Use of a Structured Knowledge Base Enhances Metadata Curation by Large Language Models - Sowmya S. Sundaram; Benjamin Solomon; Avani Khatri; Anisha Laumas; Purvesh Khatri; Mark A. Musen (CoRR, 2024)

Development of Machine Learning Classifiers for Blood-based Diagnosis and Prognosis of Suspected Acute Infections and Sepsis - Ljubomir J. Buturovic; Michael B. Mayhew; Roland Lüthy; Kirindi Choi; Uros Midic; Nandita Damaraju; Yehudit Hasin-Brumshtein; Amitesh Pratap; Rhys M. Adams; João F. Henriques; Ambika Srinath; Paul Fleming; et al. (CoRR, 2024)

Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology - Laurynas Kalesinskas; Sanjana Gupta; Purvesh Khatri (PLoS Comput. Biol., 2022)

Computational drug repositioning of atorvastatin for ulcerative colitis - Lawrence Bai; Madeleine K. D. Scott; Ethan Steinberg; Laurynas Kalesinskas; Aida Habtezion; Nigam H. Shah; Purvesh Khatri (J. Am. Medical Informatics Assoc., 2021)

SIMON: Open-Source Knowledge Discovery Platform - Adriana Tomic; Ivan Tomic; Levi Waldron; Ludwig Geistlinger; Max Kuhn; Rachel L. Spreng; Lindsay C. Dahora; Kelly E. Seaton; Georgia D. Tomaras; Jennifer Hill; Niharika A. Duggal; Ross D. Pollock; et al. (Patterns, 2021)

Formulating a gene signature for diagnosis of autoimmune and infectious diseases - Riya Gupta; Aditya M. Rao; Lara Murphy Jones; Purvesh Khatri (BCB '21: 12th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Gainesville, Florida, USA, August 1-4, 2021, 2021)

A multi-scale integrated analysis identifies KRT8 as a pan-cancer early biomarker - Madeleine Scott; Maneesha Limaye; Steven Schaffert; Robert West; Michael G. Ozawa; Pauline Chu; Viswam S. Nair; Albert C. Koong; Purvesh Khatri (Biocomputing 2021: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2021, 2021)

Chemical Space Mimicry for Drug Discovery - William Yuan; Dadi Jiang; Dhanya K. Nambiar; Lydia P. Liew; Michael P. Hay; Joshua Bloomstein; Peter Lu; Brandon Turner; Quynh-Thu Le; Robert Tibshirani; Purvesh Khatri; Mark G. Moloney; et al. (J. Chem. Inf. Model., 2017)

Gene annotation bias impedes biomedical research - Winston A. Haynes; Aurelie Tomczak; Purvesh Khatri (AMIA 2017, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 4-8, 2017, 2017)

Complementing single-cell RNA-seq using bulk transcriptional profiles - Winston A. Haynes; Francesco Vallania; Purvesh Khatri (2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, MO, USA, November 13-16, 2017, 2017)

Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility - Winston A. Haynes; Francesco Vallania; Charles Liu; Erika Bongen; Aurelie Tomczak; Marta Andres-Terrè; Shane Lofgren; Andrew Tam; Cole A. Deisseroth; Matthew D. Li; Timothy E. Sweeney; Purvesh Khatri (Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2017, 2017)

Meta-Analysis of Continuous Phenotypes Identifies a Gene Signature that Correlates with COPD Disease Status - Madeleine Scott; Francesco Vallania; Purvesh Khatri (Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2017, 2017)

The center for expanded data annotation and retrieval - Mark A. Musen; Carol A. Bean; Kei-Hoi Cheung; Michel Dumontier; Kim A. Durante; Olivier Gevaert; Alejandra N. González-Beltrán; Purvesh Khatri; Steven H. Kleinstein; Martin J. O'Connor; Yannick Pouliot; Philippe Rocca-Serra; et al. (J. Am. Medical Informatics Assoc., 2015)

Multiplex Meta-Analysis of Medulloblastoma Expression Studies with External Controls - Alexander A. Morgan; Matthew D. Li; Achal S. Achrol; Purvesh Khatri; Samuel H. Cheshier (Biocomputing 2014: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2014, 2014)

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges - Purvesh Khatri; Marina Sirota; Atul J. Butte (PLoS Comput. Biol., 2012)

Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants - Alexander A. Morgan; Purvesh Khatri; Richard Hayden Jones; Minnie M. Sarwal; Atul J. Butte (BMC Bioinform., 2010)

Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis - Bogdan Done; Purvesh Khatri; Arina Done; Sorin Draghici (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

A novel signaling pathway impact analysis - Adi L. Tarca; Sorin Draghici; Purvesh Khatri; Sonia S. Hassan; Pooja Mittal; Jung-Sun Kim; Chong Jai Kim; Juan Pedro Kusanovic; Roberto Romero (Bioinform., 2009)

Identifying uncertainty regions in Support Vector Machines using geometric margin and convex hulls - Calin Voichita; Purvesh Khatri; Sorin Draghici (Proceedings of the International Joint Conference on Neural Networks, IJCNN 2008, part of the IEEE World Congress on Computational Intelligence, WCCI 2008, Hong Kong, China, June 1-6, 2008, 2008)

Onto-Tools: new additions and improvements in 2006 - Purvesh Khatri; Calin Voichita; Khalid Kattan; Nadeem Ansari; Avani Khatri; Constantin Georgescu; Adi L. Tarca; Sorin Draghici (Nucleic Acids Res., 2007)

A System Biology Approach for the Steady-State Analysis of Gene Signaling Networks - Purvesh Khatri; Sorin Draghici; Adi L. Tarca; Sonia S. Hassan; Roberto Romero (Progress in Pattern Recognition, Image Analysis and Applications, 12th Iberoamericann Congress on Pattern Recognition, CIARP 2007, Valparaiso, Chile, November 13-16, 2007, Proceedings, 2007)

Semantic Analysis of Genome Annotations using Weighting Schemes - Bogdan Done; Purvesh Khatri; Arina Done; Sorin Draghici (Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2007, Honolulu, Hawaii, USA, April 1-5, 2007, Part of the IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2007), 2007)

Babel's tower revisited: a universal resource for cross-referencing across annotation databases - Sorin Draghici; Sivakumar Sellamuthu; Purvesh Khatri (Bioinform., 2006)

New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate - Purvesh Khatri; Valmik Desai; Adi L. Tarca; Sivakumar Sellamuthu; Derek E. Wildman; Roberto Romero; Sorin Draghici (Nucleic Acids Res., 2006)

A semantic analysis of the annotations of the human genome - Purvesh Khatri; Bogdan Done; Archana Rao; Arina Done; Sorin Draghici (Bioinform., 2005)

Ontological analysis of gene expression data: current tools, limitations, and open problems - Purvesh Khatri; Sorin Draghici (Bioinform., 2005)

Recent additions and improvements to the Onto-Tools - Purvesh Khatri; Sivakumar Sellamuthu; Pooja Malhotra; Kashyap Amin; Arina Done; Sorin Draghici (Nucleic Acids Res., 2005)

A Novel Bioinformatics Technique for Predicting Condition-specific Transcription Factor Binding Sites - Valmik Desai; Purvesh Khatri; Arina Done; Aviva Friedman; Michael A. Tainsky; Sorin Draghici (Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, Embassy Suites Hotel La Jolla, La Jolla, CA, USA, November 14 & 15, 2005, 2005)

Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax Threats - Sorin Draghici; Purvesh Khatri; Yanhong Liu; Kitty J. Chase; Elizabeth A. Bode; David A. Kulesh; Leonard P. Wasieloski; David A. Norwood; Jaques Reifman (Biocomputing 2005, Proceedings of the Pacific Symposium, Hawaii, USA, 4-8 January 2005, 2005)

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments - Purvesh Khatri; Pratik Bhavsar; Gagandeep Bawa; Sorin Draghici (Nucleic Acids Res., 2004)

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate - Sorin Draghici; Purvesh Khatri; Pratik Bhavsar; Abhik Shah; Stephen A. Krawetz; Michael A. Tainsky (Nucleic Acids Res., 2003)