Knowledge Aggregation from Organized Sets (KAOS) Applied to Clinical Data. - Indra Neil Sarkar; Paul J. Planet; Robert DeSalle; David H. Figurski (AMIA, 2001)

An integrative model for in-silico clinical-genomics discovery science. - Yves A. Lussier; Indra Neil Sarkar; Michael Cantor (AMIA, 2002)

Exploring SNOMED Using Phylogenetic Analysis Tools. - Indra Neil Sarkar; Michael N. Cantor; Robert DeSalle; Yves A. Lussier (AMIA, 2002)

Discovering protein similarity using natural language processing. - Indra Neil Sarkar; Thomas C. Rindflesch (AMIA, 2002)

Implementation Brief: Desiderata for Personal Electronic Communication in Clinical Systems. - Indra Neil Sarkar; Justin Starren (J. Am. Medical Informatics Assoc., 2002)

Characteristic attributes in cancer microarrays. - Indra Neil Sarkar; Paul J. Planet; T. E. Bael; S. E. Stanley; Mark Siddall; Robert DeSalle; David H. Figurski (J. Biomed. Informatics, 2002)

An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS®$. - Michael N. Cantor; Indra Neil Sarkar; R. Gelman; Frank W. Hartel; Olivier Bodenreider; Yves A. Lussier (MIE, 2003)

Linking Biomedical Language Information and Knowledge Resources in the 21st Century: GO and UMLS. - Indra Neil Sarkar; Michael N. Cantor; R. Gelman; Frank W. Hartel; Yves A. Lussier (Pacific Symposium on Biocomputing, 2003)

ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. - Jeffrey A. Rosenfeld; Indra Neil Sarkar; Paul J. Planet; David H. Figurski; Robert DeSalle (Bioinform., 2004)

GenesTrace: Phenomic Knowledge Discovery via Structured Terminology. - Michael N. Cantor; Indra Neil Sarkar; Olivier Bodenreider; Yves A. Lussier (Pacific Symposium on Biocomputing, 2005)

mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests. - Paul J. Planet; Indra Neil Sarkar (Bioinform., 2005)

Literature Based Discovery of Gene Clusters Using Phylogenetic Methods. - Indra Neil Sarkar; Abha Agrawal (AMIA, 2006)

zMedline: A Medline-Based Content Management System. - Chif N. Umejei; Indra Neil Sarkar (AMIA, 2006)

OrthologID: automation of genome-scale ortholog identification within a parsimony framework. - Joanna C. Chiu; Ernest K. Lee; Mary G. Egan; Indra Neil Sarkar; Gloria M. Coruzzi; Robert DeSalle (Bioinform., 2006)

Phylogenetics in the modern era. - Indra Neil Sarkar (J. Biomed. Informatics, 2006)

Session Introduction. - Indra Neil Sarkar (Pacific Symposium on Biocomputing, 2007)

Biodiversity informatics: organizing and linking information across the spectrum of life. - Indra Neil Sarkar (Briefings Bioinform., 2007)

uBioRSS: Tracking taxonomic literature using RSS. - Patrick R. Leary; David P. Remsen; Catherine N. Norton; David J. Patterson; Indra Neil Sarkar (Bioinform., 2007)

Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. - Indra Neil Sarkar; Mary G. Egan; Gloria M. Coruzzi; Ernest K. Lee; Robert DeSalle (BMC Bioinform., 2008)

LigerCat: Using "MeSH Clouds" from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature. - Indra Neil Sarkar; Ryan Schenk; Holly Miller; Catherine N. Norton (AMIA, 2009)

Selected proceedings of the First Summit on Translational Bioinformatics 2008. - Atul J. Butte; Indra Neil Sarkar; Marco Ramoni; Yves A. Lussier; Olga G. Troyanskaya (BMC Bioinform., 2009)

Selected proceedings of the 2009 Summit on Translational Bioinformatics. - Yves A. Lussier; Indra Neil Sarkar (BMC Bioinform., 2009)

Biodiversity Informatics: the emergence of a field. - Indra Neil Sarkar (BMC Bioinform., 2009)

Editorial: Bioinformatics education in the 21st century. - Indra Neil Sarkar (Briefings Bioinform., 2010)

Evaluation of family history information within clinical documents and adequacy of HL7 clinical statement and clinical genomics family history models for its representation: a case report. - Genevieve B. Melton; Nandhini Raman; Elizabeth S. Chen; Indra Neil Sarkar; Serguei V. S. Pakhomov; Robert D. Madoff (J. Am. Medical Informatics Assoc., 2010)

MeSHing molecular sequences and clinical trials: A feasibility study. - Elizabeth S. Chen; Indra Neil Sarkar (J. Biomed. Informatics, 2010)

Translational bioinformatics: linking knowledge across biological and clinical realms. - Indra Neil Sarkar; Atul J. Butte; Yves A. Lussier; Peter Tarczy-Hornoch; Lucila Ohno-Machado (J. Am. Medical Informatics Assoc., 2011)

Selected Papers from the 2011 Summit on Translational Bioinformatics. - Indra Neil Sarkar (J. Biomed. Informatics, 2011)

The joint summits on translational science: Crossing the translational chasm. - Indra Neil Sarkar; Philip R. O. Payne (J. Biomed. Informatics, 2011)

Enhancing phylogeography by improving geographical information from GenBank. - Matthew Scotch; Indra Neil Sarkar; Changjiang Mei; Robert Leaman; Kei-Hoi Cheung; Pierina Ortiz; Ashutosh Singraur; Graciela Gonzalez 001 (J. Biomed. Informatics, 2011)

Characterizing the Use and Contents of Free-Text Family History Comments in the Electronic Health Record. - Elizabeth S. Chen; Genevieve B. Melton; Timothy E. Burdick; Paul Rosenau; Indra Neil Sarkar (AMIA, 2012)

Social and Behavioral History Information in Public Health Datasets. - Genevieve B. Melton; Sharad Manaktala; Indra Neil Sarkar; Elizabeth S. Chen (AMIA, 2012)

Mining Disease Fingerprints From Within Genetic Pathways. - Ahmed Ragab Nabhan; Indra Neil Sarkar (AMIA, 2012)

Determining Compound Comorbidities for Heart Failure from Hospital Discharge Data. - Indra Neil Sarkar; Elizabeth S. Chen (AMIA, 2012)

The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. - Ahmed Ragab Nabhan; Indra Neil Sarkar (Briefings Bioinform., 2012)

A vector space model approach to identify genetically related diseases. - Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2012)

Translating standards into practice: Experiences and lessons learned in biomedicine and health care. - Elizabeth S. Chen; Genevieve B. Melton; Indra Neil Sarkar (J. Biomed. Informatics, 2012)

Development of a Comprehensive Family Health History Information Model. - Elizabeth S. Chen; Elizabeth W. Carter; Tamara Winden; Indra Neil Sarkar; Genevieve B. Melton (AMIA, 2013)

Resolving and Standardizing Providers within Administrative Data. - Indra Neil Sarkar; Elizabeth S. Chen; Steven J. Kappel (AMIA, 2013)

Bioinformatics opportunities for identification and study of medicinal plants. - Vivekanand Sharma; Indra Neil Sarkar (Briefings Bioinform., 2013)

Research and applications: Leveraging biodiversity knowledge for potential phyto-therapeutic applications. - Vivekanand Sharma; Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2013)

Leveraging concept-based approaches to identify potential phyto-therapies. - Vivekanand Sharma; Indra Neil Sarkar (J. Biomed. Informatics, 2013)

People, organizational, and leadership factors impacting informatics support for clinical and translational research. - Philip R. O. Payne; Taylor R. Pressler; Indra Neil Sarkar; Yves A. Lussier (BMC Medical Informatics Decis. Mak., 2013)

Examining the Use, Contents, and Quality of Free-Text Tobacco Use Documentation in the Electronic Health Record. - Elizabeth S. Chen; Elizabeth W. Carter; Indra Neil Sarkar; Tamara Winden; Genevieve B. Melton (AMIA, 2014)

Using Arden Syntax to Identify Registry-Eligible Very Low Birth Weight Neonates from the Electronic Health Record. - Indra Neil Sarkar; Elizabeth S. Chen; Paul Rosenau; Matthew B. Storer; Beth Anderson; Jeffrey D. Horbar (AMIA, 2014)

PubMedMiner: Mining and Visualizing MeSH-based Associations in PubMed. - Yucan Zhang; Indra Neil Sarkar; Elizabeth S. Chen (AMIA, 2014)

Drug repurposing: mining protozoan proteomes for targets of known bioactive compounds. - Adam Sateriale; Kovi Bessoff; Indra Neil Sarkar; Christopher D. Huston (J. Am. Medical Informatics Assoc., 2014)

Structural network analysis of biological networks for assessment of potential disease model organisms. - Ahmed Ragab Nabhan; Indra Neil Sarkar (J. Biomed. Informatics, 2014)

Representation of Drug Use in Biomedical Standards, Clinical Text, and Research Measures. - Elizabeth W. Carter; Indra Neil Sarkar; Genevieve B. Melton; Elizabeth S. Chen (AMIA, 2015)

Mining and Visualizing Family History Associations in the Electronic Health Record: A Case Study for Pediatric Asthma. - Elizabeth S. Chen; Genevieve B. Melton; Richard Wasserman; Paul Rosenau; Diantha B. Howard; Indra Neil Sarkar (AMIA, 2015)

Surveying Problem List Perceptions and Use in the Electronic Health Record. - Darlene Peterson; Timothy E. Burdick; Joshua Cohen; Indra Neil Sarkar; Julie Lin; Dennis Plante; Elizabeth S. Chen (AMIA, 2015)

Automated Extraction of Substance Use Information from Clinical Texts. - Yan Wang 025; Elizabeth S. Chen; Serguei V. S. Pakhomov; Elliot G. Arsoniadis; Elizabeth W. Carter; Elizabeth Lindemann; Indra Neil Sarkar; Genevieve B. Melton (AMIA, 2015)

Multi-source development of an integrated model for family health history. - Elizabeth S. Chen; Elizabeth W. Carter; Tamara Winden; Indra Neil Sarkar; Yan Wang 025; Genevieve B. Melton (J. Am. Medical Informatics Assoc., 2015)

Adapting simultaneous analysis phylogenomic techniques to study complex disease gene relationships. - Joseph D. Romano; William G. Tharp; Indra Neil Sarkar (J. Biomed. Informatics, 2015)

New Pathways Into Biomedical Informatics: Educational Outreach Programs for High School Students. - David Boone; John T. Finnell; Kim M. Unertl; Indra Neil Sarkar (AMIA, 2016)

Mining and Visualizing Sequential Patterns in the Electronic Health Record: A Case Study for Asthma With and Without Mental Disorders. - Elizabeth S. Chen; Genevieve B. Melton; Mark Howison; Erik Knoll; Ashley S. Lee; Indra Neil Sarkar (AMIA, 2016)

Report from the ED-WG Frontline: Biomedical and Health Informatics Baccalaureate (BHIB) Course. - Saif S. Khairat; Glynda Doyle; Indra Neil Sarkar; Jeff Williamson (AMIA, 2016)

Identifying Family History and Substance Use Associations for Adult Epilepsy from the Electronic Health Record. - Yan Wang 025; Elizabeth S. Chen; Ilo Leppik; Serguei V. S. Pakhomov; Indra Neil Sarkar; Genevieve B. Melton (CRI, 2016)

How to Prepare a Nursing Informatics Conference Submission. - Kaija Saranto; Elizabeth M. Borycki; Indra Neil Sarkar (Nursing Informatics, 2016)

Developing new pathways into the biomedical informatics field: the AMIA High School Scholars Program. - Kim M. Unertl; John T. Finnell; Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2016)

Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. - Laura K. Wiley; Peter Tarczy-Hornoch; Joshua C. Denny; Robert R. Freimuth; Casey L. Overby; Nigam Shah; Ross D. Martin; Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2016)

An Automated System for Categorizing Transthoracic Echocardiography Indications According to the Echocardiography Appropriate Use Criteria. - Aaron S. Eisman; Rory B. Weiner; Elizabeth S. Chen; Paul Stey; Rishi K. Wadhera; Aaron P. Kithcart; Indra Neil Sarkar (AMIA, 2017)

Comorbidity Miner: An Open Source Interactive Tool for Mining Disparate Electronic Health Data Sources. - Ashley S. Lee; Indra Neil Sarkar; Genevieve B. Melton; Yuanqing Liu; Vivekanand Sharma; Elizabeth S. Chen (AMIA, 2017)

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts. - Vivekanand Sharma; Wayne Law; Michael J. Balick; Indra Neil Sarkar (AMIA, 2017)

Assessing Data Quality within Health Information Exchanges: A Case Study for Supporting Emergency Department Research. - Margaret M. Thorsen; Indra Neil Sarkar; Elizabeth S. Chen; Elaine Fontaine; Gregory Walker; Megan L. Ranney (AMIA, 2017)

Crossing the health IT chasm: considerations and policy recommendations to overcome current challenges and enable value-based care. - Julia Adler-Milstein; Peter J. Embí; Blackford Middleton; Indra Neil Sarkar; Jeff Smith (J. Am. Medical Informatics Assoc., 2017)

Using Demographic Factors and Comorbidities to Develop a Predictive Model for ICU Mortality in Patients with Acute Exacerbation COPD. - Sukrit S. Jain; Indra Neil Sarkar; Paul Stey; Rajsavi S. Anand; Dustin R. Biron; Elizabeth S. Chen (AMIA, 2018)

Predicting Thromboembolism after Vaginal and Laparoscopic Hysterectomy in Gynecologic Oncology Patients using Machine Learning. - Justin E. Kleiner; Michael Cohen; Dilum P. Aluthge; Ishan Sinha; Indra Neil Sarkar; Elizabeth S. Chen; Dario R. Roque (AMIA, 2018)

Predicting the Costs of Medical Liability Using Artificial Neural Networks. - Jonathan T. Vu; Dilum P. Aluthge; Ishan Sinha; Elizabeth S. Chen; Indra Neil Sarkar (AMIA, 2018)

Identifying natural health product and dietary supplement information within adverse event reporting systems. - Vivekanand Sharma; Indra Neil Sarkar (PSB, 2018)

Web-Based Visualization of MeSH-Based PubMed/MEDLINE Statistics. - Maria I. Restrepo 002; Mary C. McGrath; Indra Neil Sarkar; Elizabeth S. Chen (MedInfo, 2019)

Racial Representation Disparity of Population-Level Genomic Sequencing Efforts. - Isaac E. Kim Jr.; Indra Neil Sarkar (MedInfo, 2019)

Identifying Phytochemicals from Biomedical Literature Utilizing Semantic Knowledge Sources. - Indra Neil Sarkar; Wayne Law; Michael J. Balick (MedInfo, 2019)

Machine learning approach to literature mining for the genetics of complex diseases. - Jessica Schuster; Michael Superdock; Anthony Agudelo; Paul Stey; James Padbury; Indra Neil Sarkar; Alper Uzun (Database J. Biol. Databases Curation, 2019)

Solr-Plant: efficient extraction of plant names from text. - Vivekanand Sharma; Maria Isabel Restrepo; Indra Neil Sarkar (BMC Bioinform., 2019)

Mental Health Comorbidity Analysis in Pediatric Patients with Autism Spectrum Disorder Using Rhode Island Medical Claims Data. - Katherine A. Brown; Indra Neil Sarkar; Elizabeth S. Chen (AMIA, 2020)

Extracting Angina Symptoms from Clinical Notes Using Pre-Trained Transformer Architectures. - Aaron S. Eisman; Nishant R. Shah; Carsten Eickhoff; George Zerveas; Elizabeth S. Chen; Wen-Chih Wu; Indra Neil Sarkar (AMIA, 2020)

Coding Free-Text Chief Complaints from a Health Information Exchange: A Preliminary Study. - Sotiris Karagounis; Indra Neil Sarkar; Elizabeth S. Chen (AMIA, 2020)

A Phylogenetic Approach to Analyze the Conservativeness of BRCA1 and BRCA2 Mutations. - Jiaying Lai; Indra Neil Sarkar (AMIA, 2020)

Clinical Note Section Detection Using a Hidden Markov Model of Unified Medical Language System Semantic Types. - Aaron S. Eisman; Katherine A. Brown; Elizabeth S. Chen; Indra Neil Sarkar (AMIA, 2021)

Public Health Informatics in a Global Pandemic: In the COVID response trenches. - Jessica D. Tenenbaum; Theresa Cullen; Indra Neil Sarkar; Philip R. O. Payne; Brian E. Dixon (AMIA, 2021)

An Unsupervised Cluster Analysis of Post-COVID-19 Mental Health Outcomes and Associated Comorbidities. - Katherine A. Brown; Indra Neil Sarkar; Karen Crowley; Dilum P. Aluthge; Elizabeth S. Chen (AMIA, 2022)

GenBank as a source to monitor and analyze Host-Microbiome data. - Vivek Ramanan; Shanti Mechery; Indra Neil Sarkar (Bioinform., 2022)

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. - Emily R. Pfaff; Andrew T. Girvin; Davera Gabriel; Kristin Kostka; Michele Morris; Matvey B. Palchuk; Harold P. Lehmann; Benjamin R. C. Amor; Mark Bissell; Katie R. Bradwell; Sigfried Gold; Stephanie S. Hong; et al. (J. Am. Medical Informatics Assoc., 2022)

Learning health system linchpins: information exchange and a common data model. - Aaron S. Eisman; Elizabeth S. Chen; Wen-Chih Wu; Karen Crowley; Dilum P. Aluthge; Katherine A. Brown; Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2025)

The health data utility and the resurgence of health information exchanges as a national resource. - Anjum Khurshid; Indra Neil Sarkar (J. Am. Medical Informatics Assoc., 2025)