Template Based Semantic Similarity for Security Applications. - Boanerges Aleman-Meza; Christian Halaschek-Wiener; Satya Sanket Sahoo; Amit P. Sheth; Ismailcem Budak Arpinar (ISI, 2005)

Bioinformatics Applications Of Web Services, Web Processes And Role Of Semantics. - Satya Sanket Sahoo; Amit P. Sheth (Semantic Web Services, Processes and Applications, 2006)

Knowledge modeling and its application in life sciences: a tale of two ontologies. - Satya Sanket Sahoo; Christopher Thomas 001; Amit P. Sheth; William S. York; Samir Tartir (WWW, 2006)

From "Glycosyltransferase" to "Congenital Muscular Dystrophy": Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology. - Satya Sanket Sahoo; Kelly Zeng; Olivier Bodenreider; Amit P. Sheth (MedInfo, 2007)

Capturing Workflow Event Data for Monitoring, Performance Analysis, and Management of Scientific Workflows. - Matthew D. Valerio; Satya Sanket Sahoo; Roger S. Barga; Jared Jackson (eScience, 2008)

Semantic Provenance for eScience: Managing the Deluge of Scientific Data. - Satya Sanket Sahoo; Amit P. Sheth; Cory A. Henson (IEEE Internet Comput., 2008)

Semantic Sensor Web. - Amit P. Sheth; Cory A. Henson; Satya Sanket Sahoo (IEEE Internet Comput., 2008)

An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence. - Satya Sanket Sahoo; Olivier Bodenreider; Joni L. Rutter; Karen J. Skinner; Amit P. Sheth (J. Biomed. Informatics, 2008)

Ontology-Driven Provenance Management in eScience: An Application in Parasite Research. - Satya Sanket Sahoo; D. Brent Weatherly; Raghava Mutharaju; Pramod Anantharam; Amit P. Sheth; Rick L. Tarleton (OTM Conferences (2), 2009)

Introduction. - Juliana Freire; Paolo Missier; Satya Sanket Sahoo (SWPM, 2009)

Janus: From Workflows to Semantic Provenance and Linked Open Data. - Paolo Missier; Satya Sanket Sahoo; Jun Zhao 003; Carole A. Goble; Amit P. Sheth (IPAW, 2010)

Provenance of Microarray Experiments for a Better Understanding of Experiment Results. - Helena F. Deus; Jun Zhao 003; Satya S. Sahoo; Matthias Samwald; Eric Prud'hommeaux; Michael Miller 001; M. Scott Marshall; Kei-Hoi Cheung (SWPM@ISWC, 2010)

Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. - Satya Sanket Sahoo; Olivier Bodenreider; Pascal Hitzler; Amit P. Sheth; Krishnaprasad Thirunarayan (SSDBM, 2010)

Provenance for Scientific Workflows Towards Reproducible Research. - Roger S. Barga; Yogesh L. Simmhan; Eran Chinthaka; Satya Sanket Sahoo; Jared Jackson; Nelson Araujo (IEEE Data Eng. Bull., 2010)

Towards Desiderata for Provenance Ontologies in Biomedicine. - Satya Sanket Sahoo (ICBO, 2011)

A unified framework for managing provenance information in translational research. - Satya Sanket Sahoo; Vinh Nguyen; Olivier Bodenreider; Priti Parikh; Todd Minning; Amit P. Sheth (BMC Bioinform., 2011)

Extending Semantic Provenance into the Web of Data. - Jun Zhao 003; Satya Sanket Sahoo; Paolo Missier; Amit P. Sheth; Carole A. Goble (IEEE Internet Comput., 2011)

EpiDEA: Extracting Structured Epilepsy and Seizure Information from Patient Discharge Summaries for Cohort Identification. - Licong Cui; Samden D. Lhatoo; Guo-Qiang Zhang 001; Satya Sanket Sahoo; Alireza Bozorgi (AMIA, 2012)

OPIC: Ontology-driven Patient Information Capturing System for Epilepsy. - Satya Sanket Sahoo; Meng Zhao; Lingyun Luo; Alireza Bozorgi; Deepak K. Gupta; Samden D. Lhatoo; Guo-Qiang Zhang 001 (AMIA, 2012)

A Distributed Semantic Web Approach for Cohort Identification. - Joseph Teagno; Richard C. Kiefer; Jyotishman Pathak; G. Q. Zhang; Satya Sanket Sahoo (AMIA, 2012)

An Analysis of Multi-type Relational Interactions in FMA Using Graph Motifs with Disjointness Constraints. - Guo-Qiang Zhang 001; Lingyun Luo; Chimezie Thomas-Ogbuji; Cliff A. Joslyn; José Leonardo Villaraza Mejino Jr.; Satya Sanket Sahoo (AMIA, 2012)

Role of semantic web in health informatics. - Satya Sanket Sahoo; Amit P. Sheth; Guo-Qiang Zhang 001 (IHI, 2012)

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. - Priti Parikh; Jie Zheng 001; Flora J. Logan-Klumpler; Christian J. Stoeckert Jr.; Christos Louis; Pantelis Topalis; Anna V. Protasio; Amit P. Sheth; Mark Carrington; Matthew Berriman; Satya Sanket Sahoo (J. Biomed. Semant., 2012)

A semantic proteomics dashboard (SemPoD) for data management in translational research. - Catherine P. Jayapandian; Meng Zhao; Rob M. Ewing; Guo-Qiang Zhang 001; Satya Sanket Sahoo (BMC Syst. Biol., 2012)

Cloudwave: Distributed Processing of "Big Data" from Electrophysiological Recordings for Epilepsy Clinical Research Using Hadoop. - Catherine P. Jayapandian; Chien-Hung Chen; Alireza Bozorgi; Samden D. Lhatoo; Guo-Qiang Zhang 001; Satya Sanket Sahoo (AMIA, 2013)

From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data. - Amir H. Asiaee; Prashant Doshi; Todd Minning; Satya Sanket Sahoo; Priti Parikh; Amit P. Sheth; Rick L. Tarleton (DILS, 2013)

Querying Complex Federated Clinical Data Using Ontological Mapping and Subsumption Reasoning. - Licong Cui; Remo Mueller; Satya Sanket Sahoo; Guo-Qiang Zhang 001 (ICHI, 2013)

Electrophysiological Signal Analysis and Visualization using Cloudwave for Epilepsy Clinical Research. - Catherine P. Jayapandian; Chien-Hung Chen; Alireza Bozorgi; Samden D. Lhatoo; Guo-Qiang Zhang 001; Satya Sanket Sahoo (MedInfo, 2013)

MEDCIS: Multi-Modality Epilepsy Data Capture and Integration System. - Guo-Qiang Zhang 001; Licong Cui; Samden D. Lhatoo; Satya S. Sahoo (AMIA, 2014)

Domain Ontology As Conceptual Model for Big Data Management: Application in Biomedical Informatics. - Catherine P. Jayapandian; Chien-Hung Chen; Aman Dabir; Samden D. Lhatoo; Guo-Qiang Zhang 001; Satya Sanket Sahoo (ER, 2014)

Biomedical Big Data for Clinical Research and Patient Care: Role of Semantic Computing. - Satya Sanket Sahoo (ICSC, 2014)

Heart beats in the cloud: distributed analysis of electrophysiological 'Big Data' using cloud computing for epilepsy clinical research. - Satya Sanket Sahoo; Catherine P. Jayapandian; Gaurav Garg; Farhad Kaffashi; Stephanie Chung; Alireza Bozorgi; Chien-Hung Chen; Kenneth A. Loparo; Samden D. Lhatoo; Guo-Qiang Zhang 001 (J. Am. Medical Informatics Assoc., 2014)

Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care. - Satya Sanket Sahoo; Samden D. Lhatoo; Deepak K. Gupta; Licong Cui; Meng Zhao; Catherine P. Jayapandian; Alireza Bozorgi; Guo-Qiang Zhang 001 (J. Am. Medical Informatics Assoc., 2014)

Complex epilepsy phenotype extraction from narrative clinical discharge summaries. - Licong Cui; Satya Sanket Sahoo; Samden D. Lhatoo; Gaurav Garg; Prashant Rai; Alireza Bozorgi; Guo-Qiang Zhang 001 (J. Biomed. Informatics, 2014)

Insight: Semantic provenance and analysis platform for multi-center neurology healthcare research. - Priya Ramesh; Annan Wei; Elisabeth Welter; Yvan Bamps; Shelley Stoll; Ashley Bukach; Martha Sajatovic; Satya S. Sahoo (BIBM, 2015)

A scalable neuroinformatics data flow for electrophysiological signals using MapReduce. - Catherine P. Jayapandian; Annan Wei; Priya Ramesh; Bilal Zonjy; Samden D. Lhatoo; Kenneth A. Loparo; Guo-Qiang Zhang 001; Satya S. Sahoo (Frontiers Neuroinformatics, 2015)

Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description. - Satya S. Sahoo; Joshua Valdez; Michael Rueschman (AMIA, 2016)

Comparative Evaluation for Brain Structural Connectivity Approaches: Towards Integrative Neuroinformatics Tool for Epilepsy Clinical Research. - Sheng Yang; Curtis Tatsuoka; Kaushik Ghosh; Nuria Lacuey Lecumberri; Samden D. Lhatoo; Satya Sanket Sahoo (CRI, 2016)

An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper). - Joshua Valdez; Michael Rueschman; Matthew Kim; Susan Redline; Satya S. Sahoo (OTM Conferences, 2016)

NeuroPigPen: A Scalable Toolkit for Processing Electrophysiological Signal Data in Neuroscience Applications Using Apache Pig. - Satya S. Sahoo; Annan Wei; Joshua Valdez; Li Wang; Bilal Zonjy; Curtis Tatsuoka; Kenneth A. Loparo; Samden D. Lhatoo (Frontiers Neuroinformatics, 2016)

Managing information well: Toward an ontology-driven informatics platform for data sharing and secondary use in epilepsy self-management research centers. - Satya S. Sahoo; Guo-Qiang Zhang 001; Yvan Bamps; Robert Fraser; Shelley Stoll; Samden D. Lhatoo; Curtis Tatsuoka; Johnny Sams; Elisabeth Welter; Martha Sajatovic (Health Informatics J., 2016)

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research. - Satya S. Sahoo; Priya Ramesh; Elisabeth Welter; Ashley Bukach; Joshua Valdez; Curtis Tatsuoka; Yvan Bamps; Shelley Stoll; Barbara C. Jobst; Martha Sajatovic (Int. J. Medical Informatics, 2016)

Processing Neurology Clinical Data for Knowledge Discovery: Scalable Data Flows Using Distributed Computing. - Satya S. Sahoo; Annan Wei; Curtis Tatsuoka; Kaushik Ghosh; Samden D. Lhatoo (Machine Learning for Health Informatics, 2016)

A Flexible Computational Neuroinformatics Workflow for Computing Functional Networks in Epilepsy Neurological Disorder. - Arthur L. Gershon; Bilal Zonjy; Curtis Tatsuoka; Kaushik Ghosh; Satya S. Sahoo (AMIA, 2017)

ProvCaRe Semantic Provenance Knowledgebase: Evaluating Scientific Reproducibility of Research Studies. - Joshua Valdez; Matthew Kim; Michael Rueschman; Vimig Socrates; Satya S. Sahoo (AMIA, 2017)

An Extensible Ontology Modeling Approach Using Post Coordinated Expressions for Semantic Provenance in Biomedical Research. - Joshua Valdez; Michael Rueschman; Matthew Kim; Sara ArabYarmohammadi; Susan Redline; Satya S. Sahoo (OTM Conferences (2), 2017)

Classification of Provenance Triples for Scientific Reproducibility: A Comparative Evaluation of Deep Learning Models in the ProvCaRe Project. - Joshua Valdez; Matthew Kim; Michael Rueschman; Susan Redline; Satya S. Sahoo (IPAW, 2018)

Enhancing Multi-Center Patient Cohort Studies in the Managing Epilepsy Well (MEW) Network: Integrated Data Integration and Statistical Analysis. - Xinting Hong; Chang Liu; Hasina Momotaz; Kristin Cassidy; Martha Sajatovic; Satya S. Sahoo (AMIA, 2019)

Semantic Provenance Graph for Reproducibility of Biomedical Research Studies: Generating and Analyzing Graph Structures from Published Literature. - Satya S. Sahoo; Joshua Valdez; Michael Rueschman; Matthew Kim (MedInfo, 2019)

Computation of Brain Functional Connectivity Network Measures in Epilepsy: A Web-Based Platform for EEG Signal Data Processing and Analysis. - Vimig Socrates; Arthur L. Gershon; Satya S. Sahoo (MedInfo, 2019)

ProvCaRe: Characterizing scientific reproducibility of biomedical research studies using semantic provenance metadata. - Satya S. Sahoo; Joshua Valdez; Matthew Kim; Michael Rueschman; Susan Redline (Int. J. Medical Informatics, 2019)

NeuroIntegrative Connectivity (NIC) Informatics Tool for Brain Functional Connectivity Network Analysis in Cohort Studies. - Satya S. Sahoo; Arthur L. Gershon; Nassim Shafiabadi; Kaushik Ghosh; Curtis Tatsuoka; Samden D. Lhatoo; Guadalupe Fernandez-BacaVaca (AMIA, 2020)

Parkinson and movement disorders ontology for clinically-oriented and clinicians-driven data mining of multi-center cohorts in Parkinson's disease. - Deepak K. Gupta; Massimo Marano; Raj Aurora; James Boyd; Satya S. Sahoo (AMIA, 2021)

Epilepsy-Connect: An Integrated Knowledgebase for Characterizing Alterations in Consciousness State of Pharmacoresistant Epilepsy Patients. - Katrina Prantzalos; Jianzhe Zhang; Nassim Shafiabadi; Guadalupe Fernandez-BacaVaca; Satya S. Sahoo (AMIA, 2021)

Characterizing Brain Network Dynamics using Persistent Homology in Patients with Refractory Epilepsy. - Jianzhe Zhang; Roland Bauman; Nassim Shafiabadi; Nick Gurski; Guadalupe Fernandez-BacaVaca; Satya S. Sahoo (AMIA, 2021)

Enabling Scientific Reproducibility through FAIR Data Management: An ontology-driven deep learning approach in the NeuroBridge Project. - Xiaochen Wang; Yue Wang 035; José Luis Ambite; Abhishek M. Appaji; Howard Lander; Stephen Moore; Arcot Rajasekar; Jessica A. Turner; Matthew D. Turner; Lei Wang 032; Satya S. Sahoo (AMIA, 2022)

NeuroBridge ontology: computable provenance metadata to give the long tail of neuroimaging data a FAIR chance for secondary use. - Satya S. Sahoo; Matthew D. Turner; Lei Wang 032; José Luis Ambite; Abhishek M. Appaji; Arcot Rajasekar; Howard Lander; Yue Wang 035; Jessica A. Turner (Frontiers Neuroinformatics, 2023)

NeuroBridge: a prototype platform for discovery of the long-tail neuroimaging data. - Lei Wang 032; José Luis Ambite; Abhishek M. Appaji; Janine Bijsterbosch; Jérôme Dockès; Rick Herrick; Alexander Kogan; Howard Lander; Daniel S. Marcus; Stephen Moore; Jean-Baptiste Poline; Arcot Rajasekar; et al. (Frontiers Neuroinformatics, 2023)

A 360° View for Large Language Models: Early Detection of Amblyopia in Children Using Multi-view Eye Movement Recordings. - Dipak P. Upadhyaya; Aasef G. Shaikh; Gokce Busra Cakir; Katrina Prantzalos; Pedram Golnari; Fatema F. Ghasia; Satya S. Sahoo (AIME (2), 2024)

Machine learning interpretability methods to characterize the importance of hematologic biomarkers in prognosticating patients with suspected infection. - Dipak P. Upadhyaya; Yasir Tarabichi; Katrina Prantzalos; Salman Ayub; David C. Kaelber; Satya S. Sahoo (Comput. Biol. Medicine, 2024)

Large language models for biomedicine: foundations, opportunities, challenges, and best practices. - Satya S. Sahoo; Joseph M. Plasek; Hua Xu 001; Özlem Uzuner; Trevor Cohen; Meliha Yetisgen; Hongfang Liu; Stéphane M. Meystre; Yanshan Wang (J. Am. Medical Informatics Assoc., 2024)

Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain. - Subhashini Sivagnanam; Steven Yeu; Kai Lin; S. Sakai; F. Garzon; Kenneth Yoshimoto; Katrina Prantzalos; Dipak P. Upadhyaya; Amitava Majumdar 001; Satya S. Sahoo; William W. Lytton (Database J. Biol. Databases Curation, 2024)

Large language models can extract metadata for annotation of human neuroimaging publications. - Matthew D. Turner; Abhishek M. Appaji; Nibras Ar Rakib; Pedram Golnari; Arcot K. Rajasekar; Anitha Rathnam K. V; Satya S. Sahoo; Yue Wang 035; Lei Wang 032; Jessica A. Turner (Frontiers Neuroinformatics, 2025)

Ontology accelerates few-shot learning capability of large language model: A study in extraction of drug efficacy in a rare pediatric epilepsy. - Pedram Golnari; Katrina Prantzalos; Veronica Hood; Mary Anne Meskis; Lori L. Isom; Karen Wilcox; Jack M. Parent; Dennis Lal; Samden D. Lhatoo; Howard P. Goodkin; Elaine C. Wirrell; Kelly G. Knupp; et al. (Int. J. Medical Informatics, 2025)