Selected Publications

Rajagopalan A, Nguyen TA, Guare LA, Garao Rico AL, Venkatesh R, Caruth L, Regeneron Genetics Center, Penn Medicine BioBank, Verma A, Ritchie MD, Hall MA, Setia-Verma S, & Romano JD: DRIVE-KG: Enhancing variant-phenotype association discovery in understudied complex diseases using heterogeneous knowledge graphs. 2026 Pacific Symposium on Biocomputing 2026, Jan 2026 Notes: (Accepted; In-press. Drs. Romano and Setia-Verma are co-corresponding/co-senior authors on this publication.).

Kumar R, Romano JD, & Ritchie MD: Learnable Protein Representations in Computational Biology for Predicting Drug-Target Affinity. Journal of Cheminformatics 2026 Notes: (accepted; in press).

Kumar R, Romano JD, & Ritchie MD: Network-based analyses of multiomics data in biomedicine. BioData Mining 18: 37, May 2025 Notes: (accepted; in-press).

Romano JD: Ista: An Ontology-Driven Toolkit for Biomedical Knowledge Base Assembly. Studies in Health Technology and Informatics May 2025 Notes: Accepted; in-press.

Donnelly HK, Ashcraft LE, Romano JD, Daniels S, and Mowery D: Using Topic Modeling to Understand Implementation Science in the Biomedical Literature. AMIA 2025 Informatics Summit March 2025.

Nguyen TA & Romano JD: Uterine Leiomyoma Prediction using Geometric Deep Learning and Freely Available Electronic Health Record Data. AMIA 2025 Informatics Summit March 2025.

Pan IT, & Romano JD: Enhancing Molecular Representation Learning through the Combination of 3D and 2D Graph Machine Learning. The 39th Annual AAAI Conference on Artificial Intelligence 39, February 2025 Notes: (accepted; in press).

Haredasht FN, Kim D, Romano JD, Tison G, Daneshjou R, & Chen JH: Session Introduction: AI and Machine Learning in Clinical Medicine: Generative and Interactive Systems at the Human-Machine Interface. Pacific Symposium on Biocomputing 30: 33-39, Jan 2025.

Kumar R, Romano JD, & Ritchie MD: CASTER-DTA: Equivariant Graph Neural Networks for Predicting Drug-Target Affinity. Briefings in Bioinformatics 2025 Notes: (Accepted; in-press).

Aldeia GSI, Romano JD, de Franca FO, Herman DS, & La Cava WG: Towards symbolic regression for interpretable clinical decision scores. Philosophical Transactions A 2025 Notes: (Accepted: In-press).