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
State-resolved sc+spatial atlas of IDH-associated differences in glioma.
Type: paper
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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
Perspective on AI virtual cell platforms for environmental perturbation modelling.
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
Spatial + single-cell dissection of medulloblastoma hierarchies (2026).
An operational perturbation proteomics-based virtual cell model.
Sun R et al. · Nature · 2026-09-09
Nature 2026: operational perturbation-proteomics-based virtual cell model.
A world model of the virtual cell
Xing et al. · Cell · 2026-09
Cell peer-reviewed version of VCWM: persistent multimodal virtual-cell world model vs task-specific predictors.
Predicting cellular responses to perturbation across diverse contexts with State.
Adduri AK et al. · Cell · 2026-08-31
State (Arc Institute): state-embedding + transition model across 70 contexts; Cell 2026.
Virtual Cell Challenge 2026: Benchmarking zero-shot generalization across cellular contexts.
Arc Virtual Cell Initiative Team, Goodarzi H. · Cell · 2026-08-26
Virtual Cell Challenge 2026 paper: benchmarking zero-shot generalization across contexts.
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
Critique of the DMG generative growth study (domain shift, nesting).
UniPert-G2CP bridges genetic and chemical screens from molecular representation to phenotype modeling
Li et al. · Cell · 2026-08
UniPert-G2CP: unified genetic/chemical perturbagen embeddings + CRISPR-to-drug phenotype transfer for AIVC.
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
Assessing scale and predictive diversity of Geneformer-based models.
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 organoid-brain slice infiltration model (Nat Protoc).
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
Attention-derived edge scores in scFMs add no GRN information beyond baselines.
A World Model of the Virtual Cell (ICML 2026)
ICML 2026 · ICML 2026 · 2026-07
Proposes virtual cell world model (VCWM) as operational definition.
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
Oligodendrocyte fatty-acid remodeling in brain metastasis (sc+spatial).
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
Automated personalized GBM organoid drug screening platform.
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
Generative AI forecasting spatial tumor growth on MRI in pediatric DMG.
TumorTwin: a Python framework for patient-specific digital twins in oncology
Kapteyn et al. · BMC Med Inform Decis Mak · 2026-05-11
Open modular Python framework for patient-specific tumor digital twins; HGG growth/RT response demo.
TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects.
Wenkel F et al. · Nature biotechnology · 2026-05-01
TxPert: multiple knowledge graphs for transcriptomic perturbation prediction.
Discovery of candidate therapeutic targets with Geneformer.
Zhang Y, Venkatesh MS, Theodoris CV. · Nature protocols · 2026-04-23
Nature Protocols: discovering therapeutic targets with Geneformer in silico perturbation.
A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.
Sussman JH et al. · Cell reports. Medicine · 2026-04-23
Longitudinal single-cell & spatial atlas of pediatric high-grade glioma.
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
Review: current landscape of single-cell genomics in meningioma.
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
MRI foundation model for brain tumor molecular profiling and progression.
Anatomically aware simulation of patient-specific glioblastoma xenografts
Malik et al. · PLoS Comput Biol · 2026-01-20
Patient-specific GBM xenograft growth/invasion model on mouse brain anatomy; ABC fit; treatment via parameter perturbation.
Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations
Suter et al. · Nature Communications · 2026-01-07
scFOCAL/ISOSCELES links GBM cell states to L1000 signatures; predicts state-specific sensitivity and OLIG2i+Depatux-M combo.
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.
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.
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.
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.
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.
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.
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.
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).
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).
How to build the virtual cell with artificial intelligence: Priorities and opportunities.
Bunne C et al. · Cell · 2024-12-01
Landmark perspective defining the AI Virtual Cell (AIVC): multiscale, multimodal, universal representations and virtual instruments.
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
In silico exploration of GBM attractors from scRNA-seq (Boolean network).
GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model.
Yang X et al. · Cell research · 2024-10-08
GeneCompass: knowledge-informed cross-species foundation model (CAS).
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
In vivo Perturb-seq of GBM and microenvironment dissects drivers and radiotherapy responses.
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: 100M-parameter model on ~50M human cells (Tsinghua/BioMap).
Hypoxia coordinates the spatial landscape of myeloid cells within glioblastoma to affect survival.
Haley MJ et al. · Science advances · 2024-05-17
Hypoxia coordinates spatial landscape of myeloid cells in GBM.
Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
Greenwald AC et al. · Cell · 2024-04-22
Greenwald et al.: multi-layered spatial organization of GBM.
Towards a general-purpose foundation model for computational pathology.
Chen RJ et al. · Nature medicine · 2024-03-19
UNI: general-purpose computational pathology foundation model (incl. brain tumor tasks).
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: generative pretrained transformer on 33M cells (Bo Wang lab).
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
Agent-based hybrid model of GBM cell biophysics and treatment.
Disentanglement of single-cell data with biolord.
Piran Z, Cohen N, Hoshen Y, Nitzan M. · Nature biotechnology · 2024-01-15
biolord: disentangled representations for counterfactual cell prediction.
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: neural optimal transport for single-cell perturbation responses.
Predicting transcriptional outcomes of novel multigene perturbations with GEARS.
Roohani Y, Huang K, Leskovec J. · Nature biotechnology · 2023-08-17
GEARS: knowledge-graph GNN predicting multigene perturbation outcomes.
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
Cellular origins and drivers of brain metastasis by scRNA-seq.
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: context-aware transformer enabling in silico deletion/network predictions.
Predicting cellular responses to complex perturbations in high-throughput screens.
Lotfollahi M et al. · Molecular systems biology · 2023-05-08
CPA: compositional perturbation autoencoder for drug/dose/combination responses.
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
Single-cell atlas of GBM evolution under therapy.
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
Liu et al.: tumor cell states and spatial organization of H3-K27M DMG across ages.
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
Spatial transcriptomic landscape of NSCLC brain metastasis.
Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma.
Ravi VM et al. · Cancer cell · 2022-06-01
Ravi et al.: spatial multi-omics of tumor-host interdependence in GBM.
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
Single-cell profiling of human dura and meningioma.
Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy.
Couturier CP et al. · Nature communications · 2020-07-08
Couturier et al.: GBM recapitulates neurodevelopmental hierarchy.
A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity.
Jacob F et al. · Cell · 2019-12-26
Jacob et al.: patient-derived GBM organoid biobank (GBO).
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
Vladoiu et al.: medulloblastoma progenitors & developmental origins.
scGen predicts single-cell perturbation responses.
Lotfollahi M, Wolf FA, Theis FJ. · Nature methods · 2019-07-29
scGen: early VAE-based single-cell perturbation response prediction.
Resolving medulloblastoma cellular architecture by single-cell genomics.
Hovestadt V et al. · Nature · 2019-07-24
Hovestadt et al.: medulloblastoma cellular architecture by single-cell genomics.
An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma.
Neftel C et al. · Cell · 2019-07-18
Neftel et al.: four GBM malignant states (NPC/OPC/AC/MES), plasticity and genetics.
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 et al.: OPC-like programs in H3K27M gliomas.
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 et al.: IDH-mutant glioma lineages and microenvironment by scRNA-seq.
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
Multiscale DTI-based glioma spread model.
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 et al.: 'virtual and real brain tumors' — classic proliferation-invasion model.