Nigam H. Shah

Tobias Wittkop, Emily TerAvest, Uday S. Evani, K. Mathew Fleisch, Ari E. Berman, Corey Powell, Nigam H. Shah, Sean D. Mooney: STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. BMC Bioinformatics 14: 53 (2013)

Ryen W. White, Nicholas P. Tatonetti, Nigam H. Shah, Russ B. Altman, Eric Horvitz: Web-scale pharmacovigilance: listening to signals from the crowd. JAMIA 20(3): 404-408 (2013)

Rave Harpaz, Santiago Vilar, William DuMouchel, Hojjat Salmasian, Krystl Haerian, Nigam H. Shah, Herbert S. Chase, Carol Friedman: Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions. JAMIA 20(3): 413-419 (2013)

Udo Hahn, Kevin Bretonnel Cohen, Yael Garten, Nigam H. Shah: Mining the pharmacogenomics literature - a survey of the state of the art. Briefings in Bioinformatics 13(4): 460-494 (2012)

Mark A. Musen, Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne D. Storey, Barry Smith: The National Center for Biomedical Ontology. JAMIA 19(2): 190-195 (2012)

Yi Liu, Adrien Coulet, Paea LePendu, Nigam H. Shah: Using ontology-based annotation to profile disease research. JAMIA 19(e1) (2012)

Nigam H. Shah, Jessica D. Tenenbaum: The coming age of data-driven medicine: translational bioinformatics' next frontier. JAMIA 19(e1) (2012)

Stephen Tze-Inn Wu, Hongfang Liu, Dingcheng Li, Cui Tao, Mark A. Musen, Christopher G. Chute, Nigam H. Shah: Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. JAMIA 19(e1) (2012)

Cameron Neylon, Jan Aerts, C. Brown, Simon J. Coles, Les Hatton, Daniel Lemire, K. Millman, Peter Murray-Rust, Fernando Perez, Neil F. W. Saunders, Nigam Shah, Arfon Smith, Gaël Varoquaux, Egon L. Willighagen: Changing computational research. The challenges ahead. Source Code for Biology and Medicine 7: 2 (2012)

Byambajargal Byambajav, Tomasz Wiktor Wlodarczyk, Chunming Rong, Paea LePendu, Nigam Shah: Performance of Left Outer Join on Hadoop with Right Side within Single Node Memory Size. AINA Workshops 2012: 1075-1080

Alejandro Rodríguez González, Jyotishman Pathak, Mark Wilkinson, Nigam Shah, Robert Stevens, Richard Boyce, Ángel García-Crespo (Eds.): Proceedings of the Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine, Boston, USA, November 12, 2012. CEUR Workshop Proceedings 930, CEUR-WS.org 2012

Atul J. Butte, Nigam H. Shah: Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. JAMIA 18(4): 352-353 (2011)

Patricia L. Whetzel, Natalya Fridman Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, Mark A. Musen: 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(Web-Server-Issue): 541-545 (2011)

Clement Jonquet, Paea LePendu, Sean M. Falconer, Adrien Coulet, Natalya Fridman Noy, Mark A. Musen, Nigam H. Shah: NCBO Resource Index: Ontology-based search and mining of biomedical resources. J. Web Sem. 9(3): 316-324 (2011)

Cui Tao, Natalya Fridman Noy, Harold R. Solbrig, Nigam H. Shah, Mark A. Musen, Christopher G. Chute: Proposed SKOS Extensions for BioPortal Terminology Services. JIST 2011: 342-349

Paea LePendu, Mark A. Musen, Nigam H. Shah: The Age of Data-Driven Medicine: Mining the Electronic Health Record. ICBO 2011

Patricia L. Whetzel, Clement Jonquet, Cherie Youn, Michael Dorf, Ray W. Fergerson, Mark A. Musen, Nigam Shah: The NCBO Annotator: Ontology-Based Annotation as a Web Service. ICBO 2011

Patricia L. Whetzel, Natasha F. Noy, Nigam Shah, Paul R. Alexander, Michael Dorf, Ray W. Fergerson, Margaret-Anne D. Storey, Barry Smith, Christopher G. Chute, Mark A. Musen: Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse. ICBO 2011

Kevin Bretonnel Cohen, Yael Garten, Udo Hahn, Nigam H. Shah: Workshop Introduction. Pacific Symposium on Biocomputing 2011: 362-363

Christophe Roeder, Clement Jonquet, Nigam H. Shah, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter: A UIMA wrapper for the NCBO annotator. Bioinformatics 26(14): 1800-1801 (2010)

Adrien Coulet, Nigam H. Shah, Yael Garten, Mark A. Musen, Russ B. Altman: Using text to build semantic networks for pharmacogenomics. Journal of Biomedical Informatics 43(6): 1009-1019 (2010)

Adrien Coulet, Nigam H. Shah, Lawrence Hunter, Chitta Baral, Russ B. Altman: Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application. Pacific Symposium on Biocomputing 2010: 485-487

Paea LePendu, Natalya Fridman Noy, Clement Jonquet, Paul R. Alexander, Nigam H. Shah, Mark A. Musen: Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases. International Semantic Web Conference (1) 2010: 486-501

Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen: Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 10(S-2) (2009)

Nigam H. Shah, Nipun Bhatia, Clement Jonquet, Daniel L. Rubin, Annie P. Chiang, Mark A. Musen: Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinformatics 10(S-9): 14 (2009)

Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Daniel L. Rubin, Margaret-Anne D. Storey, Christopher G. Chute, Mark A. Musen: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37(Web-Server-Issue): 170-173 (2009)

Amir Ghazvinian, Natalya Fridman Noy, Clement Jonquet, Nigam H. Shah, Mark A. Musen: What Four Million Mappings Can Tell You about Two Hundred Ontologies. International Semantic Web Conference 2009: 229-242

Syed Hamid Tirmizi, Stuart Aitken, Dilvan A. Moreira, Chris Mungall, Juan Sequeda, Nigam H. Shah, Daniel P. Miranker: OBO & OWL: Roundtrip Ontology Transformations. SWAT4LS 2009

Nigam Shah: Biomedical Data/Content Acquisition, Curation. Encyclopedia of Database Systems 2009: 224-229

Nikesh Kotecha, Kyle Bruck, William Lu, Nigam Shah: Pathway knowledge base: An integrated pathway resource using BioPAX. Applied Ontology 3(4): 235-245 (2008)

Daniel L. Rubin, Nigam Shah, Natalya Fridman Noy: Biomedical ontologies: a functional perspective. Briefings in Bioinformatics 9(1): 75-90 (2008)

Robert J. Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H. Shah, Wijan Prapong, Michael Nitzberg, Zachariah K. Zachariah, Gavin Sherlock, Yasodha Natkunam, Robert B. West, Matt van de Rijn, Patrick O. Brown, Catherine A. Ball: The Stanford Tissue Microarray Database. Nucleic Acids Research 36(Database-Issue): 871-877 (2008)

Clement Jonquet, Mark A. Musen, Nigam Shah: A System for Ontology-Based Annotation of Biomedical Data. DILS 2008: 144-152

Natalya Fridman Noy, Nigam Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Michael Montegut, Daniel L. Rubin, Cherie Youn, Mark A. Musen: BioPortal: A Web Repository for Biomedical Ontologies and Data Resources. International Semantic Web Conference (Posters & Demos) 2008

Balaji S. Srinivasan, Nigam H. Shah, Jason Flannick, Eduardo Abeliuk, Antal F. Novak, Serafim Batzoglou: Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics 8(5): 318-332 (2007)

Nigam H. Shah, Daniel L. Rubin, Inigo Espinosa, Kelli Montgomery, Mark A. Musen: Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics 8 (2007)

Woei-Jyh Lee, Louiqa Raschid, Padmini Srinivasan, Nigam Shah, Daniel L. Rubin, Natasha Fridman Noy: Using Annotations from Controlled Vocabularies to Find Meaningful Associations. DILS 2007: 247-263

Harith Alani, Natasha Fridman Noy, Nigam Shah, Nigel Shadbolt, Mark A. Musen: Searching ontologies based on content: experiments in the biomedical domain. K-CAP 2007: 55-62

Stephen A. Racunas, Nigam Shah, Nina V. Fedoroff: A case study in pathway knowledgebase verification. BMC Bioinformatics 7: 196 (2006)

N. H. Shah: Inventory model for deteriorating items and time value of money for a finite time horizon under the permissible delay in payments. Int. J. Systems Science 37(1): 9-15 (2006)

N. H. Shah, Nina V. Fedoroff: CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology. Bioinformatics 20(7): 1196-1197 (2004)

Stephen A. Racunas, Christopher Griffin, Nigam Shah: A Finite Model Theory for Biological Hypotheses. CSB 2004: 616-620

Stephen A. Racunas, N. H. Shah, I. Albert, Nina V. Fedoroff: HyBrow: a prototype system for computer-aided hypothesis evaluation. ISMB/ECCB (Supplement of Bioinformatics) 2004: 257-264

N. H. Shah, D. C. King, P. N. Shah, Nina V. Fedoroff: A tool-kit for cDNA microarray and promoter analysis. Bioinformatics 19(14): 1846-1848 (2003)

Nigam Shah, Jorge Lepre, Yuhai Tu, Gustavo Stolovitzky: Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data? CSB 2003: 94-103

Steve Racunas, Nigam Shah, Nina V. Fedoroff: A Contradiction-Based Framework for Testing Gene Regulation Hypotheses. CSB 2003: 634-638

Muhammad Younas, N. H. Shah, Kuo-Ming Chao: A Multi-agent Approach to SACReD Transactions for E-commerce Applications. EC-Web 2002: 119-128