Pathway knowledge base: An integrated pathway resource using BioPAX. - Nikesh Kotecha; Kyle Bruck; William Lu; Nigam Shah (Appl. Ontology, 2008)

NetworkPainter: dynamic intracellular pathway animation in Cytobank. - Jonathan R. Karr; Harendra Guturu; Edward Y. Chen; Stuart L. Blair; Jonathan M. Irish; Nikesh Kotecha; Markus W. Covert (BMC Bioinform., 2015)

Informatics Architecture for the Future of Cancer Immunotherapy Research. - Theresa L. Walunas; Abel N. Kho; Nikesh Kotecha; Nike Beaubier (AMIA, 2019)

Evaluation of GPT-3.5 and GPT-4 for supporting real-world information needs in healthcare delivery. - Debadutta Dash; Rahul Thapa; Juan M. Banda; Akshay Swaminathan; Morgan Cheatham; Mehr Kashyap; Nikesh Kotecha; Jonathan H. Chen; Saurabh Gombar; Lance Downing; Rachel Pedreira; Ethan Goh; et al. (CoRR, 2023)

DEPLOYR: a technical framework for deploying custom real-time machine learning models into the electronic medical record. - Conor K. Corbin; Rob Maclay; Aakash Acharya; Sreedevi Mony; Soumya Punnathanam; Rahul Thapa; Nikesh Kotecha; Nigam H. Shah; Jonathan H. Chen (J. Am. Medical Informatics Assoc., 2023)

Standing on FURM ground - A framework for evaluating Fair, Useful, and Reliable AI Models in healthcare systems. - Alison Callahan; Duncan C. McElfresh; Juan M. Banda; Gabrielle Bunney; Danton Char; Jonathan H. Chen; Conor K. Corbin; Debadutta Dash; Norman L. Downing; Sneha S. Jain; Nikesh Kotecha; Jonathan Masterson; et al. (CoRR, 2024)

MedHELM: Holistic Evaluation of Large Language Models for Medical Tasks. - Suhana Bedi; Hejie Cui; Miguel Fuentes; Alyssa Unell; Michael Wornow; Juan M. Banda; Nikesh Kotecha; Timothy Keyes; Yifan Mai 001; Mert Oez; Hao Qiu; Shrey Jain; et al. (CoRR, 2025)