Research
My work spans generative molecular design, virtual cell modeling, and agentic systems for scientific discovery. For a complete list of publications, see my Google Scholar profile.
Projects
AI models that predict and explain how cells respond to chemical and genetic perturbations, to accelerate the discovery of new therapies. This is the team I currently lead at Valence Labs.
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An LLM-orchestrated workflow engine for drug discovery and one of the earliest agentic AI systems in the space. LOWE composes ML models, lab automation, and proprietary data to help researchers formulate, test, and prioritize hypotheses at scale.
A molecular representation framework that enables a single generative model to handle all major molecular design tasks: de novo generation, scaffold decoration, and linker design.
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An open-source ecosystem of Python packages for molecular processing, including datamol (molecular manipulation), molfeat (molecular featurization), and safe (SAFE molecular design).
Selected Publications
TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation PredictionWenkel F., ..., Noutahi E., Denton A. K.
Nature Biotechnology, 2025
SeedER: Seed-and-Expand Retrieval from Knowledge GraphsShirzad H., Wenkel F., Beaini D., Sutherland D. J., Noutahi E.
arXiv, 2026
Unpaired Multimodal Learning for Biological DatasetsJi Z., Eastwood C., Goldenberg A., Liang P. P., Hartford J., Krishnan R. G., Noutahi E.
MIDL, 2026
- A Cross Modal Knowledge Distillation & Data Augmentation Recipe for Improving Transcriptomics Representations through Morphological Features
Bendidi I., El Mesbahi Y., Denton A. K., Suri K., Kenyon-Dean K., Genovesio A., Noutahi E.
ICML, 2025
- Benchmarking Transcriptomics Foundation Models for Perturbation Analysis: One PCA Still Rules Them All
Bendidi I., Whitfield S., Kenyon-Dean K., Ben Yedder H., El Mesbahi Y., Noutahi E., Denton A. K.
NeurIPS AIDrugX Workshop, 2024
Gotta be SAFE: A New Framework for Molecular DesignNoutahi E., Gabellini C., Craig M., Lim J.S., Tossou P.
Digital Discovery, 2024
Real-World Molecular Out-Of-Distribution: Specification and InvestigationTossou P., Wognum C., Craig M., Mary H., Noutahi E.
J. Chem. Inf. Model., 2023
Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement LearningHorwood J., Noutahi E.
ACS Omega, 2020
Rapid Genetic Code Evolution in Green Algal Mitochondrial GenomesNoutahi E., Calderon V., Blanchette M., El-Mabrouk N., Lang B.F.
Molecular Biology and Evolution, 2019
Efficient Gene Tree Correction Guided by Genome EvolutionNoutahi E., Semeria M., Lafond M., et al.
PLoS ONE, 2016