Protein Complexes in Bacteria. - J. Harry Caufield; Marco Abreu; Christopher Wimble; Peter Uetz (PLoS Comput. Biol., 2015)

Bacterial protein meta-interactomes predict cross-species interactions and protein function. - J. Harry Caufield; Christopher Wimble; Shary Semarjit; Stefan Wuchty; Peter Uetz (BMC Bioinform., 2017)

Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inference. - Yichao Zhou 001; Yu Yan; Rujun Han; J. Harry Caufield; Kai-Wei Chang; Yizhou Sun; Peipei Ping; Wei Wang 010 (AAAI, 2021)

CREATe: Clinical Report Extraction and Annotation Technology. - Yichao Zhou 001; Wei-Ting Chen; Bowen Zhang 002; David Lee; J. Harry Caufield; Kai-Wei Chang; Yizhou Sun; Peipei Ping; Wei Wang 010 (ICDE, 2021)

Clinical Named Entity Recognition using Contextualized Token Representations. - Yichao Zhou 001; Chelsea Ju; J. Harry Caufield; Kevin Shih; Calvin Yu-Chian Chen; Yizhou Sun; Kai-Wei Chang; Peipei Ping; Wei Wang 010 (CoRR, 2021)

KG-Hub - Building and Exchanging Biological Knowledge Graphs. - J. Harry Caufield; Tim E. Putman; Kevin Schaper; Deepak R. Unni; Harshad Hegde; Tiffany J. Callahan; Luca Cappelletti; Sierra A. T. Moxon; Vida Ravanmehr; Seth Carbon; Lauren E. Chan; Katherina Cortes; et al. (CoRR, 2023)

Gene Set Summarization using Large Language Models. - Marcin P. Joachimiak; J. Harry Caufield; Nomi L. Harris; Hyeongsik Kim 001; Christopher J. Mungall (CoRR, 2023)

MapperGPT: Large Language Models for Linking and Mapping Entities. - Nicolas Matentzoglu; J. Harry Caufield; Harshad B. Hegde; Justin T. Reese; Sierra A. T. Moxon; Hyeongsik Kim 001; Nomi L. Harris; Melissa A. Haendel; Christopher J. Mungall (CoRR, 2023)

Initial achievements in relation extraction from RNA-focused scientific papers. - Emanuele Cavalleri; Mauricio Soto Gomez; Ali Pashaeibarough; Dario Malchiodi; J. Harry Caufield; Justin T. Reese; Christopher J. Mungall; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (SEBD, 2024)

SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning. - Emanuele Cavalleri; Mauricio Soto Gomez; Ali Pashaeibarough; Dario Malchiodi; J. Harry Caufield; Justin T. Reese; Chris Mungall; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (VLDB Workshops, 2024)

The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies. - Marcin P. Joachimiak; Mark A. Miller; J. Harry Caufield; Ryan Ly; Nomi L. Harris; Andrew J. Tritt; Christopher J. Mungall; Kristofer E. Bouchard (Appl. Ontology, 2024)

CurateGPT: A flexible language-model assisted biocuration tool. - J. Harry Caufield; Carlo Kroll; Shawn T. O'Neil; Justin T. Reese; Marcin P. Joachimiak; Harshad Hegde; Nomi L. Harris; Madan Krishnamurthy; James A. McLaughlin; Damian Smedley; Melissa A. Haendel; Peter N. Robinson; et al. (CoRR, 2024)

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. - J. Harry Caufield; Harshad Hegde; Vincent Emonet; Nomi L. Harris; Marcin P. Joachimiak; Nicolas Matentzoglu; Hyeongsik Kim 001; Sierra A. T. Moxon; Justin T. Reese; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (Bioinform., 2024)

An evaluation of GPT models for phenotype concept recognition. - Tudor Groza; J. Harry Caufield; Dylan Gration; Gareth Baynam; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall; Justin T. Reese (BMC Medical Informatics Decis. Mak., 2024)

A change language for ontologies and knowledge graphs. - Harshad Hegde; Jennifer Vendetti; Damien Goutte-Gattat; J. Harry Caufield; John B. Graybeal; Nomi L. Harris; Naouel Karam; Christian Kindermann; Nicolas Matentzoglu; James A. Overton; Mark A. Musen; Christopher J. Mungall (Database J. Biol. Databases Curation, 2025)