Nigam H. Shah

According to our database1, Nigam H. Shah
  • authored at least 104 papers between 2002 and 2017.
  • has a "Dijkstra number"2 of four.

Timeline

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Bibliography

2017
Synergistic drug combinations from electronic health records and gene expression.
JAMIA, 2017

Learning Effective Representations from Clinical Notes.
CoRR, 2017

Open Data for Discovery Science.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Learning Attributes of Disease Progression from Trajectories of Sparse Lab Values.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2016
An unsupervised learning method to identify reference intervals from a clinical database.
Journal of Biomedical Informatics, 2016

Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.
JAMIA, 2016

Learning statistical models of phenotypes using noisy labeled training data.
JAMIA, 2016

Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature.
BMC Bioinformatics, 2016

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.
J. Biomedical Semantics, 2016

RegenBase: a knowledge base of spinal cord injury biology for translational research.
Database, 2016

The digital revolution in phenotyping.
Briefings in Bioinformatics, 2016

Discovering Patient Phenotypes Using Generalized Low Rank Models.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Session Introduction.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Learning Effective Treatment Pathways for Type-2 Diabetes from a clinical data warehouse.
Proceedings of the AMIA 2016, 2016

Big Data for Healthcare and Life Sciences: Learning Useful Insights from Imperfect Data.
Proceedings of the AMIA 2016, 2016

Ensuring Reproducibility in Observational Research: Building and Sharing Knowledge Resources in the OHDSI Network.
Proceedings of the AMIA 2016, 2016

2015
A formal concept analysis and semantic query expansion cooperation to refine health outcomes of interest.
BMC Med. Inf. & Decision Making, 2015

Implications of non-stationarity on predictive modeling using EHRs.
Journal of Biomedical Informatics, 2015

A method for systematic discovery of adverse drug events from clinical notes.
JAMIA, 2015

Functional evaluation of out-of-the-box text-mining tools for data-mining tasks.
JAMIA, 2015

Provenance-Centered Dataset of Drug-Drug Interactions.
CoRR, 2015

Special issue on bio-ontologies and phenotypes.
J. Biomedical Semantics, 2015

Provenance-Centered Dataset of Drug-Drug Interactions.
Proceedings of the Semantic Web - ISWC 2015, 2015

Analyzing Search Behavior of Healthcare Professionals for Drug Safety Surveillance.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

The Value of an Open-Source Observational Research Collaboratory: Results from the OHDSI Initiative.
Proceedings of the AMIA 2015, 2015

Recent Advances in Computational Drug Repositioning.
Proceedings of the AMIA 2015, 2015

2014
Mining clinical text for signals of adverse drug-drug interactions.
JAMIA, 2014

Toward personalizing treatment for depression: predicting diagnosis and severity.
JAMIA, 2014

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomedical Semantics, 2014

Finding progression stages in time-evolving event sequences.
Proceedings of the 23rd International World Wide Web Conference, 2014

Session introduction.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

Medicine in the age of electronic health records.
Proceedings of the 20th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2014

2013
Web-scale pharmacovigilance: listening to signals from the crowd.
JAMIA, 2013

Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions.
JAMIA, 2013

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.
BMC Bioinformatics, 2013

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomedical Semantics, 2013

Refining Health Outcomes of Interest using Formal Concept Analysis and Semantic Query Expansion.
Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2013

Session introduction.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Empirical bayes model to combine signals of adverse drug reactions.
Proceedings of the 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2013

Mining Biomedical Ontologies and Data Using RDF Hypergraphs.
Proceedings of the 12th International Conference on Machine Learning and Applications, 2013

Refining health outcomes of interest using formal concept analysis and semantic query expansion.
Proceedings of the Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, 2013

Learning Practice-based Evidence from Unstructured Clinical Notes.
Proceedings of the AMIA 2013, 2013

Predictive Models in Mental Health: From Diagnosis to Treatment.
Proceedings of the AMIA 2013, 2013

2012
Changing computational research. The challenges ahead.
Source Code for Biology and Medicine, 2012

Chapter 9: Analyses Using Disease Ontologies.
PLoS Computational Biology, 2012

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
JAMIA, 2012

The coming age of data-driven medicine: translational bioinformatics' next frontier.
JAMIA, 2012

The National Center for Biomedical Ontology.
JAMIA, 2012

Using ontology-based annotation to profile disease research.
JAMIA, 2012

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomedical Semantics, 2012

Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes.
J. Biomedical Semantics, 2012

Mining the pharmacogenomics literature - a survey of the state of the art.
Briefings in Bioinformatics, 2012

Session introduction.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Performance of Left Outer Join on Hadoop with Right Side within Single Node Memory Size.
Proceedings of the 26th International Conference on Advanced Information Networking and Applications Workshops, 2012

2011
NCBO Resource Index: Ontology-based search and mining of biomedical resources.
J. Web Sem., 2011

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, 2011

Enabling enrichment analysis with the Human Disease Ontology.
Journal of Biomedical Informatics, 2011

Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA.
JAMIA, 2011

Mapping between the OBO and OWL ontology languages.
J. Biomedical Semantics, 2011

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomedical Semantics, 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.
J. Biomedical Semantics, 2011

HyQue: evaluating hypotheses using Semantic Web technologies.
J. Biomedical Semantics, 2011

Workshop Introduction.
Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The NCBO Annotator: Ontology-Based Annotation as a Web Service.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

The Age of Data-Driven Medicine: Mining the Electronic Health Record.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Proposed SKOS Extensions for BioPortal Terminology Services.
Proceedings of the Semantic Web - Joint International Semantic Technology Conference, 2011

2010
Using text to build semantic networks for pharmacogenomics.
Journal of Biomedical Informatics, 2010

Selected papers from the 12th annual Bio-Ontologies meeting.
J. Biomedical Semantics, 2010

Building a biomedical ontology recommender web service.
J. Biomedical Semantics, 2010

A UIMA wrapper for the NCBO annotator.
Bioinformatics, 2010

Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases.
Proceedings of the Semantic Web - ISWC 2010 - 9th International Semantic Web Conference, 2010

Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Indexation et intégration de ressources textuelles à l'aide d'ontologies : application au domaine biomédical.
Proceedings of the IC 2010 : 21es Journées Ingénierie des Connaissances 2010 (Proceedings of the 21st French Knowledge Engineering Conference), 2010

2009
Ontologies for Formal Representation of Biological Systems.
Proceedings of the Handbook on Ontologies, 2009

Biomedical Data/Content Acquisition, Curation.
Proceedings of the Encyclopedia of Database Systems, 2009

BioPortal: ontologies and integrated data resources at the click of a mouse.
Nucleic Acids Research, 2009

Ontology-driven indexing of public datasets for translational bioinformatics.
BMC Bioinformatics, 2009

Comparison of concept recognizers for building the Open Biomedical Annotator.
BMC Bioinformatics, 2009

OBO & OWL: Roundtrip Ontology Transformations.
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2009

What Four Million Mappings Can Tell You about Two Hundred Ontologies.
Proceedings of the Semantic Web - ISWC 2009, 8th International Semantic Web Conference, 2009

2008
The Stanford Tissue Microarray Database.
Nucleic Acids Research, 2008

Biomedical ontologies: a functional perspective.
Briefings in Bioinformatics, 2008

Pathway knowledge base: An integrated pathway resource using BioPAX.
Applied Ontology, 2008

BioPortal: A Web Repository for Biomedical Ontologies and Data Resources.
Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference (ISWC2008), 2008

A System for Ontology-Based Annotation of Biomedical Data.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

UMLS-Query: A Perl Module for Querying the UMLS.
Proceedings of the AMIA 2008, 2008

Comparison of Ontology-based Semantic-Similarity Measures.
Proceedings of the AMIA 2008, 2008

2007
Annotation and query of tissue microarray data using the NCI Thesaurus.
BMC Bioinformatics, 2007

Current progress in network research: toward reference networks for key model organisms.
Briefings in Bioinformatics, 2007

Searching ontologies based on content: experiments in the biomedical domain.
Proceedings of the 4th International Conference on Knowledge Capture (K-CAP 2007), 2007

Using Annotations from Controlled Vocabularies to Find Meaningful Associations.
Proceedings of the Data Integration in the Life Sciences, 4th International Workshop, 2007

Interpretation Errors related to the GO Annotation File Format.
Proceedings of the AMIA 2007, 2007

2006
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, 2006

A case study in pathway knowledgebase verification.
BMC Bioinformatics, 2006

Ontology-based Annotation and Query of Tissue Microarray Data.
Proceedings of the AMIA 2006, 2006

2004
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.
Bioinformatics, 2004

HyBrow: a prototype system for computer-aided hypothesis evaluation.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

A Finite Model Theory for Biological Hypotheses.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003
A tool-kit for cDNA microarray and promoter analysis.
Bioinformatics, 2003

Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data?
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

A Contradiction-Based Framework for Testing Gene Regulation Hypotheses.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
A Multi-agent Approach to SACReD Transactions for E-commerce Applications.
Proceedings of the E-Commerce and Web Technologies, Third International Conference, 2002


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