Tag: Perturb-seq
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A Genome-Scale CRISPRi Atlas of Human iPSCs Is a Data Resource, Not a Model: What It Adds for Cell Foundation Models (A Reading of the Journal Abstract)
Analysis based on information available as of 2026-10-23. 30-second summary What: Nourreddine, Doctor, Dailamy and colleagues (22 authors; corresponding author Prashant Mali) published in Nature Biotechnology (online July 2026) a CRISPR interference (CRISPRi) perturbation atlas in the human induced pluripotent stem cell (iPSC) line KOLF2.1J. The abstract reports transcriptional phenotypes for 11,692 perturbed genes across…
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A Preprint Benchmark of Six Single-Cell and Spatial Transcriptomics Foundation Models Finds No Overall Winner, on Curated Datasets and Without a Reported Simple-Baseline Comparison
Analysis based on information available as of 2026-08-02. 30-second summary What: A preprint (arXiv:2607.17227, submitted 2026-07-19, q-bio.GN) evaluates six single-cell and spatial transcriptomics foundation models (FMs) under one harmonised framework: Nicheformer, CellPLM, scGPT-spatial, GenePT, scELMo and Novae. Tasks were clustering, supervised annotation, marker-gene concordance and perturbation prediction, across scRNA-seq, spatial transcriptomics and Perturb-seq data. The…
