FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. - John A. Bachman; Benjamin M. Gyori; Peter K. Sorger (BMC Bioinform., 2018)

Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models. - Rebecca Sharp; Adarsh Pyarelal; Benjamin M. Gyori; Keith Alcock; Egoitz Laparra; Marco Antonio Valenzuela-Escárcega; Ajay Nagesh; Vikas Yadav; John A. Bachman; Zheng Tang; Heather C. Lent; Fan Luo; et al. (NAACL-HLT (Demonstrations), 2019)

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. - Charles Tapley Hoyt; Daniel Domingo-Fernández; Rana Aldisi; Lingling Xu; Kristian Kolpeja; Sandra Spalek; Esther Wollert; John A. Bachman; Benjamin M. Gyori; Patrick Greene 001; Martin Hofmann-Apitius (Database J. Biol. Databases Curation, 2019)

INDRA-IPM: interactive pathway modeling using natural language with automated assembly. - Petar V. Todorov; Benjamin M. Gyori; John A. Bachman; Peter K. Sorger (Bioinform., 2019)

Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. - Albert Steppi; Benjamin M. Gyori; John A. Bachman (J. Open Source Softw., 2020)

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs. - Helena Balabin; Charles Tapley Hoyt; Benjamin M. Gyori; John A. Bachman; Alpha Tom Kodamullil; Martin Hofmann-Apitius; Daniel Domingo-Fernández (SWAT4HCLS, 2022)

STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. - Helena Balabin; Charles Tapley Hoyt; Colin Birkenbihl; Benjamin M. Gyori; John A. Bachman; Alpha Tom Kodamullil; Paul G. Plöger; Martin Hofmann-Apitius; Daniel Domingo-Fernández (Bioinform., 2022)