scPRINT-2: Towards the next-generation of cell foundation models and benchmarks
Kalfon J, Peyré G, Cantini L. · bioRxiv · 2025-12-15
scPRINT-2：新一代细胞基础模型与基准。
年份：2025
共 41 条，按时间倒序。
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
胶质瘤-免疫生态可变剪接单细胞图谱。
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
综述：AI虚拟细胞在临床前研究中的技术路径与验证机制。
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：基于图的空间转录组基础模型。
NeurIPS 2025: Altos Labs wins Generalist Prize at Arc's Virtual Cell Challenge
GEN (Fay Lin) · GEN · 2025-12-08
GEN报道挑战赛结果。
Virtual Cell Challenge 2025 Wrap-Up: Winners and Reflections
Arc Institute · Arc news · 2025-12-06
2025挑战赛结果：百图生科第一、四川大学第二；指标可被“刷分”的教训。
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
脑肿瘤MRI基础模型：WHO分级与亚型。
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：整合全切片图像与空间转录组的生成模型。
BRD2 bromodomain-mediated regulation of cell state plasticity modulates therapy response in glioblastoma.
Vadla R et al. · Neuro-oncology · 2025-11-01
BRD2调控GBM状态可塑性与治疗反应。
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：单细胞+空间组学基础模型（Theis团队）。
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：IDH野生型GBM单细胞与空间参考图谱。
DELPHAI, AI Agent for Predicting Drug Response and Resistance
Peng et al. · preprint · 2025-09-17
DELPHAI：GBM类器官+TMZ的单细胞扰动预测与LLM机制解读；最优传输+PCA优于基线。
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：剔除系统性变异后评估扰动预测。
rBio: reasoning model trained on virtual cell simulations
Chan Zuckerberg Initiative · CZI blog · 2025-08-20
rBio：以TranscriptFormer为软验证器训练的生物推理大模型。
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
多尺度机制模型+强化学习优化胶质瘤联合治疗时序。
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等：深度模型未超越简单线性基线。
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories.
Johnson JAI et al. · Cell · 2025-07-26
可解释“语法”驱动的多细胞主体模型，降低虚拟细胞实验室门槛（含肿瘤示例）。
Can AI build a virtual cell? Scientists race to model life's smallest unit.
Callaway E. · Nature · 2025-07-01
Nature新闻特稿：科学家竞相构建AI虚拟细胞。
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
脑膜瘤纵向单细胞演化轨迹。
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
多模态基础模型表示的扰动预测基准。
Predicting cellular responses to perturbation across diverse contexts with State
Adduri AK et al. · bioRxiv · 2025-06-27
State模型预印本。
Arc Institute's first virtual cell model: State
Arc Institute · Arc news · 2025-06-23
Arc发布State模型新闻。
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：Xaira全基因组Perturb-seq数据集。
Bioptimus: multimodal biology foundation model (NVIDIA compute)
Bioptimus · Bioptimus news · 2025-06-11
法国Bioptimus多尺度生物基础模型。
Virtual Cell Challenge: Toward a Turing test for the virtual cell.
Roohani YH et al. · Cell · 2025-06-01
Arc研究所发起虚拟细胞挑战赛，作为虚拟细胞的“图灵测试”。
A visual-omics foundation model to bridge histopathology with spatial transcriptomics.
Chen W et al. · Nature methods · 2025-05-29
病理图像与空间转录组桥接的视觉-组学基础模型。
Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma.
Hara T et al. · Cancer cell · 2025-05-27
免疫细胞驱动GBM向间充质样状态转变。
Virtual Cells: Predict, Explain, Discover (arXiv 2505.14613)
Recursion / Valence Labs · arXiv · 2025-05-20
Recursion观点：虚拟细胞应能预测、解释、发现。
Spatial epigenomic niches underlie glioblastoma cell state plasticity
Kint S et al. · bioRxiv · 2025-05-14
空间表观生态位决定GBM状态可塑性。
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
CZI的TranscriptFormer：跨12物种、1.12亿细胞的生成式模型。
TranscriptFormer model overview (blog)
Chan Zuckerberg Initiative · CZI blog · 2025-04-29
CZI介绍TranscriptFormer的博客。
Benchmarking foundation cell models for post-perturbation RNA-seq prediction.
Csendes G, Sanz G, Szalay KZ, Szalai B. · BMC genomics · 2025-04-23
Csendes等：基础模型扰动预测不如简单基线。
Zero-shot evaluation reveals limitations of single-cell foundation models.
Kedzierska KZ, Crawford L, Amini AP, Lu AX. · Genome biology · 2025-04-18
Kedzierska等：零样本评估揭示单细胞基础模型局限。
Scaling Large Language Models for Next-Generation Single-Cell Analysis
Rizvi SA et al. · bioRxiv · 2025-04-17
C2S-Scale（耶鲁/谷歌）：270亿参数单细胞LLM，含虚拟药物筛选。
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
GBM核心到边缘的空间结构。
Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases.
Tagore S et al. · Nature medicine · 2025-02-27
非小细胞肺癌脑转移单细胞与空间图谱。
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：1亿细胞、1100药物×50肿瘤细胞系。
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
上述扰动蛋白组虚拟细胞模型预印本。
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：面向空间转录组的持续预训练。
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
面向肿瘤研究的虚拟细胞评论（中国团队）。
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：超1亿细胞的数据平台（含胶质瘤数据集）。