scPRINT-2: Towards the next-generation of cell foundation models and benchmarks
Kalfon J, Peyré G, Cantini L. · bioRxiv · 2025-12-15
scPRINT-2: next-gen cell foundation models and benchmarks.
Year: 2025
41 items, newest first.
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A single-cell atlas of RNA alternative splicing in the glioma-immune ecosystem.
Song X, Tiek D, Lu M, Yu X, Wu R, Walker M, He Q, Sisbarro D, Hu B, Cheng SY. · Genome biology · 2025-12-12
Single-cell atlas of alternative splicing in glioma-immune ecosystem.
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.
Ma C, Zhang H, Rao Y, Jiang X, Liu B, Sun Z, Song Z, Gao Y, Cui Y, Liu X, Li Z. · NPJ digital medicine · 2025-12-11
Review of AI virtual cell models in preclinical research: technical pathways and validation.
Novae: a graph-based foundation model for spatial transcriptomics data.
Blampey Q, Benkirane H, Bercovici N, Mulder K, Gessain G, Ginhoux F, André F, Cournède PH. · Nature methods · 2025-12-10
Novae: graph-based foundation model for spatial transcriptomics.
NeurIPS 2025: Altos Labs wins Generalist Prize at Arc's Virtual Cell Challenge
GEN (Fay Lin) · GEN · 2025-12-08
GEN coverage of challenge results, quotes Hani Goodarzi.
Virtual Cell Challenge 2025 Wrap-Up: Winners and Reflections
Arc Institute · Arc news · 2025-12-06
Winners: BioMap (1st), Sichuan Univ XLearning (2nd), Outlier (3rd), Altos Labs (Generalist); metrics gaming lessons.
A foundation model for brain tumor MRI analysis: WHO grading and subtype classification.
Li J, Liu R, Xing Y, Gao X, Yin Q, Su Q. · Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology · 2025-11-19
Foundation model for brain tumor MRI: WHO grading & subtyping.
STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.
Huang T, Liu T, Babadi M, Ying R, Jin W. · NPJ digital medicine · 2025-11-14
STPath: generative model linking WSIs and spatial transcriptomics.
BRD2 bromodomain-mediated regulation of cell state plasticity modulates therapy response in glioblastoma.
Vadla R et al. · Neuro-oncology · 2025-11-01
BRD2 regulates GBM cell-state plasticity and therapy response.
Nicheformer: a foundation model for single-cell and spatial omics.
Tejada-Lapuerta A, Schaar AC, Gutgesell R, Palla G, Halle L, Minaeva M, Vornholz L, Dony L, Drummer F, Richter T, Bahrami M, Theis FJ. · Nature methods · 2025-10-30
Nicheformer (Theis lab): single-cell + spatial foundation model, Nat Methods 2025.
Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap.
Ruiz-Moreno C et al. · Neuro-oncology · 2025-10-01
GBmap: single-cell & spatial reference atlas of IDH-wt GBM (>1M cells).
DELPHAI, AI Agent for Predicting Drug Response and Resistance
Peng et al. · preprint · 2025-09-17
DELPHAI: AI agent for sc perturbation prediction + LLM mechanism on GBM organoids with TMZ; OT+PCA beat baselines.
Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation.
Viñas Torné R, Wiatrak M, Piran Z, Fan S, Jiang L, Teichmann SA, Nitzan M, Brbić M. · Nature biotechnology · 2025-08-25
Systema: evaluating perturbation prediction beyond systematic variation.
rBio: reasoning model trained on virtual cell simulations
Chan Zuckerberg Initiative · CZI blog · 2025-08-20
rBio: Qwen2.5-3B reasoning LLM post-trained with TranscriptFormer as soft verifier.
Multiscale mathematical model-informed reinforcement learning optimizes combination treatment scheduling in glioblastoma evolution.
Liu Z, Zhang J, Hong L, Nie Q, Sun X. · Science advances · 2025-08-08
Multiscale mechanistic model + reinforcement learning to optimize glioma combination scheduling.
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.
Ahlmann-Eltze C, Huber W, Anders S. · Nature methods · 2025-08-04
Ahlmann-Eltze, Huber, Anders: deep models don't beat simple linear baselines for perturbation prediction.
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories.
Johnson JAI et al. · Cell · 2025-07-26
Human-interpretable grammar for multicellular agent-based models (PhysiCell) to democratize virtual cell labs.
Can AI build a virtual cell? Scientists race to model life's smallest unit.
Callaway E. · Nature · 2025-07-01
Nature news feature: the race to build an AI virtual cell.
Single-cell analysis reveals a longitudinal trajectory of meningioma evolution and heterogeneity.
Lee JY, Lee EJ, Seo BY, Kim J, Song Y, Lee D, Moon N, Koo H, Park CK, Kim MS, Park SI, Nam DH, Kong DS, Sa JK. · Nature communications · 2025-07-01
Longitudinal single-cell trajectory of meningioma evolution.
Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction
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.
Predicting cellular responses to perturbation across diverse contexts with State
Adduri AK et al. · bioRxiv · 2025-06-27
State preprint (bioRxiv June 2025).
Arc Institute's first virtual cell model: State
Arc Institute · Arc news · 2025-06-23
Announcement of State (~170M observational + 100M perturbed cells).
X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models
Huang AC et al. · bioRxiv · 2025-06-16
X-Atlas/Orion: genome-wide Perturb-seq datasets (Xaira).
Bioptimus: multimodal biology foundation model (NVIDIA compute)
Bioptimus · Bioptimus news · 2025-06-11
French startup building multiscale biology FMs (H-Optimus pathology models).
Virtual Cell Challenge: Toward a Turing test for the virtual cell.
Roohani YH et al. · Cell · 2025-06-01
Arc Institute perspective launching the Virtual Cell Challenge as a 'Turing test' for virtual cells.
A visual-omics foundation model to bridge histopathology with spatial transcriptomics.
Chen W et al. · Nature methods · 2025-05-29
OmiCLIP/Loki: visual-omics foundation model bridging H&E and spatial transcriptomics.
Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma.
Hara T et al. · Cancer cell · 2025-05-27
Hara et al.: immune–cancer interactions drive MES-like transitions in GBM.
Virtual Cells: Predict, Explain, Discover (arXiv 2505.14613)
Recursion / Valence Labs · arXiv · 2025-05-20
Recursion/Valence perspective: virtual cells should predict, explain, discover via lab-in-the-loop.
Spatial epigenomic niches underlie glioblastoma cell state plasticity
Kint S et al. · bioRxiv · 2025-05-14
Spatial epigenomic niches underlie GBM cell-state plasticity.
A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model
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.
TranscriptFormer model overview (blog)
Chan Zuckerberg Initiative · CZI blog · 2025-04-29
CZI blog post introducing TranscriptFormer (Theofanis Karaletsos et al.).
Benchmarking foundation cell models for post-perturbation RNA-seq prediction.
Csendes G, Sanz G, Szalay KZ, Szalai B. · BMC genomics · 2025-04-23
Csendes et al.: foundation cell models vs simple baselines for post-perturbation prediction.
Zero-shot evaluation reveals limitations of single-cell foundation models.
Kedzierska KZ, Crawford L, Amini AP, Lu AX. · Genome biology · 2025-04-18
Kedzierska et al.: zero-shot limitations of scGPT/Geneformer.
Scaling Large Language Models for Next-Generation Single-Cell Analysis
Rizvi SA et al. · bioRxiv · 2025-04-17
C2S-Scale (Yale/Google): scaling LLMs to 27B for single-cell analysis and virtual screening.
Mapping the spatial architecture of glioblastoma from core to edge delineates niche-specific tumor cell states and intercellular interactions
Khan SM et al. · bioRxiv · 2025-04-04
Spatial architecture of GBM from core to edge; niche-specific states.
Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases.
Tagore S et al. · Nature medicine · 2025-02-27
Single-cell & spatial landscape of NSCLC brain metastases (Nat Med 2025).
Tahoe-100M : A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling
Zhang J et al. · bioRxiv · 2025-02-24
Tahoe-100M preprint: 100M cells, 1,100 drugs x 50 cancer cell lines.
A perturbation proteomics-based foundation model for virtual cell construction
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.
scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics
Wang C, Cui H, Zhang A, Xie R, Goodarzi H, Wang B. · bioRxiv · 2025-02-08
scGPT-spatial: continual pretraining for spatial transcriptomics.
Build the virtual cell with artificial intelligence: a perspective for cancer research.
Yang T, Wang YY, Ma F, Xu BH, Qian HL. · Military Medical Research · 2025-01-27
Commentary on building virtual cells for cancer research (Chinese authors).
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data.
CZI Cell Science Program et al. · Nucleic acids research · 2025-01-01
CZ CELLxGENE Discover: 100M+ cell data platform (contains glioma datasets).