Nigam Shah, Ph.D. - Publications

2005 Pennsylvania State University, State College, PA, United States 
Molecular Biology, Computer Science

79 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Winnenburg R, Shah NH. Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature. Bmc Bioinformatics. 17: 250. PMID 27333889 DOI: 10.1186/s12859-016-1080-z  0.76
2016 Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH. Reply to R.L. Bowen et al, M. Froehner et al, J.L. Leow et al, and C. Brady et al. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. PMID 27298415 DOI: 10.1200/JCO.2016.67.9449  0.76
2016 Hripcsak G, Ryan PB, Duke JD, Shah NH, Park RW, Huser V, Suchard MA, Schuemie MJ, DeFalco FJ, Perotte A, Banda JM, Reich CG, Schilling LM, Matheny ME, Meeker D, et al. Characterizing treatment pathways at scale using the OHDSI network. Proceedings of the National Academy of Sciences of the United States of America. PMID 27274072 DOI: 10.1073/pnas.1510502113  0.76
2016 Banda JM, Evans L, Vanguri RS, Tatonetti NP, Ryan PB, Shah NH. A curated and standardized adverse drug event resource to accelerate drug safety research. Scientific Data. 3: 160026. PMID 27193236 DOI: 10.1038/sdata.2016.26  0.76
2016 Callahan A, Abeyruwan SW, Al-Ali H, Sakurai K, Ferguson AR, Popovich PG, Shah NH, Visser U, Bixby JL, Lemmon VP. RegenBase: a knowledge base of spinal cord injury biology for translational research. Database : the Journal of Biological Databases and Curation. 2016. PMID 27055827 DOI: 10.1093/database/baw040  0.76
2016 Schroeder LF, Giacherio D, Gianchandani R, Engoren M, Shah NH. Postmarket Surveillance of Point-of-Care Glucose Meters through Analysis of Electronic Medical Records. Clinical Chemistry. PMID 26988586 DOI: 10.1373/clinchem.2015.251827  0.76
2016 Mitra M, Shah N, Ghosh A, Chatterjee S, Kaur I, Bhattacharya N, Basu S. Efficacy and Safety of Vi-Tetanus Toxoid conjugated Typhoid vaccine (PedaTyph(TM)) in Indian Children: School Based Cluster Randomized Study. Human Vaccines & Immunotherapeutics. 0. PMID 26901576 DOI: 10.1080/21645515.2015.1117715  0.32
2015 Shah NH, Cooke JP, Leeper NJ. Reply. Gastroenterology. PMID 26721609 DOI: 10.1053/j.gastro.2015.12.017  0.76
2015 Poole S, Schroeder LF, Shah N. An unsupervised learning method to identify reference intervals from a clinical database. Journal of Biomedical Informatics. PMID 26707631 DOI: 10.1016/j.jbi.2015.12.010  0.76
2015 Gaskin GL, Pershing S, Cole TS, Shah NH. Predictive modeling of risk factors and complications of cataract surgery. European Journal of Ophthalmology. 0. PMID 26692059 DOI: 10.5301/ejo.5000706  0.76
2015 Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH. Special issue on bio-ontologies and phenotypes. Journal of Biomedical Semantics. 6: 40. PMID 26682035 DOI: 10.1186/s13326-015-0040-2  0.76
2015 Nead KT, Gaskin G, Chester C, Swisher-McClure S, Leeper NJ, Shah NH. Androgen Deprivation Therapy and Future Alzheimer's Disease Risk. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. PMID 26644522 DOI: 10.1200/JCO.2015.63.6266  0.76
2015 Low YS, Gallego B, Shah NH. Comparing high-dimensional confounder control methods for rapid cohort studies from electronic health records. Journal of Comparative Effectiveness Research. PMID 26634383 DOI: 10.2217/cer.15.53  0.76
2015 Harpaz R, DuMochel W, Shah N. Big Data and Adverse Drug Reaction Detection. Clinical Pharmacology and Therapeutics. PMID 26575203 DOI: 10.1002/cpt.302  0.76
2015 Jung K, Shah NH. Implications of non-stationarity on predictive modeling using EHRs. Journal of Biomedical Informatics. PMID 26483171 DOI: 10.1016/j.jbi.2015.10.006  0.76
2015 Banda JM, Callahan A, Winnenburg R, Strasberg HR, Cami A, Reis BY, Vilar S, Hripcsak G, Dumontier M, Shah NH. Feasibility of Prioritizing Drug-Drug-Event Associations Found in Electronic Health Records. Drug Safety. PMID 26446143 DOI: 10.1007/s40264-015-0352-2  0.76
2015 Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW, Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE, et al. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Studies in Health Technology and Informatics. 216: 574-8. PMID 26262116 DOI: 10.3233/978-1-61499-564-7-574  0.76
2015 Wang G, Jung K, Winnenburg R, Shah NH. A method for systematic discovery of adverse drug events from clinical notes. Journal of the American Medical Informatics Association : Jamia. PMID 26232442 DOI: 10.1093/jamia/ocv102  0.76
2015 Shah NH, LePendu P, Bauer-Mehren A, Ghebremariam YT, Iyer SV, Marcus J, Nead KT, Cooke JP, Leeper NJ. Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population. Plos One. 10: e0124653. PMID 26061035 DOI: 10.1371/journal.pone.0124653  0.76
2015 Curé OC, Maurer H, Shah NH, Le Pendu P. A formal concept analysis and semantic query expansion cooperation to refine health outcomes of interest. Bmc Medical Informatics and Decision Making. 15: S8. PMID 26043839 DOI: 10.1186/1472-6947-15-S1-S8  0.76
2015 Tamang S, Patel MI, Blayney DW, Kuznetsov J, Finlayson SG, Vetteth Y, Shah N. Detecting unplanned care from clinician notes in electronic health records. Journal of Oncology Practice / American Society of Clinical Oncology. 11: e313-9. PMID 25980019 DOI: 10.1200/JOP.2014.002741  0.76
2015 Gallego B, Walter SR, Day RO, Dunn AG, Sivaraman V, Shah N, Longhurst CA, Coiera E. Bringing cohort studies to the bedside: framework for a 'green button' to support clinical decision-making. Journal of Comparative Effectiveness Research. 1-7. PMID 25959863 DOI: 10.2217/cer.15.12  0.76
2015 Ghebremariam YT, Cooke JP, Khan F, Thakker RN, Chang P, Shah NH, Nead KT, Leeper NJ. Proton pump inhibitors and vascular function: A prospective cross-over pilot study. Vascular Medicine (London, England). PMID 25835348 DOI: 10.1177/1358863X14568444  0.76
2015 Harpaz R, DuMouchel W, Shah NH. Comment on: "Zoo or savannah? Choice of training ground for evidence-based pharmacovigilance". Drug Safety. 38: 113-4. PMID 25432779 DOI: 10.1007/s40264-014-0245-9  0.76
2015 Jung K, LePendu P, Iyer S, Bauer-Mehren A, Percha B, Shah NH. Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. Journal of the American Medical Informatics Association : Jamia. 22: 121-31. PMID 25336595 DOI: 10.1136/amiajnl-2014-002902  0.76
2014 Harpaz R, Callahan A, Tamang S, Low Y, Odgers D, Finlayson S, Jung K, LePendu P, Shah NH. Text mining for adverse drug events: the promise, challenges, and state of the art. Drug Safety. 37: 777-90. PMID 25151493 DOI: 10.1007/s40264-014-0218-z  0.76
2014 Longhurst CA, Harrington RA, Shah NH. A 'green button' for using aggregate patient data at the point of care. Health Affairs (Project Hope). 33: 1229-35. PMID 25006150 DOI: 10.1377/hlthaff.2014.0099  0.76
2014 Shah N. Mining the internet for drug information. Clinical Advances in Hematology & Oncology : H&O. 12: 391-3. PMID 25003570  0.76
2014 Huang SH, LePendu P, Iyer SV, Tai-Seale M, Carrell D, Shah NH. Toward personalizing treatment for depression: predicting diagnosis and severity. Journal of the American Medical Informatics Association : Jamia. 21: 1069-75. PMID 24988898 DOI: 10.1136/amiajnl-2014-002733  0.76
2014 Ghebremariam YT, Lee JC, LePendu P, Erlanson DA, Slaviero A, Shah NH, Leiper JM, Cooke JP. Response to letters regarding article, "unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine". Circulation. 129: e428. PMID 24687654 DOI: 10.1161/CIRCULATIONAHA.114.009343  0.76
2014 Jung K, LePendu P, Chen WS, Iyer SV, Readhead B, Dudley JT, Shah NH. Automated detection of off-label drug use. Plos One. 9: e89324. PMID 24586689 DOI: 10.1371/journal.pone.0089324  0.76
2014 Iyer SV, Harpaz R, LePendu P, Bauer-Mehren A, Shah NH. Mining clinical text for signals of adverse drug-drug interactions. Journal of the American Medical Informatics Association : Jamia. 21: 353-62. PMID 24158091 DOI: 10.1136/amiajnl-2013-001612  0.76
2013 Shah NH. Mining the ultimate phenome repository. Nature Biotechnology. 31: 1095-7. PMID 24316646 DOI: 10.1038/nbt.2757  0.76
2013 Cole TS, Frankovich J, Iyer S, Lependu P, Bauer-Mehren A, Shah NH. Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research. Pediatric Rheumatology Online Journal. 11: 45. PMID 24299016 DOI: 10.1186/1546-0096-11-45  0.76
2013 Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, et al. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 155: 70-80. PMID 24074861 DOI: 10.1016/j.cell.2013.08.030  0.76
2013 Lyalina S, Percha B, LePendu P, Iyer SV, Altman RB, Shah NH. Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records. Journal of the American Medical Informatics Association : Jamia. 20: e297-305. PMID 23956017 DOI: 10.1136/amiajnl-2013-001933  0.76
2013 Ghebremariam YT, LePendu P, Lee JC, Erlanson DA, Slaviero A, Shah NH, Leiper J, Cooke JP. Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine. Circulation. 128: 845-53. PMID 23825361 DOI: 10.1161/CIRCULATIONAHA.113.003602  0.76
2013 Leeper NJ, Bauer-Mehren A, Iyer SV, Lependu P, Olson C, Shah NH. Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notes. Plos One. 8: e63499. PMID 23717437 DOI: 10.1371/journal.pone.0063499  0.76
2013 White RW, Tatonetti NP, Shah NH, Altman RB, Horvitz E. Web-scale pharmacovigilance: listening to signals from the crowd. Journal of the American Medical Informatics Association : Jamia. 20: 404-8. PMID 23467469 DOI: 10.1136/amiajnl-2012-001482  0.76
2013 Wittkop T, TerAvest E, Evani US, Fleisch KM, Berman AE, Powell C, Shah NH, Mooney SD. STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. Bmc Bioinformatics. 14: 53. PMID 23409969 DOI: 10.1186/1471-2105-14-53  0.76
2013 Harpaz R, Vilar S, Dumouchel W, Salmasian H, Haerian K, Shah NH, Chase HS, Friedman C. Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions. Journal of the American Medical Informatics Association : Jamia. 20: 413-9. PMID 23118093 DOI: 10.1136/amiajnl-2012-000930  0.76
2012 Shah NH, Cole T, Musen MA. Chapter 9: Analyses using disease ontologies. Plos Computational Biology. 8: e1002827. PMID 23300417 DOI: 10.1371/journal.pcbi.1002827  0.76
2012 Hahn U, Cohen KB, Garten Y, Shah NH. Mining the pharmacogenomics literature--a survey of the state of the art. Briefings in Bioinformatics. 13: 460-94. PMID 22833496 DOI: 10.1093/bib/bbs018  0.76
2012 Shah NH, Tenenbaum JD. The coming age of data-driven medicine: translational bioinformatics' next frontier. Journal of the American Medical Informatics Association : Jamia. 19: e2-4. PMID 22718035 DOI: 10.1136/amiajnl-2012-000969  0.76
2012 Neylon C, Aerts J, Brown CT, Coles SJ, Hatton L, Lemire D, Millman KJ, Murray-Rust P, Perez F, Saunders N, Shah N, Smith A, Varoquaux G, Willighagen E. Changing computational research. The challenges ahead. Source Code For Biology and Medicine. 7: 2. PMID 22640749 DOI: 10.1186/1751-0473-7-2  0.76
2012 Lependu P, Iyer SV, Fairon C, Shah NH. Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. Journal of Biomedical Semantics. 3: S5. PMID 22541596 DOI: 10.1186/2041-1480-3-S1-S5  0.76
2012 Liu Y, Coulet A, LePendu P, Shah NH. Using ontology-based annotation to profile disease research. Journal of the American Medical Informatics Association : Jamia. 19: e177-86. PMID 22494789 DOI: 10.1136/amiajnl-2011-000631  0.76
2012 Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B. The National Center for Biomedical Ontology. Journal of the American Medical Informatics Association : Jamia. 19: 190-5. PMID 22081220 DOI: 10.1136/amiajnl-2011-000523  0.76
2011 Jonquet C, Lependu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Web Semantics (Online). 9: 316-324. PMID 21918645 DOI: 10.1016/j.websem.2011.06.005  0.76
2011 Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Research. 39: W541-5. PMID 21672956 DOI: 10.1093/nar/gkr469  0.76
2011 Butte AJ, Shah NH. Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. Journal of the American Medical Informatics Association : Jamia. 18: 352-3. PMID 21672904 DOI: 10.1136/amiajnl-2011-000343  0.76
2011 Callahan A, Dumontier M, Shah NH. HyQue: evaluating hypotheses using Semantic Web technologies. Journal of Biomedical Semantics. 2: S3. PMID 21624158 DOI: 10.1186/2041-1480-2-S2-S3  0.76
2011 LePendu P, Musen MA, Shah NH. Enabling enrichment analysis with the Human Disease Ontology. Journal of Biomedical Informatics. 44: S31-8. PMID 21550421 DOI: 10.1016/j.jbi.2011.04.007  0.76
2011 Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP. Mapping between the OBO and OWL ontology languages. Journal of Biomedical Semantics. 2: S3. PMID 21388572 DOI: 10.1186/2041-1480-2-S1-S3  0.76
2010 Xu R, Musen MA, Shah NH. A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2010: 907-11. PMID 21347110  0.76
2010 Parai GK, Jonquet C, Xu R, Musen MA, Shah NH. The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2010: 587-91. PMID 21347046  0.76
2010 Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, ... ... Shah N, et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 28: 935-42. PMID 20829833 DOI: 10.1038/nbt.1666  0.76
2010 Coulet A, Shah NH, Garten Y, Musen M, Altman RB. Using text to build semantic networks for pharmacogenomics. Journal of Biomedical Informatics. 43: 1009-19. PMID 20723615 DOI: 10.1016/j.jbi.2010.08.005  0.76
2010 Jonquet C, Musen MA, Shah NH. Building a biomedical ontology recommender web service. Journal of Biomedical Semantics. 1: S1. PMID 20626921 DOI: 10.1186/2041-1480-1-S1-S1  0.76
2010 Roeder C, Jonquet C, Shah NH, Baumgartner WA, Verspoor K, Hunter L. A UIMA wrapper for the NCBO annotator Bioinformatics. 26: 1800-1801. PMID 20505005 DOI: 10.1093/bioinformatics/btq250  0.76
2010 Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, et al. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Human Mutation. 31: 335-46. PMID 20052762 DOI: 10.1002/humu.21192  0.76
2009 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 Research. 37: W170-3. PMID 19483092 DOI: 10.1093/nar/gkp440  0.76
2008 Musen MA, Musen M, Shah NH, Shah N, Noy NF, Noy N, Dai BY, Dai B, Dorf M, Dorf M, Griffith N, Griffith N, Buntrok J, Buntrock JD, Jonquet C, et al. BioPortal: ontologies and data resources with the click of a mouse. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1223-4. PMID 18999306  0.76
2008 Shah NH, Shah N, Muse MA, Musen M. UMLS-Query: a perl module for querying the UMLS. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 652-6. PMID 18998805  0.76
2008 Rubin DL, Shah NH, Noy NF. Biomedical ontologies: a functional perspective. Briefings in Bioinformatics. 9: 75-90. PMID 18077472 DOI: 10.1093/bib/bbm059  0.76
2008 Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. The Stanford Tissue Microarray Database. Nucleic Acids Research. 36: D871-7. PMID 17989087 DOI: 10.1093/nar/gkm861  0.76
2007 Moreira DA, Shah NH, Musen MA. Interpretation errors related to the GO annotation file format. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 538-42. PMID 18693894  0.76
2007 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, ... ... Shah N, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. 25: 1251-5. PMID 17989687 DOI: 10.1038/nbt1346  0.76
2007 Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S. Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics. 8: 318-32. PMID 17728341 DOI: 10.1093/bib/bbm038  0.76
2007 Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. Annotation and query of tissue microarray data using the NCI Thesaurus. Bmc Bioinformatics. 8: 296. PMID 17686183 DOI: 10.1186/1471-2105-8-296  0.76
2006 Shah NH, Rubin DL, Supekar KS, Musen MA. Ontology-based annotation and query of tissue microarray data. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 709-13. PMID 17238433  0.76
2006 Racunas SA, Shah NH, Fedoroff NV. A case study in pathway knowledgebase verification. Bmc Bioinformatics. 7: 196. PMID 16603083 DOI: 10.1186/1471-2105-7-196  0.76
2005 Mahalingam R, Shah N, Scrymgeour A, Fedoroff N. Temporal evolution of the Arabidopsis oxidative stress response. Plant Molecular Biology. 57: 709-30. PMID 15988565 DOI: 10.1007/s11103-005-2860-4  0.76
2004 Racunas SA, Shah NH, Albert I, Fedoroff NV. HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics (Oxford, England). 20: i257-64. PMID 15262807 DOI: 10.1093/bioinformatics/bth905  0.76
2004 Shah NH, Fedoroff NV. CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology. Bioinformatics (Oxford, England). 20: 1196-7. PMID 14764555 DOI: 10.1093/bioinformatics/bth056  0.76
2003 Shah N, Lepre J, Tu Y, Stolovitzky G. Can we identify cellular pathways implicated in cancer using gene expression data? Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 94-103. PMID 16452783 DOI: 10.1109/CSB.2003.1227308  0.76
2003 Shah NH, King DC, Shah PN, Fedoroff NV. A tool-kit for cDNA microarray and promoter analysis. Bioinformatics (Oxford, England). 19: 1846-8. PMID 14512358 DOI: 10.1093/bioinformatics/btg253  0.76
2003 Mahalingam R, Gomez-Buitrago A, Eckardt N, Shah N, Guevara-Garcia A, Day P, Raina R, Fedoroff NV. Characterizing the stress/defense transcriptome of Arabidopsis. Genome Biology. 4: R20. PMID 12620105  0.76
2002 Mitra M, Shah N, Mueller L, Pin S, Fedoroff N. StressDB: a locally installable web-based relational microarray database designed for small user communities. Comparative and Functional Genomics. 3: 91-6. PMID 18628845 DOI: 10.1002/cfg.153  0.76
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