Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. - Manuel Lafond; Emmanuel Noutahi; Nadia El-Mabrouk (CPM, 2016)

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. - Emmanuel Noutahi; Virginie Calderon; Mathieu Blanchette; B. Franz Lang; Nadia El-Mabrouk (Bioinform., 2017)

Reconstructing the History of Syntenies Through Super-Reconciliation. - Mattéo Delabre; Nadia El-Mabrouk; Katharina T. Huber; Manuel Lafond; Vincent Moulton; Emmanuel Noutahi; Miguel Sautie Castellanos (RECOMB-CG, 2018)

GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution. - Emmanuel Noutahi; Nadia El-Mabrouk (BMC Genom., 2018)

Towards Interpretable Sparse Graph Representation Learning with Laplacian Pooling. - Emmanuel Noutahi; Dominique Beaini; Julien Horwood; Prudencio Tossou (CoRR, 2019)

Evolution through segmental duplications and losses: a Super-Reconciliation approach. - Mattéo Delabre; Nadia El-Mabrouk; Katharina T. Huber; Manuel Lafond; Vincent Moulton; Emmanuel Noutahi; Miguel Sautie Castellanos (Algorithms Mol. Biol., 2020)

Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learning. - Julien Horwood; Emmanuel Noutahi (CoRR, 2020)

Gotta be SAFE: A New Framework for Molecular Design. - Emmanuel Noutahi; Cristian Gabellini; Michael Craig; Jonathan S. C. Lim; Prudencio Tossou (CoRR, 2023)

Role of Structural and Conformational Diversity for Machine Learning Potentials. - Nikhil Shenoy; Prudencio Tossou; Emmanuel Noutahi; Hadrien Mary; Dominique Beaini; Jiarui Ding (CoRR, 2023)

Graph Classification Gaussian Processes via Hodgelet Spectral Features. - Mathieu Alain; So Takao; Xiaowen Dong 001; Bastian Rieck; Emmanuel Noutahi (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)

SAFE setup for generative molecular design. - Yassir El Mesbahi; Emmanuel Noutahi (CoRR, 2024)

Real-World Molecular Out-Of-Distribution: Specification and Investigation. - Prudencio Tossou; Cas Wognum; Michael Craig; Hadrien Mary; Emmanuel Noutahi (J. Chem. Inf. Model., 2024)

Graph and Simplicial Complex Prediction Gaussian Process via the Hodgelet Representations. - Mathieu Alain; So Takao; Xiaowen Dong 001; Bastian Rieck; Emmanuel Noutahi (CoRR, 2025)

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)

Conditional Chemical Language Models are Versatile Tools in Drug Discovery. - Lu Zhu; Emmanuel Noutahi (CoRR, 2025)