Nigam H Shah

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc 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 Ontology-based annotation and query of tissue microarray data
    Nigam H Shah
    Stanford Medical Informatics, Stanford University School of Medicine and the National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA
    AMIA Annu Symp Proc . 2006
  3. doi request reprint Synergistic drug combinations from electronic health records and gene expression
    Yen S Low
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
    J Am Med Inform Assoc . 2016
  4. 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
  5. 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
  6. 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
  7. 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
  8. pmc HyQue: evaluating hypotheses using Semantic Web technologies
    Alison Callahan
    Department of Biology, Carleton University, Ottawa, Ontario, Canada
    J Biomed Semantics 2:S3. 2011
  9. 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
  10. 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

Collaborators

Detail Information

Publications56

  1. pmc 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 Ontology-based annotation and query of tissue microarray data
    Nigam H Shah
    Stanford Medical Informatics, Stanford University School of Medicine and the National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA
    AMIA Annu Symp Proc . 2006
    ..Our approach provides the basis for a data-driven ontology alignment by mapping annotations of experimental data...
  3. doi request reprint Synergistic drug combinations from electronic health records and gene expression
    Yen S Low
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
    J Am Med Inform Assoc . 2016
    ..EHRs provide real-world treatment and outcome patterns, while complementary biomolecular data, including disease-specific gene expression and drug-protein interactions, provide mechanistic understanding...
  4. 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
    ....
  5. 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
    ....
  6. 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
    ....
  7. 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
    ..These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL...
  8. 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...
  9. 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
    ....
  10. 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
    ....
  11. 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...
  12. 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...
  13. 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...
  14. pmc BioPortal: ontologies and integrated data resources at the click of a mouse
    Natalya F Noy
    Stanford Center for Biomedical Informatics Research, Stanford University
    Nucleic Acids Res 37:W170-3. 2009
    ..Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources...
  15. 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
    ....
  16. 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...
  17. pmc Influence of age on androgen deprivation therapy-associated Alzheimer's disease
    Kevin T Nead
    Stanford Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, California, 94305, USA
    Sci Rep 6:35695. 2016
    ..Future work should investigate the ADT Alzheimer's disease association in advanced age populations given the greater potential clinical impact...
  18. 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
    ....
  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 NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources
    Clement Jonquet
    Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305 5479, USA
    Web Semant 9:316-324. 2011
    ..Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics "under the hood."..
  21. 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...
  22. doi request reprint Association Between Androgen Deprivation Therapy and Risk of Dementia
    Kevin T Nead
    Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California2Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia
    JAMA Oncol 3:49-55. 2017
    ..A growing body of evidence supports a link between androgen deprivation therapy (ADT) and cognitive dysfunction, including Alzheimer disease. However, it is currently unknown whether ADT may contribute to the risk of dementia more broadly...
  23. pmc Functional evaluation of out-of-the-box text-mining tools for data-mining tasks
    Kenneth Jung
    Program in Biomedical Informatics, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 22:121-31. 2015
    ..We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug-drug interactions, and learning used-to-treat relationships between drugs and indications...
  24. pmc Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature
    Rainer Winnenburg
    Stanford Center for Biomedical Informatics Research, 1265 Welch Road, MSOB, Stanford, CA, 94305, USA
    BMC Bioinformatics 17:250. 2016
    ..Here, we assess how defining a selection of adverse event terms from MeSH, based on information content, can improve the detection of adverse events for drugs and drug classes...
  25. pmc Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population
    Nigam H Shah
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United States of America
    PLoS ONE 10:e0124653. 2015
    ..Recent pre-clinical results suggest that this risk might extend to subjects without any prior history of cardiovascular disease. We explore this potential risk in the general population via data-mining approaches...
  26. 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...
  27. 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
    ....
  28. 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
    ....
  29. pmc DISCOVERING PATIENT PHENOTYPES USING GENERALIZED LOW RANK MODELS
    Alejandro Schuler
    Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA, 94305, USA
    Pac Symp Biocomput 21:144-55. 2016
    ..We demonstrate that low rank modeling successfully captures known and putative phenotypes in these vastly different datasets. ..
  30. pmc Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research
    Tyler S Cole
    Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, 1265 Welch Road, MSOB, X 215, Stanford, CA 94305 5479, USA
    Pediatr Rheumatol Online J 11:45. 2013
    ..Knowledge of clinical associations will improve risk stratification. Based on clinical observation, we hypothesized that allergic conditions are associated with chronic uveitis in juvenile idiopathic arthritis patients...
  31. pmc Androgen Deprivation Therapy and Future Alzheimer's Disease Risk
    Kevin T Nead
    Kevin T Nead, Greg Gaskin, and Nigam H Shah, Stanford University Cariad Chester and Nicholas J Leeper, Stanford University School of Medicine, Stanford, CA Kevin T Nead and Samuel Swisher McClure, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA and Joel T Dudley, Icahn School of Medicine at Mount Sinai, New York, NY
    J Clin Oncol 34:566-71. 2016
    ..To test the association of androgen deprivation therapy (ADT) in the treatment of prostate cancer with subsequent Alzheimer's disease risk...
  32. pmc Text mining for adverse drug events: the promise, challenges, and state of the art
    Rave Harpaz
    Center for Biomedical Informatics Research, Stanford University, 1265 Welch Road, Stanford, CA, 94305 5479, USA
    Drug Saf 37:777-90. 2014
    ....
  33. 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...
  34. 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...
  35. pmc Analyzing search behavior of healthcare professionals for drug safety surveillance
    David J Odgers
    Center for Biomedical Informatics, Stanford University, 1265 Welch Road, Stanford, CA 94305 5479, USA
    Pac Symp Biocomput . 2015
    ..Despite these promising results additional research is required to better understand users' search behavior, biasing factors, and the overall utility of analyzing healthcare professional search logs for drug safety surveillance. ..
  36. pmc Toward personalizing treatment for depression: predicting diagnosis and severity
    Sandy H Huang
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 21:1069-75. 2014
    ..Toward the goal of personalizing treatment for depression, we develop and evaluate computational models that use electronic health record (EHR) data for predicting the diagnosis and severity of depression, and response to treatment...
  37. 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. ..
  38. 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)...
  39. 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 number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use...
  40. 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...
  41. 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]...
  42. pmc Repurposing cAMP-modulating medications to promote β-cell replication
    Zhenshan Zhao
    Department of Medicine and Division of Endocrinology, Gerontology, and Metabolism Z Z, N A A, S A S, J P A and Stanford Center for Biomedical Informatics Research Y S L, Stanford University School of Medicine, Stanford, California 94306 Department of Stem Cell and Regenerative Biology J H R, A C A, Harvard University, Cambridge, Massachusetts 02138 and Section of Islet Cell and Regenerative Biology J H L, G C W, Joslin Diabetes Center, Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
    Mol Endocrinol 28:1682-97. 2014
    ..This work provides new mechanistic insights into cAMP-dependent growth regulation of β-cells and highlights the potential of commonly prescribed medications to influence β-cell growth...
  43. pmc Interpretation errors related to the GO annotation file format
    Dilvan A Moreira
    Stanford University, Stanford, CA, USA
    AMIA Annu Symp Proc . 2007
    ..We propose a complementary format to represent GO annotation files as knowledge bases using the W3C recommended Web Ontology Language (OWL)...
  44. pmc RegenBase: a knowledge base of spinal cord injury biology for translational research
    Alison Callahan
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
    Database (Oxford) 2016:. 2016
    ..RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org. ..
  45. pmc Rapid identification of slow healing wounds
    Kenneth Jung
    Program in Biomedical Informatics, Stanford University, Stanford, California
    Wound Repair Regen 24:181-8. 2016
    ..00018. Early, accurate prediction of delayed healing wounds can improve patient care by allowing clinicians to increase the aggressiveness of intervention in patients most at risk. ..
  46. pmc Building the graph of medicine from millions of clinical narratives
    Samuel G Finlayson
    Center for Biomedical Informatics Research, Stanford University, Stanford, California 94305, USA
    Sci Data 1:140032. 2014
    ..This dataset can be leveraged to quantitatively assess comorbidity, drug-drug, and drug-disease patterns for a range of clinical, epidemiological, and financial applications. ..
  47. pmc A method for systematic discovery of adverse drug events from clinical notes
    Guan Wang
    Stanford University, Center for Biomedical Informatics, Stanford, California, USA
    J Am Med Inform Assoc 22:1196-204. 2015
    ..The authors have developed a data-mining method for systematic, automated detection of ADEs from electronic medical records...
  48. pmc Implications of non-stationarity on predictive modeling using EHRs
    Kenneth Jung
    Program in Biomedical Informatics, Stanford University, Stanford, CA, United States Electronic address
    J Biomed Inform 58:168-74. 2015
    ..Ignoring non-stationarity can thus lead to sub-optimal model selection in this task...
  49. 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...
  50. 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...
  51. 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
    ....
  52. 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...
  53. 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...
  54. 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...
  55. 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...