Author

Nima Alidoust

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:perturbation response prediction· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Assay:scRNA-seq· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

Daniele MericoiD· 3 shared Hani GoodarziiD· 3 shared Johnny X. YuiD· 3 shared Umair KhaniD· 3 shared Valentine SvenssoniD· 3 shared Airol A. Ubas· 2 shared Matthew G. JonesiD· 2 shared Nicole Thomas· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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3 shared papersGenomics

Daniele MericoORCID

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Author profile →

3 papers

Recent·Most cited

Back to basics: Observed statistics are sufficient to predict drug responses

Valentine Svensson, Umair Khan, Hamed Heydari, Airol A. Ubas, Nicole Thomas, Daniele Merico, Hani Goodarzi, Johnny X. Yu, Nima Alidoust, Shreshth Gandhi

The paper introduces Rhaister, a perturbation-response predictor that uses summary statistics to predict drug responses, outperforming virtual-cell models in speed and accuracy.

bioRxiv · Jun 12, 2026 · PreprintGenomics

Tahoe-x1: Scaling Perturbation-Trained Single-CellFoundation Models to 3 Billion Parameters

Shreshth Gandhi, Farnoosh Javadi, Valentine Svensson, Umair Khan, Matthew G. Jones, John Yu, Daniele Merico, Hani Goodarzi, Nima Alidoust

The paper introduces Tahoe-x1, a large-scale perturbation-trained single-cell foundation model with 3 billion parameters, achieving state-of-the-art performance in cancer-related tasks.

bioRxiv · Oct 23, 2025 · PreprintSystems Biology

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

Jesse M. Zhang, Airol A. Ubas, Richard de Borja, Valentine Svensson, Nicole Thomas, Neha Thakar, Ian K. Lai, Aidan F. Winters, Umair Khan, Matthew G. Jones, John D. Thompson, Vuong Tran, Joseph Pangallo, Efthymia Papalexi, Ajay Sapre, , Johnny X. Yu

A 100-million-cell atlas: 50 cancer lines pooled as spheroid villages, treated with 379 drugs at several doses, profiled by combinatorial-barcoding scRNA-seq and embedded with a 10-dimensional scVI model.

bioRxiv · Feb 20, 2025 · PreprintGenomics✦ In-depth digest