28 items, newest first.
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Metzner E, Guruvayurappan K, Southard KM, Ardy RC, Dey KK, Norman TM. · bioRxiv · 2026-10-12
Norman/Dey labs (MSKCC): CRISPRa Multiome Perturb-seq of 119 TFs + dual-guide Perturb-seq of 1,225 TF pairs in RPE-1; chromatin priming predicts emergent states; Mosaic (Transformer) predicts TF-pair interaction residuals (r=0.484) and nominated a validated triple-TF combination.
Sanaki Y, Shigenobu S, Niwa R. · bioRxiv · 2026-09-24
ISP3 platform: Geneformer-based sequential multi-gene in silico perturbation.
Yu et al. · bioRxiv · 2026-08-12
PerturbLDM: Tahoe-100M-pretrained latent diffusion for conditional sc response generation across drug/dose/cell-line.
Denvis O. · Research Square · 2026-07-22
Empirical comparison of virtual cell models: the baseline gap persists.
Mayfield JD. · bioRxiv · 2026-04-23
Proteome-calibrated mechanistic digital twin of the GBM astrocyte (bioRxiv 2026).
Vollenweider M, Bühlmann P. · bioRxiv · 2026-04-22
Signal, Bounds, and Baselines: principles for evaluating virtual cell perturbation models.
Cheng et al. · bioRxiv · 2026-04-14
VCHarness: autonomous AI coding agent that searches/refines perturbation-response model architectures for virtual cells.
Wang C et al. · bioRxiv · 2026-03-20
X-Cell (Xaira): 4.9B-param diffusion model, perturbation scaling laws.
Li et al. · bioRxiv · 2026-03-16
AetherCell unifies clinical RNA-seq and perturbation assays for generative response prediction and in vivo repurposing.
Chuai et al. · bioRxiv · 2026-03-05
AlphaCell: genome-wide virtual-cell world model with OT conditional flow matching for cross-context perturbation dynamics.
Swinderman JT et al. · bioRxiv · 2026-02-05
Probe-based scalable single-cell profiling for virtual-cell perturbation mapping.
Zhang Y, Su Y, Wefers Z, Su S, Li H, Li T, Wang C, Burgess J, Lozano A, Zhou L, Ding D, Nirschl J, Lundberg E, Yeung-Levy S. · bioRxiv · 2026-01-20
CellFluxV2: image generative foundation model for virtual cell modeling.
Kalfon J, Peyré G, Cantini L. · bioRxiv · 2025-12-15
scPRINT-2: next-gen cell foundation models and benchmarks.
Hasanaj E, Cole E, Mohammadi S, Addagudi S, Zhang X, Song L, Xing EP. · bioRxiv · 2025-06-28
Multimodal benchmarking of FM representations for perturbation response.
Adduri AK et al. · bioRxiv · 2025-06-27
State preprint (bioRxiv June 2025).
Recursion / Valence Labs · arXiv · 2025-05-20
Recursion/Valence perspective: virtual cells should predict, explain, discover via lab-in-the-loop.
Kint S et al. · bioRxiv · 2025-05-14
Spatial epigenomic niches underlie GBM cell-state plasticity.
Pearce JD, Simmonds SE, Mahmoudabadi G, Krishnan L, Palla G, Istrate A, Tarashansky A, Nelson B, Valenzuela O, Li D, Quake SR, Karaletsos T. · bioRxiv · 2025-04-29
TranscriptFormer (CZI): generative cross-species cell atlas, 112M cells, 12 species.
Rizvi SA et al. · bioRxiv · 2025-04-17
C2S-Scale (Yale/Google): scaling LLMs to 27B for single-cell analysis and virtual screening.
Khan SM et al. · bioRxiv · 2025-04-04
Spatial architecture of GBM from core to edge; niche-specific states.
Sun R, Qian L, Li Y, Cheng H, Xue Z, Zhang X, Tan L, Zhan Y, Hu W, Xiao Q, Liu Z, Zhang G, Weinan E, Zhou P, Wen H, Zhu Y, Guo T. · bioRxiv · 2025-02-10
Preprint of the perturbation-proteomics foundation model for virtual cells.
Wang C, Cui H, Zhang A, Xie R, Goodarzi H, Wang B. · bioRxiv · 2025-02-08
scGPT-spatial: continual pretraining for spatial transcriptomics.
Ho N, Ellington CN, Hou J, Addagudi S, Mo S, Tao T, Li D, Zhuang Y, Wang H, Cheng X, Song L, Xing EP. · bioRxiv · 2024-12-03
AIDO.Cell (GenBio AI): dense transcriptome-scale context single-cell models.
Wenteler A, Occhetta M, Branson N, Curean V, Huebner M, Dee W, Connell W, Chung SP, Hawkins-Hooker A, Ektefaie Y, Valdez Córdova CM, Gallagher-Syed A. · bioRxiv · 2024-10-03
PertEval-scFM: benchmarking scFMs for perturbation effect prediction.
Rosen Y, Roohani Y, Agrawal A, Samotorcan L, Tabula Sapiens Consortium, Quake SR, Quake SR, Leskovec J. · bioRxiv · 2023-11-29
Universal Cell Embeddings (UCE), cross-species zero-shot cell embedding (Leskovec/Quake).
Wen H, Tang W, Dai X, Ding J, Jin W, Xie Y, Tang J. · bioRxiv · 2023-10-05
CellPLM: cell language model beyond single cells (spatial context).
Levine D et al. · bioRxiv · 2023-09-14
Cell2Sentence: cells as text for LLMs.
Yang F, Wang W, Wang F, Fang Y, Tang D, Huang J, Lu H, Yao J. · bioRxiv · 2021-12-07
scBERT: early pretrained language model for cell type annotation.