From clusters to queries: exploiting uncertainty in the modularity landscape of complex networks. - James P. Gilbert; Jamie Twycross (CoRR, 2018)

Gsmodutils: a python based framework for test-driven genome scale metabolic model development. - James P. Gilbert; Nicole Pearcy; Rupert Norman; Thomas Millat; Klaus Winzer; John R. King; Charlie Hodgman; Nigel P. Minton; Jamie Twycross (Bioinform., 2019)

Cell Model Passports - a hub for clinical, genetic and functional datasets of preclinical cancer models. - Dieudonne van der Meer; Syd Barthorpe; Wanjuan Yang; Howard Lightfoot; Caitlin Hall; James P. Gilbert; Hayley E. Francies; Mathew Garnett (Nucleic Acids Res., 2019)

A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications. - Nicole Pearcy; Marco Garavaglia; Thomas Millat; James P. Gilbert; Yoseb Song; Hassan Hartman; Craig Woods; Claudio Tomi-Andrino; Rajesh Reddy Bommareddy; Byung-Kwan Cho; David A. Fell; Mark Poolman; et al. (PLoS Comput. Biol., 2022)

Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research. - Martijn J. Schuemie; Jenna Reps; Adam Black; Frank J. DeFalco; Lee Evans; Egill A. Fridgeirsson; James P. Gilbert; Chris Knoll; Martin Lavallee; Gowtham A. Rao; Peter R. Rijnbeek; Katy Sadowski; et al. (MedInfo, 2023)

Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study. - Anna Ostropolets; Yasser Albogami; Mitchell Conover; Juan M. Banda; William A. Baumgartner Jr.; Clair Blacketer; Priyamvada Desai; Scott L. DuVall; Stephen P. Fortin; James P. Gilbert; Asieh Golozar; Joshua Ide; et al. (J. Am. Medical Informatics Assoc., 2023)