Author

Ash Holland

Wellcome Sanger InstituteORCID 0000-0002-4606-7740Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:scRNA-seq· 2 Approach:transformer / foundation model· 2 Research Focus:cell type annotation· 1 Research Focus:perturbation response prediction· 1

Frequent Co-Authors

Amirhossein VahidiiD· 2 shared Anindita RoyiD· 2 shared April Rose FosteriD· 2 shared Berthold GöttgensiD· 2 shared Daniela Basurto-LozadaiD· 2 shared Daniyal J. JafreeiD· 2 shared David HorsfalliD· 2 shared Deena IskanderiD· 2 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Amirhossein VahidiORCID

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2 papers

Recent·Most cited

Self-supervised learning for a gene program-centric view of cell states

Marie Moullet, Tomoya Isobe, Amirhossein Vahidi, Carlo Leonardi, Licyel Paulas-Condori, Christopher J. Soelistyo, Lloyd Steele, Kevin Chi Hao Ly, Mariana Quiroga Londoño, Nicole Mende, Emily Stephenson, Deena Iskander, Simone Webb, Issac Goh, M. S. Vijayabaskar, , Mohammad Lotfollahi

Tripso, a self-supervised transformer model, identifies gene program-specific embeddings and discovers novel gene programs, revealing biological insights in hematopoietic development and disease.

bioRxiv · Mar 26, 2026 · PreprintBioinformatics

Predicting how perturbations reshape cellular trajectories with PerturbGen

Kevin Chi Hao Ly, Adib Miraki Feriz, Tomoya Isobe, Amirhossein Vahidi, Delshad Vaghari, Anthony Rostron, Mariana Quiroga Londoño, Nicole Mende, M. S. Vijayabaskar, Marie Moullet, April Rose Foster, Emily J Graves, Fereshteh Torabi, Chloe Admane, David Horsfall, , Mohammad Lotfollahi

PerturbGen predicts how genetic perturbations affect cellular trajectories across time in human datasets, showing effects on immune responses, hematopoiesis, and skin development.

bioRxiv · Mar 5, 2026 · PreprintBioinformatics