A State-Resolved Single-Cell and Spatial Atlas Reveals IDH-Associated Differences in Malignant and Immune Architecture in Diffuse Glioma.
Zaman A et al. · MedComm · 2026-10-04
IDH相关胶质瘤状态分辨图谱。
类型：论文
共 75 条，按时间倒序。
Beyond the drug-centric view: Advancing AI virtual cell platforms for environmental perturbation modelling.
Ukaegbu D, Curean V, Bender A, Maertens A. · ALTEX · 2026-09-17
观点：虚拟细胞用于环境暴露/毒理扰动建模。
Spatial and single-cell dissection of medulloblastoma identifies developmental hierarchies and a prognostic PPIA-BSG tumor-immune axis.
Chen M, Duan B, Zhang J, Daniels C, Hu C, Yuan J, Guo J, Taylor MD, Shi X, Zhang L, Li D, Sun T. · Journal of translational medicine · 2026-09-15
髓母细胞瘤空间与单细胞层级（2026）。
An operational perturbation proteomics-based virtual cell model.
Sun R et al. · Nature · 2026-09-09
Nature 2026：基于扰动蛋白质组的可操作虚拟细胞模型。
A world model of the virtual cell
Xing et al. · Cell · 2026-09
Cell正式版VCWM：持久多模态虚拟细胞世界模型，区别于任务型预测基础模型。
Predicting cellular responses to perturbation across diverse contexts with State.
Adduri AK et al. · Cell · 2026-08-31
Arc的State模型：跨70种细胞情境预测扰动反应（Cell 2026）。
Virtual Cell Challenge 2026: Benchmarking zero-shot generalization across cellular contexts.
Arc Virtual Cell Initiative Team, Goodarzi H. · Cell · 2026-08-26
2026挑战赛论文：跨细胞情境零样本泛化基准。
Biological domain shift and statistical nesting concerns in generative AI-based spatial tumor growth prediction for pediatric diffuse midline glioma.
Li W, Sun X, Pei S. · BMC medicine · 2026-08-12
对上述DMG生成模型的方法学批评。
UniPert-G2CP bridges genetic and chemical screens from molecular representation to phenotype modeling
Li et al. · Cell · 2026-08
UniPert-G2CP：统一基因/化学扰动表征，并把CRISPR筛查迁移到药物表型预测。
Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer.
Chen J, Schmidt F, Henao R. · PLoS computational biology · 2026-07-30
评估Geneformer类模型的规模效应。
Core2Edge: a human glioblastoma organoid-brain slice model capturing infiltration and transcriptional heterogeneity from core to single-cell dispersion.
Melhem A et al. · Nature protocols · 2026-07-28
Core2Edge：GBM类器官-脑片浸润模型。
Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction.
Kendiukhov I. · BMC genomics · 2026-07-22
单细胞基础模型注意力边得分未增加调控网络信息。
A World Model of the Virtual Cell (ICML 2026)
ICML 2026 · ICML 2026 · 2026-07
提出“虚拟细胞世界模型”的操作性定义。
Single-cell and spatial transcriptomes reveal oligodendrocyte remodeling fatty acid metabolism microenvironment of lung cancer brain metastases.
Yang Y, Gao Y, Qi Z, Li S, Wang Z, Li D, Chen L, Zhou C, Feng M, Chen X, Hao B, Wu X, Li L, Cao Y. · Journal of translational medicine · 2026-06-16
脑转移中少突胶质细胞脂肪酸代谢重塑。
Automated and personalized glioblastoma tumor organoid drug screening platform exposes sensitivity to proteasome and HDAC inhibitors.
Jungwirth G et al. · NPJ precision oncology · 2026-06-16
自动化个体化GBM类器官药筛平台。
Generative AI for spatial tumor growth on MRI: a proof-of-principle study in pediatric diffuse midline glioma.
Laslo D et al. · BMC medicine · 2026-05-18
生成式AI预测儿童DMG的MRI空间生长。
TumorTwin: a Python framework for patient-specific digital twins in oncology
Kapteyn et al. · BMC Med Inform Decis Mak · 2026-05-11
开源模块化Python肿瘤数字孪生框架；演示高级别胶质瘤生长与放疗反应。
TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects.
Wenkel F et al. · Nature biotechnology · 2026-05-01
TxPert：多知识图谱预测转录组扰动效应。
Discovery of candidate therapeutic targets with Geneformer.
Zhang Y, Venkatesh MS, Theodoris CV. · Nature protocols · 2026-04-23
Nature Protocols：用Geneformer进行靶点发现的流程。
A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.
Sussman JH et al. · Cell reports. Medicine · 2026-04-23
儿童高级别胶质瘤纵向单细胞/空间图谱。
Current landscape of single-cell genomics in meningioma.
Ellenbogen Y, Landry AP, Yefet LS, Ajisebutu A, Gui C, Persaud P, Kaloti R, Nassiri F. · Neuro-oncology advances · 2026-02-27
综述：脑膜瘤单细胞基因组学现状。
Foundation Model Based on Routine Magnetic Resonance Imaging for Brain Tumor Molecular Profiling and Progression Prediction.
Li J, Liu R, Xing Y, Gao X, Yin Q, Su Q. · JCO precision oncology · 2026-02-20
基于常规MRI的脑肿瘤分子分型基础模型。
Anatomically aware simulation of patient-specific glioblastoma xenografts
Malik et al. · PLoS Comput Biol · 2026-01-20
基于小鼠脑解剖的患者特异性GBM异种移植生长/侵袭模型；ABC拟合；通过扰动参数模拟治疗。
Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations
Suter et al. · Nature Communications · 2026-01-07
scFOCAL/ISOSCELES：把GBM细胞状态接到L1000药签，预测状态敏感度并验证OLIG2抑制剂+Depatux-M。
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。
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）。
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。
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）。
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。
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。
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。
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。
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）。
How to build the virtual cell with artificial intelligence: Priorities and opportunities.
Bunne C et al. · Cell · 2024-12-01
奠基性综述：提出“AI虚拟细胞”定义与多尺度、多模态路线图。
A method for in silico exploration of potential glioblastoma multiforme attractors using single-cell RNA sequencing.
Vieira Junior MG, de Almeida Côrtes AM, Gonçalves Carneiro FR, Carels N, Silva FABD. · Scientific reports · 2024-10-29
基于单细胞数据的GBM吸引子计算探索。
GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model.
Yang X et al. · Cell research · 2024-10-08
GeneCompass：知识引导的跨物种基础模型（中科院）。
In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma.
Liu SJ et al. · Genome biology · 2024-10-07
GBM体内Perturb-seq：解析驱动基因与放疗反应——脑肿瘤虚拟细胞的关键训练数据类型。
Large-scale foundation model on single-cell transcriptomics.
Hao M, Gong J, Zeng X, Liu C, Guo Y, Cheng X, Wang T, Ma J, Zhang X, Song L. · Nature methods · 2024-06-06
scFoundation：清华/百图生科的1亿参数单细胞基础模型。
Hypoxia coordinates the spatial landscape of myeloid cells within glioblastoma to affect survival.
Haley MJ et al. · Science advances · 2024-05-17
缺氧协调GBM髓系细胞空间格局。
Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
Greenwald AC et al. · Cell · 2024-04-22
Greenwald等：GBM多层次空间组织。
Towards a general-purpose foundation model for computational pathology.
Chen RJ et al. · Nature medicine · 2024-03-19
UNI：通用病理基础模型（含脑肿瘤分型任务）。
scGPT: toward building a foundation model for single-cell multi-omics using generative AI.
Cui H, Wang C, Maan H, Pang K, Luo F, Duan N, Wang B. · Nature methods · 2024-02-26
scGPT：基于3300万细胞的生成式单细胞基础模型（王波团队）。
A simple agent-based hybrid model to simulate the biophysics of glioblastoma multiforme cells and the concomitant evolution of the oxygen field.
Saucedo-Mora L, Sanz MÁ, Montáns FJ, Benítez JM. · Computer methods and programs in biomedicine · 2024-01-26
GBM细胞生物物理主体模型。
Disentanglement of single-cell data with biolord.
Piran Z, Cohen N, Hoshen Y, Nitzan M. · Nature biotechnology · 2024-01-15
biolord：解耦表示进行反事实细胞预测。
Learning single-cell perturbation responses using neural optimal transport.
Bunne C, Stark SG, Gut G, Del Castillo JS, Levesque M, Lehmann KV, Pelkmans L, Krause A, Rätsch G. · Nature methods · 2023-09-28
CellOT：神经最优传输预测扰动反应。
Predicting transcriptional outcomes of novel multigene perturbations with GEARS.
Roohani Y, Huang K, Leskovec J. · Nature biotechnology · 2023-08-17
GEARS：知识图谱图神经网络预测多基因扰动。
Single-cell transcriptomic analyses provide insights into the cellular origins and drivers of brain metastasis from lung adenocarcinoma.
Wang Z, Wang Y, Chang M, Wang Y, Liu P, Wu J, Wang G, Tang X, Hui X, Liu P, Guo X, Xing B, Wang Y, Han Z, Ma W. · Neuro-oncology · 2023-07-01
脑转移细胞起源与驱动。
Transfer learning enables predictions in network biology.
Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. · Nature · 2023-05-31
Geneformer：支持“计算机模拟敲除”的单细胞基础模型。
Predicting cellular responses to complex perturbations in high-throughput screens.
Lotfollahi M et al. · Molecular systems biology · 2023-05-08
CPA：组合扰动自编码器，预测药物/剂量/组合反应。
A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets.
Wang L, Jung J, Babikir H, Shamardani K, Jain S, Feng X, Gupta N, Rosi S, Chang S, Raleigh D, Solomon D, Phillips JJ, Diaz AA. · Nature cancer · 2022-12-20
治疗下GBM演化单细胞图谱。
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.
Liu I et al. · Nature genetics · 2022-12-05
H3-K27M弥漫中线胶质瘤跨年龄细胞状态与空间组织。
The spatial transcriptomic landscape of non-small cell lung cancer brain metastasis.
Zhang Q, Abdo R, Iosef C, Kaneko T, Cecchini M, Han VK, Li SS. · Nature communications · 2022-10-10
肺癌脑转移空间转录组。
Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma.
Ravi VM et al. · Cancer cell · 2022-06-01
Ravi等：GBM空间多组学揭示肿瘤-宿主相互依存。
Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response.
Wang AZ et al. · Genome medicine · 2022-05-10
硬脑膜与脑膜瘤单细胞图谱。
Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy.
Couturier CP et al. · Nature communications · 2020-07-08
GBM重演神经发育层级。
A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity.
Jacob F et al. · Cell · 2019-12-26
Jacob等：患者来源GBM类器官库。
Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse.
Zhang L et al. · Cancer cell · 2019-08-29
髓母细胞瘤起源祖细胞。
scGen predicts single-cell perturbation responses.
Lotfollahi M, Wolf FA, Theis FJ. · Nature methods · 2019-07-29
scGen：早期基于VAE的单细胞扰动预测。
Resolving medulloblastoma cellular architecture by single-cell genomics.
Hovestadt V et al. · Nature · 2019-07-24
髓母细胞瘤单细胞结构。
An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma.
Neftel C et al. · Cell · 2019-07-18
Neftel等：GBM四种恶性细胞状态及可塑性——虚拟细胞建模的核心“状态空间”。
Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.
Filbin MG et al. · Science (New York, N.Y.) · 2018-04-01
Filbin等：H3K27M胶质瘤的发育与致瘤程序。
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.
Venteicher AS et al. · Science (New York, N.Y.) · 2017-03-01
Venteicher等：IDH突变胶质瘤单细胞谱系。
Glioma follow white matter tracts: a multiscale DTI-based model.
Engwer C, Hillen T, Knappitsch M, Surulescu C. · Journal of mathematical biology · 2014-09-12
基于DTI的多尺度胶质瘤扩散模型。
Virtual and real brain tumors: using mathematical modeling to quantify glioma growth and invasion.
Swanson KR, Bridge C, Murray JD, Alvord EC. · Journal of the neurological sciences · 2003-12-01
Swanson等：“虚拟脑肿瘤”经典增殖-侵袭模型。