Automated Discovery of Pairwise Interactions from Unstructured Data. - Zuheng Xu; Moksh Jain; Ali Denton; Shawn Whitfield; Aniket Didolkar; Berton Earnshaw; Jason S. Hartford (CoRR, 2024)

Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all. - Ihab Bendidi; Shawn Whitfield; Kian Kenyon-Dean; Hanene Ben Yedder; Yassir El Mesbahi; Emmanuel Noutahi; Alisandra K. Denton (CoRR, 2024)

Virtual Cells: Predict, Explain, Discover. - Emmanuel Noutahi; Jason S. Hartford; Prudencio Tossou; Shawn Whitfield; Alisandra K. Denton; Cas Wognum; Kristina Ulicna; Michael Craig; Jonathan Hsu; Michael Cuccarese; Emmanuel Bengio; Dominique Beaini; et al. (CoRR, 2025)

TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation Prediction. - Frederik Wenkel; Wilson Tu; Cassandra Masschelein; Hamed Shirzad; Cian Eastwood; Shawn Whitfield; Ihab Bendidi; Craig Russell; Liam Hodgson; Yassir El Mesbahi; Jiarui Ding; Marta M. Fay; et al. (CoRR, 2025)