Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning. - Felix Stiehler; Marvin Steinborn; Stephan Scholz; Daniela Dey; Andreas P. M. Weber; Alisandra K. Denton (Bioinform., 2021)

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)

A Cross Modal Knowledge Distillation & Data Augmentation Recipe for Improving Transcriptomics Representations through Morphological Features. - Ihab Bendidi; Yassir El Mesbahi; Alisandra K. Denton; Karush Suri; Kian Kenyon-Dean; Auguste Genovesio; Emmanuel Noutahi (CoRR, 2025)