est, Campus Scientifique BP 239 54506 Vandoeuvre lès Nancy Cedex, France
    J Biomed Semantics 2:S10. 2011
    ....
  9. pmc Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting
    Larisa N Soldatova
    Aberystwyth University, Wales, UK
    J Biomed Semantics 2:I1. 2011
    ....
  10. pmc Ontology-driven indexing of public datasets for translational bioinformatics
    Nigam H Shah
    Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 10:S1. 2009
    ..The key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts...
  11. pmc Comparison of concept recognizers for building the Open Biomedical Annotator
    Nigam H Shah
    Centre for Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 10:S14. 2009
    ..The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data...
  12. pmc Annotation and query of tissue microarray data using the NCI Thesaurus
    Nigam H Shah
    Stanford Medical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 8:296. 2007
    ..These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult...
  13. ncbi request reprint Biomedical ontologies: a functional perspective
    Daniel L Rubin
    Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
    Brief Bioinform 9:75-90. 2008
    ....
  14. pmc The National Center for Biomedical Ontology
    Mark A Musen
    Center for Biomedical Informatics Research, Stanford University, Stanford, California 94305 5479, USA
    J Am Med Inform Assoc 19:190-5. 2012
    ....
  15. pmc Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records
    Svetlana Lyalina
    Department of Bioengineering, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 20:e297-305. 2013
    ..We investigated how EMR-based text mining and statistical analysis could elucidate the phenotypic boundaries of three important neuropsychiatric illnesses-autism, bipolar disorder, and schizophrenia...
  16. pmc Using ontology-based annotation to profile disease research
    Yi Liu
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California 94305, USA
    J Am Med Inform Assoc 19:e177-86. 2012
    ..Analyzing over a decade of funding data and publication data, the trends of disease research are profiled across topics, across institutions, and over time...
  17. pmc Enabling enrichment analysis with the Human Disease Ontology
    Paea Lependu
    Stanford Center for Biomedical Informatics Research, 251 Campus Drive, Medical School Office Building, Mail Code 5479, Stanford University, Stanford, CA 94305 5479, USA
    J Biomed Inform 44:S31-8. 2011
    ....
  18. ncbi request reprint Current progress in network research: toward reference networks for key model organisms
    Balaji S Srinivasan
    318 Campus Drive, Clark Center S251, Stanford, CA 94305, USA
    Brief Bioinform 8:318-32. 2007
    ....
  19. pmc BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications
    Patricia L Whetzel
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 39:W541-5. 2011
    ..Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection...
  20. pmc Mining clinical text for signals of adverse drug-drug interactions
    Srinivasan V Iyer
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 21:353-62. 2014
    ..We present an approach for identifying DDI signals directly from the textual portion of EHRs...
  21. pmc Analyzing patterns of drug use in clinical notes for patient safety
    Paea Lependu
    Stanford University, Stanford, CA
    AMIA Summits Transl Sci Proc 2012:63-70. 2012
    ..Given our ability to quantify adverse event risks using the clinical notes, this will enable us to address patient safety because we can now rank-order off-label drug use and prioritize the search for their adverse event profiles...
  22. pmc Automated detection of off-label drug use
    Kenneth Jung
    Program in Biomedical Informatics, Stanford University, Stanford, California, United States of America
    PLoS ONE 9:e89324. 2014
    ..We validated 403 predicted uses across independent data sources. Finally, we prioritize well-supported novel usages for further investigation on the basis of drug safety and cost. ..
  23. pmc Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notes
    Nicholas J Leeper
    Division of Vascular Surgery and Cardiovascular Medicine, Stanford University, Stanford, California, United States of America
    PLoS ONE 8:e63499. 2013
    ..To assess the validity of this black box warning, we employed a novel text-analytics pipeline to quantify the adverse events associated with Cilostazol use in a clinical setting, including patients with congestive heart failure (CHF)...
  24. pmc The Stanford Tissue Microarray Database
    Robert J Marinelli
    Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA, USA
    Nucleic Acids Res 36:D871-7. 2008
    ..The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license...
  25. pmc The open biomedical annotator
    Clement Jonquet
    Stanford Center for Biomedical Informatics Research and the National Center for Biomedical Ontology, Stanford University, Stanford, CA
    Summit on Translat Bioinforma 2009:56-60. 2009
    ..The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data.[1]...
  26. pmc Building a biomedical ontology recommender web service
    Clement Jonquet
    Center for Biomedical Informatics Research, Stanford University, CA 94305, USA
    J Biomed Semantics 1:S1. 2010
    ..The Recommender service (alpha version) is available to the community and is embedded into BioPortal...
  27. pmc Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine
    Yohannes T Ghebremariam
    Department of Cardiovascular Sciences, Texas Methodist Hospital Research Institute, Houston, TX 77030, USA
    Circulation 128:845-53. 2013
    ..The mechanism of this possible adverse effect is not known. Whether the general population might also be at risk has not been addressed...
  28. pmc Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes
    Paea Lependu
    Stanford Center for Biomedical Informatics Research, Stanford University, USA
    J Biomed Semantics 3:S5. 2012
    ..With the increasing access to large volumes of electronic medical data-in particular the clinical notes-it may be possible to computationally encode and to test drug safety signals in an active manner...
  29. pmc Using temporal patterns in medical records to discern adverse drug events from indications
    Yi Liu
    Stanford University, Stanford, CA
    AMIA Summits Transl Sci Proc 2012:47-56. 2012
    ....
  30. pmc Using text to build semantic networks for pharmacogenomics
    Adrien Coulet
    Department of Medicine, 300 Pasteur Drive, Room S101, Mail Code 5110, Stanford University, Stanford, CA 94305, USA
    J Biomed Inform 43:1009-19. 2010
    ..This network is used to guide the curation of PGx knowledge and provide a computable resource for knowledge discovery...
  31. pmc An ontology-neutral framework for enrichment analysis
    Rob Tirrell
    Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
    AMIA Annu Symp Proc 2010:797-801. 2010
    ..We outline the methodology of enrichment analysis, the associated challenges, and discuss novel analyses enabled by RANSUM...
  32. pmc A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations
    Rong Xu
    Center for Biomedical Informatics Research, Stanford University School of Medicine Stanford, CA 94305, USA
    AMIA Annu Symp Proc 2010:907-11. 2010
    ..This filtered and augmented UMLS Metathesaurus can potentially be used to improve efficiency and precision of UMLS-based information retrieval and NLP tasks...
  33. pmc A case study in pathway knowledgebase verification
    Stephen A Racunas
    Computational Learning Laboratory, Stanford University, CA, USA
    BMC Bioinformatics 7:196. 2006
    ..But before we can reliably use a pathway knowledge-base as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference...