Awesome Virtual Cell

A curated list of papers, datasets, benchmarks, talks, and community resources for AI-powered virtual cell research.

Here, AIVC stands for Artificial Intelligence Virtual Cell, a term popularized by the Cell perspective "How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities." The focus of this repository is broad but practical: resources that help researchers understand, model, benchmark, or build virtual cells and related cellular foundation models.

For scientific figure ideas and plotting templates, see Awesome Scientific Figures.

Scope

In scope: virtual cell perspectives, perturbation modeling, single-cell and multimodal foundation models, spatial and morphology modeling, biological AI agents, datasets, benchmarks, and community resources closely connected to virtual cell research.
Also included: adjacent work that is broadly useful for the virtual cell community, especially when it contributes data, evaluation methods, or modeling tools for cellular systems.
Usually out of scope: generic biomedical AI work with weak cell-modeling relevance, low-confidence secondary sources, broken links, or items that do not add clear value beyond more central references already listed here.

Inclusion Rules

Prefer peer-reviewed papers, high-signal preprints, official project pages, and primary-source links.
Include code, datasets, project pages, or Chinese summaries when they are clearly useful.
Keep entries concise and broadly reusable for readers who are scanning the field.
Use lightweight tags in Research Papers only as browsing aids. They are intentionally approximate, not rigid taxonomy.

Overview Papers

[Nature News] Can AI Build a Virtual Cell? Scientists Race to Model Life's Smallest Unit (Nature 2025) [paper] [中文解读]
[Nature Perspective] Towards Multimodal Foundation Models in Molecular Cell Biology (Nature 2025) [paper] [中文解读]
[Nature Methods] The virtual cell (Nature Methods 2025) [paper]
[Nature] The Human Cell Atlas from a cell census to a unified foundation model (Nature 2024) [paper]
[Nature Review] Interpretation, extrapolation and perturbation of single cells (Nature Reviews Genetics 2026) [paper]
[Nature Review] Revisiting the blueprint for an interpretable virtual cell (Nature Reviews Genetics 2026) [paper]
[npj Digital Medicine] AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential (npj Digital Medicine 2025) [paper]
[Nature Review] Adapting systems biology to address the complexity of human disease in the single-cell era (Nature Reviews Genetics 2025) [paper]
[Nature Genetics] Causal machine learning for single-cell genomics (Nature Genetics 2025) [paper]
[Nature Methods] Multimodal foundation transformer models for multiscale genomics (Nature Methods 2025) [paper]
[Cell Perspective] Empowering Biomedical Discovery with AI Agents (Cell 2024) [paper] [中文解读]
[Cell Perspective] How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities (Cell 2024) [paper] [中文解读]
[Cell Review] Toward a Foundation Model of Causal Cell and Tissue Biology with a Perturbation Cell and Tissue Atlas (Cell 2024) [paper] [中文解读]

Research Papers

Tag hints: [Virtual Cell], [Perturbation], [Foundation Model], [Spatial], [Morphology], [Agent], [Benchmark], [Tool], [Related]. Tags are lightweight and non-exhaustive.

2026

[Dataset Size & Diversity] [Foundation Model] Evaluating the role of pretraining dataset size and diversity on single-cell foundation model performance (Nature Methods 2026) [paper] [code]
[Lingshu-Cell] [Virtual Cell] Lingshu-Cell: A generative cellular world model for transcriptome modeling toward virtual cells (arXiv 2026) [paper] [homepage]
[SCALE] [Perturbation] SCALE: Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction (arXiv 2026) [paper]
[Conditional Monge Gap] [Perturbation] Conditional Monge Gap enables generalizable single-cell perturbation modelling (Nature Machine Intelligence 2026) [paper] [code]
[ProtiCelli] [Virtual Cell] Generative machine learning unlocks the first proteome-wide image of human cells (bioRxiv 2026) [paper] [code]
[AetherCell] [Virtual Cell] AetherCell: A generative engine for virtual cell perturbation and in vivo drug discovery (bioRxiv 2026) [paper] [code]
[AlphaCell] [Virtual Cell] Towards building a World Model to simulate perturbation-induced cellular dynamics by AlphaCell (bioRxiv 2026) [paper]
[VCWorld] [Virtual Cell] VCWorld: A Biological World Model for Virtual Cell Simulation (ICLR 2026 Poster) [paper] [code] [ask deepwiki]
[Spatial Perturb-seq] [Spatial] Spatial perturb-seq: single-cell functional genomics within intact tissue architecture (Nature Communications 2026) [paper][code]
[Celcomen] [Spatial] Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling (Nature Communications 2026) [paper] [code]
[stVCR] [Spatial] stVCR: spatiotemporal dynamics of single cells (Nature Methods 2026) [paper] [code]
[CONCORD] [Foundation Model] Revealing a coherent cell-state landscape across single-cell datasets with CONCORD (Nature Biotechnology 2026) [paper][code]
[AI Scientist] [Related] Towards end-to-end automation of AI research (Nature 2026) [paper] [code]
[Conformation Description Language] [Related] Bridging three-dimensional molecular structures and artificial intelligence with a conformation description language (Nature Machine Intelligence 2026) [paper]
[CRISPRi Map] [Perturbation] A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines (Cell Genomics 2026) [paper]
[TxPert] [Perturbation] TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects (Nature Biotechnology 2026) [paper] [code]
[Therapeutic Design] [Related] Deep-learning-based de novo discovery and design of therapeutics that reverse disease-associated transcriptional phenotypes (Cell 2026) [paper]
[X-Pert] [Perturbation] Unified Multimodal Learning Enables Generalized Cellular Response Prediction to Diverse Perturbations (bioRxiv) [paper] [code] [ask deepwiki]
[MVCBench] [Benchmark] MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes (bioRxiv) [paper] [code] [ask deepwiki]
[HarmonyCell] [Perturbation] HarmonyCell: Automating Single-Cell Perturbation Modeling under Semantic and Distribution Shifts (bioRxiv) [paper]
[scDFM] [Perturbation] scDFM: Distributional Flow Matching Model for Robust Single-Cell Perturbation Prediction (ICLR 2026 Poster) [paper] [code]
[Doloris] [Perturbation] Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation (ICLR 2026 Poster) [paper] [code]
[Departures] [Perturbation] Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges (AAAI 2026) [paper] [preprint]
[PETRI] [Foundation Model] PETRI: Learning Unified Cell Embeddings from Unpaired Modalities via Early-Fusion Joint Reconstruction (ICLR 2026 Poster) [paper]
[STRAND] [Perturbation] STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations (arXiv 2026) [paper]
[PerturbDiff] [Perturbation] PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling (arXiv 2026) [paper] [code] [project]
[scBIG] [Perturbation] Beyond Independent Genes: Learning Module-Inductive Representations for Gene Perturbation Prediction (arXiv 2026) [paper] [code] [code]
[CellxPert] [Perturbation] CellxPert: Inference-Time MCMC Steering of a Multi-Omics Single-Cell Foundation Model for In-Silico Perturbation (arXiv 2026) [paper]
[Perturbation Representation] [Perturbation] What Makes a Representation Good for Single-Cell Perturbation Prediction? (arXiv 2026) [paper]
[CisTransCell] [Perturbation] CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context (arXiv 2026) [paper]
[Latent Causal Processes] [Perturbation] Learning Latent Dynamical Causal Processes for Single-Cell Perturbation Prediction (arXiv 2026) [paper]
[msInfer] [Tool] Large-scale proteome inference from unpaired single-cell transcriptomic and proteomic data by msInfer (Research Square 2026) [paper]
[Stack] [Foundation Model] Stack: In-Context Learning of Single-Cell Biology (bioRxiv) [paper] [code] [ask deepwiki]
[BioWorldModel] [Related] BioWorldModel: a single architecture predicts phenotype from genotype across four kingdoms of life (bioRxiv 2026) [paper]
[Gene Importance] [Foundation Model] Scoring gene importance by interpreting single-cell foundation models (Nature Biotechnology 2026) [paper]
[Hi-C FM] [Foundation Model] A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species (Nature Methods 2026) [paper]
[Virtual Spatial Tumor] [Virtual Cell] Cellular architecture and neighborhood-informed virtual spatial tumor profiling from histopathology (Cell 2026) [paper]
[SynCell] [Virtual Cell] A framework for building a synthetic cell from the SynCell Asia Initiative (Nature Biotechnology 2026) [paper]
[3D Genome FM] [Foundation Model] A foundation model to help understand the regulatory implications of 3D genome organization (Nature Methods 2026) [paper]
[Tissueformer] [Foundation Model] Tissueformer: extending single-cell foundation models to predict population-level phenotypes (BMC Bioinformatics 2026) [paper]
[CytoSignal] [Spatial] CytoSignal detects locations and dynamics of ligand–receptor signaling at cellular resolution from spatial transcriptomic data (Nature Genetics 2026) [paper]
[graphene-seq] [Spatial] In situ graphene-seq: spatial transcriptomics and chronic electrophysiological characterization of tissue microenvironments (Nature Communications 2026) [paper]
[Deep Molecular Profiling] [Spatial] Deep molecular profiling in three dimensions (Nature Methods 2026) [paper]
[SpaMosaic] [Spatial] Mosaic integration of spatial multi-omics with SpaMosaic (Nature Genetics 2026) [paper]
[Computational Landscape] [Perturbation] Charting the computational landscape of single-cell genetic perturbation (Journal of Advanced Research 2026) [paper]
[veloAgent] [Agent] Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent (Molecular Systems Biology 2026) [paper] [code]
[Morphodynamics] [Morphology] Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation (Molecular Systems Biology 2026) [paper]
[Single Cell Notebooks] [Tool] The Single Cell Notebooks for inclusive and accessible training in single-cell and spatial omics (Nature Genetics 2026) [paper]

2025

[Pertpy] [Tool] Pertpy: an End-to-end Framework for Perturbation Analysis (Nature Methods) [paper] [code] [ask deepwiki]
[Benchmarking] [Benchmark] Benchmarking Algorithms for Generalizable Single-Cell Perturbation Response Prediction (Nature Methods) [paper] [code] [ask deepwiki]
[Scouter] [Perturbation] Scouter predicts transcriptional responses to genetic perturbations with large language model embeddings (Nature Computational Science 2025) [paper]
[GPerturb] [Perturbation] GPerturb: Gaussian process modelling of single-cell perturbation data (Nature Communications 2025) [paper] [code]
[Squidiff] [Perturbation] Squidiff: Predicting Cellular Development and Responses to Perturbations using a Diffusion Model (Nature Methods) [paper] [code] [ask deepwiki]
[Nicheformer] [Spatial] Nicheformer: A Foundation Model for Single-Cell and Spatial Omics (Nature Methods) [paper] [中文解读] [code] [ask deepwiki]
[NicheCompass] [Spatial] Quantitative characterization of cell niches in spatially resolved omics data (Nature Genetics 2025) [paper] [code]
[STAMP] [Tool] STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging (Cell 2025) [paper]
[Perturb-FISH] [Spatial] Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits (Cell 2025) [paper]
[ADLF] [Perturbation] Active Learning Framework Leveraging Transcriptomics Identifies Modulators of Disease Phenotypes (Science) [paper] [code]
[Tahoe-x1] [Foundation Model] Tahoe-x1: Scaling Perturbation-Trained Single-Cell Foundation Models to 3 Billion Parameters (bioRxiv 2025) [paper] [code] [ask deepwiki] [hugging face files]
[LPM] [Perturbation] In Silico Biological Discovery with Large Perturbation Models (Nature Computational Science 2025) [paper] [中文解读] [code] [ask deepwiki]
[CellNavi] [Perturbation] CellNavi Predicts Genes Directing Cellular Transitions by Learning a Gene Graph-Enhanced Cell State Manifold (Nature Cell Biology 2025) [paper] [中文解读] [code] [ask deepwiki]
[EpiAgent] [Foundation Model] EpiAgent: Foundation Model for Single-Cell Epigenomics (Nature Methods 2025) [paper] [中文解读] [code] [ask deepwiki]
[CellWhisperer] [Tool] Multimodal learning enables chat-based exploration of single-cell data (Nature Biotechnology 2025) [paper] [code]
[CRISPR-GPT] [Agent] CRISPR-GPT for Agentic Automation of Gene-Editing Experiments (Nature Biomedical Engineering 2025) [paper] [中文解读] [code] [ask deepwiki]
[Cell-o1] [Agent] Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning (arXiv 2025) [paper] [code] [hugging face] [ask deepwiki]
[Systema] [Benchmark] Systema: A Framework for Evaluating Genetic Perturbation Response Prediction Beyond Systematic Variation (Nature Biotechnology 2025) [paper] [中文解读] [code] [ask deepwiki]
[RegVelo] [Perturbation] RegVelo: Gene-Regulatory-Informed Dynamics of Single Cells (bioRxiv) [paper] [code] [ask deepwiki]
[IMPA] [Morphology] Predicting cell morphological responses to perturbations using generative modeling (Nature Communications 2025) [paper] [code]
[PhenoProfiler] [Morphology] PhenoProfiler: Advancing Morphology Representations for Image-based Drug Discovery (Nature Communications 2025) [paper] [code] [webserver] [ask deepwiki]
[PERISCOPE] [Morphology] A genome-wide atlas of human cell morphology (Nature Methods 2025) [paper] [dataset] [code]
[Morph Map] [Morphology] Morphological map of under- and overexpression of genes in human cells (Nature Methods 2025) [paper] [dataset] [code]
[MorphDiff] [Morphology] Prediction of Cellular Morphology Changes under Perturbations with a Transcriptome-Guided Diffusion Model (Nature Communications 2025) [paper] [中文解读] [code] [ask deepwiki]
[rBio-1] [Agent] rBio1-Training Scientific Reasoning LLMs with Biological World Models as Soft Verifiers (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[TranscriptFormer] [Foundation Model] A Cross-Species Generative Cell Atlas across 1.5 Billion Years of Evolution: The Transcriptformer Single-Cell Model (bioRxiv 2025) [paper] [code] [ask deepwiki]
[CellAtria] [Agent] An Agentic AI Framework for Ingestion and Standardization of Single-Cell RNA-Seq Data Analysis (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[Scvi-hub] [Tool] Scvi-hub: An Actionable Repository for Model-Driven Single-Cell Analysis (Nature Methods 2025) [paper] [中文解读] [code] [ask deepwiki]
[GraphVelo] [Spatial] GraphVelo Allows for Accurate Inference of Multimodal Velocities and Molecular Mechanisms for Single Cells (Nature Communications 2025) [paper] [中文解读] [code] [ask deepwiki]
[Stereo-Cell] [Spatial] Stereo-Cell: Spatial Enhanced-Resolution Single-Cell Sequencing with High-Density DNA Nanoball-Patterned Arrays (Science 2025) [paper] [中文解读] [code] [ask deepwiki]
[SToFM] [Spatial] SToFM: A Multi-scale Foundation Model for Spatial Transcriptomics (ICML 2025 Poster) [paper] [中文解读] [code] [ask deepwiki]
[NicheFlow] [Spatial] Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow (NeurIPS 2025) [paper] [code]
[scGPT-spatial] [Spatial] scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics (bioRxiv 2025) [paper] [code]
[SpatialAgent] [Agent] SpatialAgent: An Autonomous AI Agent for Spatial Biology (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[CellFlux] [Morphology] CellFlux: Simulating Cellular Morphology Changes via Flow Matching (ICML 2025 Poster) [paper] [code] [ask deepwiki]
[CellCLIP] [Morphology] CellCLIP: Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning (NeurIPS 2025) [paper] [code]
[CELTIC] [Morphology] Cell context-dependent in silico organelle localization in label-free microscopy images (Nature Methods 2025) [paper] [code]
[MorphoDiff] [Morphology] MorphoDiff: Cellular Morphology Painting with Diffusion Models (ICLR 2025) [paper] [preprint] [code]
[PRESCRIBE] [Perturbation] PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation (NeurIPS 2025 Poster) [paper]
[GDE] [Related] Generative Distribution Embeddings: Lifting Autoencoders to the Space of Distributions for Multiscale Representation Learning (NeurIPS 2025 Poster) [paper] [preprint]
[CellPB] [Benchmark] Benchmarking AI Models for in Silico Gene Perturbation of Cells (bioRxiv 2025) [paper] [code] [ask deepwiki]
[PerturBench] [Benchmark] Benchmarking Machine Learning Models for Cellular Perturbation Analysis (NeurIPS 2025 Datasets and Benchmarks Track) [paper] [code]
[CellForge] [Agent] CellForge: Agentic Design of Virtual Cell Models (arXiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[Cradle-VAE] [Perturbation] Cradle-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement (AAAI 2025) [paper] [code] [code]
[XTransferCDR] [Perturbation] Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses (AAAI 2025) [paper] [code]
[Brief Communication] [Benchmark] Deep-Learning-Based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines (Nature Methods 2025) [paper] [code] [ask deepwiki]
[Brief Communication] [Benchmark] Limitations of Cell Embedding Metrics Assessed Using Drifting Islands (Nature Biotechnology 2025) [paper] [code] [ask deepwiki]
[GeneAgent] [Agent] GeneAgent: Self-Verification Language Agent for Gene-Set Analysis Using Domain Databases (Nature Methods 2025) [paper] [code] [ask deepwiki]
[Theory] [Virtual Cell] Human Interpretable Grammar Encodes Multicellular Systems Biology Models to Democratize Virtual Cell Laboratories (Cell 2025) [paper] [code] [ask deepwiki]
[GREmLN] [Foundation Model] GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[CellVoyager] [Agent] CellVoyager: AI CompBio Agent Generates New Insights by Autonomously Analyzing Biological Data (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[CausCell] [Perturbation] Causal Disentanglement for Single-Cell Representations and Controllable Counterfactual Generation (Nature Communications 2025) [paper] [中文解读] [code] [ask deepwiki]
[CLIP^n] [Morphology] Transitive Prediction of Small-Molecule Function through Alignment of High-Content Screening Resources (Nature Biotechnology 2025) [paper] [code] [ask deepwiki]
[DrugPT] [Perturbation] DrugPT: A Flexible Framework for Integrating Gene and Chemical Representations in Perturbation Modeling (bioRxiv 2025) [paper]
[OmniPert] [Perturbation] OmniPert: A Deep Learning Foundation Model for Predicting Responses to Genetic and Chemical Perturbations in Single Cancer Cells (bioRxiv 2025) [paper]
[UNAGI] [Perturbation] A Deep Generative Model for Deciphering Cellular Dynamics and in Silico Drug Discovery in Complex Diseases (Nature Biomedical Engineering 2025) [paper] [code] [ask deepwiki]
[OmiCLIP] [Spatial] A Visual-Omics Foundation Model to Bridge Histopathology with Spatial Transcriptomics (Nature Methods 2025) [paper] [code] [ask deepwiki]
[Biomni] [Agent] Biomni: A General-Purpose Biomedical AI Agent (bioRxiv 2025) [paper] [code] [ask deepwiki]
[OCTO-vc] [Virtual Cell] OCTO-vc: Virtual Cells in Real Tissue (© by Noetik 2025) [technical report] [online demonstration]
[STATE] [Perturbation] Predicting Cellular Responses to Perturbation across Diverse Contexts with STATE (bioRxiv 2025) [paper] [code] [ask deepwiki]
[UniPert-G2CP] [Perturbation] Genetic-To-Chemical Perturbation Transfer Learning through Unified Multimodal Molecular Representations (bioRxiv 2025) [paper] [code] [ask deepwiki]
[UniCure] [Perturbation] Unicure: A Foundation Model for Predicting Personalized Cancer Therapy Response (bioRxiv 2025) [paper] [code] [ask deepwiki]
[Cell-GraphCompass] [Foundation Model] Cell-GraphCompass: Modeling Single Cells with Graph Structure Foundation Model (National Science Review 2025) [paper] [code] [ask deepwiki]
[scPRINT] [Foundation Model] scPRINT: Pre-training on 50 Million Cells Allows Robust Gene Network Predictions (Nature Communications 2025) [paper] [code] [ask deepwiki]
[CellFM] [Foundation Model] CellFM: A Large-Scale Foundation Model Pre-trained on Transcriptomics of 100 Million Human Cells (Nature Communications 2025) [paper] [中文解读] [code] [ask deepwiki]
[C2S-Scale] [Foundation Model] C2S-Scale: Scaling Large Language Models for Next-Generation Single-Cell Analysis (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[scNET] [Foundation Model] scNET: Learning Context-Specific Gene and Cell Embeddings by Integrating Single-Cell Gene Expression Data with Protein-Protein Interactions (Nature Methods 2025) [paper] [code] [ask deepwiki]
[ProCyon] [Foundation Model] ProCyon: A multimodal foundation model for protein phenotypes (bioRxiv) [paper] [project] [code]
[SubCell] [Foundation Model] SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology (bioRxiv 2025) [paper] [code] [ask deepwiki]
[Token-Mol 1.0] [Related] Token-Mol 1.0: Tokenized Drug Design with Large Language Models (Nature Communications 2025) [paper] [code] [ask deepwiki]
[Comment] [Virtual Cell] Virtual Cells for Predictive Immunotherapy (Nature Biotechnology Comment 2025) [paper]
[Recursion] [Virtual Cell] Virtual Cells: Predict, Explain, Discover (arXiv 2025) [paper]

2024

[Zero-Shot Perturbation] [Perturbation] Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction (arXiv 2024) [paper]
[Cell Maps] [Virtual Cell] Multimodal cell maps as a foundation for structural and functional genomics (Nature 2025) [paper] [project]
[CellFlow] [Morphology] CellFlow Enables Generative Single-Cell Phenotype Modeling with Flow Matching (bioRxiv 2025) [paper] [code] [ask deepwiki]
[Cell Shapes] [Morphology] Cell shapes decode molecular phenotypes in image-based spatial proteomics (bioRxiv 2025) [paper]
[Prophet] [Perturbation] Scalable and Universal Prediction of Cellular Phenotypes (bioRxiv 2025) [paper] [code] [ask deepwiki]
[Morphology] Evaluating Feature Extraction in Ovarian Cancer Cell Line Co-Cultures Using Deep Neural Networks (Communications Biology 2025) [paper]
[ProteinTalks] [Foundation Model] A Perturbation Proteomics-Based Foundation Model for Virtual Cell Construction (bioRxiv 2025) [paper] [中文解读] [code] [ask deepwiki]
[Virtual Cell] Grow AI Virtual Cells: Three Data Pillars and Closed-Loop Learning (Cell Research 2025) [paper] [中文解读]
[Virtual Cell] Build the Virtual Cell with Artificial Intelligence: A Perspective for Cancer Research (Military Medical Research 2025) [paper]
[PS] [Perturbation] Decoding Heterogeneous Single-Cell Perturbation Responses (Nature Cell Biology 2025) [paper] [code] [ask deepwiki]
[Mixscale] [Perturbation] Systematic Reconstruction of Molecular Pathway Signatures Using Scalable Single-Cell Perturbation Screens (Nature Cell Biology 2025) [paper] [code] [ask deepwiki]
[scDrugMap] [Benchmark] scDrugMap: benchmarking large foundation models for drug response prediction (Nature Communications 2025) [paper]
[VCC Commentary] [Benchmark] Virtual Cell Challenge: Toward a Turing Test for the Virtual Cell (Cell Commentary 2025) [paper] [homepage] [beginner's guidance]
[CZI Evaluation] [Benchmark] Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop (arXiv 2025) [paper] [中文解读]
[Virtual Organs] [Benchmark] From Virtual Cell Challenge to Virtual Organs: Navigating the Deep Waters of Medical AI Models (iCell 2025) [paper]
[GET] [Foundation Model] A Foundation Model of Transcription across Human Cell Types (Nature 2025) [paper] [code] [ask deepwiki]

2024

[TranSiGen] [Perturbation] Deep Representation Learning of Chemical-Induced Transcriptional Profile for Phenotype-Based Drug Discovery (Nature Communications 2024) [paper] [code] [ask deepwiki]
[PRnet] [Perturbation] Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery (Nature Communications 2024) [paper]
[GenePT] [Foundation Model] Simple and Effective Embedding Model for Single-Cell Biology Built from ChatGPT (Nature Biomedical Engineering 2024) [paper] [code] [ask deepwiki]
[SCimilarity] [Foundation Model] A Cell Atlas Foundation Model for Scalable Search of Similar Human Cells (Nature 2024) [paper] [code] [ask deepwiki]
[scLong] [Foundation Model] scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics (bioRxiv 2024) [paper] [code] [ask deepwiki]
[scFoundation] [Foundation Model] Large-Scale Foundation Model on Single-Cell Transcriptomics (Nature Methods 2024) [paper] [code] [ask deepwiki]
[scGPT] [Foundation Model] scGPT: Toward Building a Foundation Model for Single-Cell Multi-Omics Using Generative AI (Nature Methods 2024) [paper] [code] [ask deepwiki]
[TamGen] [Related] TamGen: Drug Design with Target-Aware Molecule Generation through a Chemical Language Model (Nature Communications 2024) [paper] [code] [ask deepwiki]
[GeneCompass] [Foundation Model] GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with a Knowledge-Informed Cross-Species Foundation Model (Cell Research 2024) [paper] [code] [ask deepwiki]
[scTab] [Foundation Model] scTab: Scaling Cross-Tissue Single-Cell Annotation Models (Nature Communications 2024) [paper] [code] [ask deepwiki]
[SATURN] [Foundation Model] Toward Universal Cell Embeddings: Integrating Single-Cell RNA-Seq Datasets across Species with SATURN (Nature Methods 2024) [paper] [code] [ask deepwiki]
[UCE] [Foundation Model] Universal Cell Embeddings: A Foundation Model for Cell Biology (bioRxiv 2024) [paper] [code] [ask deepwiki]
[Cell2Sentence] [Foundation Model] Cell2Sentence: Teaching Large Language Models the Language of Biology (ICML 2024 Poster) [paper] [code] [ask deepwiki]
[LangCell] [Foundation Model] LangCell: Language-Cell Pre-training for Cell Identity Understanding (ICML 2024 Poster) [paper] [code] [ask deepwiki]
[CellPLM] [Foundation Model] CellPLM: Pre-training of Cell Language Model beyond Single Cells (ICLR 2024 Poster) [paper] [code] [ask deepwiki]
[Stanford PhD Thesis] [Virtual Cell] Engineering Cells Using Artificial Intelligence (© by Yusuf Roohani 2024) [paper] [GitHub Homepage] [Arc profile]

Datasets

Perturbation and Cell-State Atlases

[Arc Virtual Cell Atlas] Large-scale perturbation atlas and codebase from Arc Institute [resource] [repo]
[Tahoe-100M] Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling (bioRxiv 2025) [paper] [code]
[X-Atlas/Orion] Genome-Wide Perturb-Seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models (bioRxiv 2025) [paper] [dataset]
[scPerturb] scPerturb: Harmonized Single-Cell Perturbation Data (Nature Methods 2024) [paper] [dataset] [code]
[CIGS] High-Throughput Profiling of Chemical-Induced Gene Expression across 93,644 Perturbations (Nature Methods 2025) [paper] [dataset] [code]
[L1000/CMap] A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles (Cell 2017) [paper] [dataset]
[Sci-Plex] Massively Multiplex Chemical Transcriptomics at Single-Cell Resolution (Science 2019) [paper] [dataset] [code]
[Perturb-seq datasets] Genome-scale and combinatorial Perturb-seq datasets from Replogle, Norman, Dixit, Adamson, and related screens [overview]
[Virtual Cell Challenge] Community perturbation-prediction challenge and hidden evaluation resources [homepage]

Single-Cell Reference Atlases

[scBaseCount] scBaseCount: An AI Agent-Curated, Uniformly Processed, and Continually Expanding Single Cell Data Repository (bioRxiv 2025) [paper] [code-scRecounter] [code-SRAgent]
[CZ CELLxGENE Discover] A single-cell data platform for scalable exploration, analysis, and modeling of aggregated data (NAR 2025) [paper] [dataset]
[Human Cell Atlas] International atlas of human cells and tissues [portal] [paper]
[Tabula Sapiens] A multiple-organ single-cell transcriptomic atlas of humans (Science 2022) [paper] [dataset]
[Human BioMolecular Atlas Program] HuBMAP healthy human tissue atlas and common coordinate framework [portal] [paper]
[GTEx] Genotype-Tissue Expression project for human tissue expression baselines [portal] [overview]

Multimodal, Morphology, and Imaging

[scGeneScope] scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling (NeurIPS 2025 Datasets and Benchmarks Track) [paper] [dataset]
[CPJUMP1] Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations (Nature Methods 2024) [paper] [dataset] [code]
[Cell Painting Gallery] Public high-content cell painting datasets from Broad and partners [dataset] [overview]
[RxRx] Recursion high-content cellular imaging datasets for perturbation and batch-correction research [datasets]
[CM4AI] Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines (bioRxiv 2024) [paper] [dataset]
[STAMP] Single-cell transcriptomics analysis and multimodal profiling through imaging (Cell 2025) [paper]

Spatial and Tissue Context

[HEST-1k] HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis (NeurIPS 2024) [paper] [code]
[Spatial Perturb-seq] Spatial perturb-seq data for functional genomics within intact tissue architecture (Nature Communications 2026) [paper] [code]
[Perturb-FISH] CRISPR screening with imaging-based spatial transcriptomics (Cell 2025) [paper]
[10x Genomics spatial datasets] Visium, Xenium, and related public spatial transcriptomics example datasets [datasets]
[Vizgen MERFISH datasets] Public MERFISH example datasets for spatial transcriptomics [datasets]

Protein, Organelle, and Molecular Priors

[Human Protein Atlas] Subcellular and tissue protein expression atlases [resource] [subcellular] [paper]
[OpenCell] Endogenous protein tagging, localization, and interaction data for human cellular organization (Science 2022) [paper] [dataset]
[ProtiCelli] Proteome-wide image generation resources for human cell protein localization (bioRxiv 2026) [paper] [code]
[SubCell] Proteome-aware microscopy foundation model resources based on HPA images (bioRxiv 2025) [paper] [code]
[STRING] Protein functional association and interaction networks [resource] [paper]
[OmniPath] Signaling, ligand-receptor, and causal network priors for multi-omics analysis [resource] [paper]

Chemical, Drug, and Target Resources

[Drug Repurposing Hub] Curated compound library with targets, mechanisms, and clinical annotations (Nature Medicine 2017) [paper] [resource]
[DepMap/CCLE/PRISM] Cancer dependency, molecular profile, and drug-response resources for cell-line perturbation modeling [resource] [paper]
[ChEMBL] Drug-like molecules, bioactivities, targets, and assays [resource] [paper]
[BindingDB] Protein-small molecule binding affinity knowledgebase [resource] [paper]
[PubChem] Compound identifiers, structures, assays, and bioactivity records [resource] [paper]

Reports and Blogs

[Post] Chan Zuckerberg Initiative's rBio Uses Virtual Cells to Train AI, Bypassing Lab Work (© by Michael Nuñez 2025) [blog]
[Blog] What Are Virtual Cells? Learning "Universal Representations" of Life's Fundamental Unit (© by Elliot Hershberg 2025) [blog]

Videos

[Arc Institute] Predicting Cellular Responses to Perturbation across Diverse Contexts with STATE [YouTube]
[Valence Labs] Virtual Cells: Predict, Explain, Discover [YouTube]
[EPFL] Virtual Cells and Digital Twins: AI in Personalized Medicine [YouTube]
[SciLifeLab] Emma Lundberg: AI Virtual Cells Could Revolutionize Biological Science [YouTube]
[Chan Zuckerberg Initiative] AI Virtual Cell Models: How AI is Accelerating Science [YouTube]
[Chan Zuckerberg Initiative] CZI's Vision for AI-Powered "Virtual Cells" [YouTube]
[Podcast] Google DeepMind CEO: We Want to Build a Virtual Cell [YouTube]

Historical and Foundational Works

[HPA Cell Atlas] [Morphology] A subcellular map of the human proteome (Science 2017) [paper] [resource]
[OpenCell] [Morphology] OpenCell: Endogenous tagging for the cartography of human cellular organization (Science 2022) [paper] [dataset]
[Perturb-seq] [Perturbation] Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq (Cell 2022) [paper] [code]
[GEARS] [Perturbation] Predicting transcriptional outcomes of novel multigene perturbations with GEARS (Nature Biotechnology 2023) [paper] [code] [ask deepwiki]
[Geneformer] [Foundation Model] Transfer Learning Enables Predictions in Network Biology (Nature 2023) [paper] [code] [ask deepwiki]
[CellOT] [Perturbation] Learning Single-Cell Perturbation Responses Using Neural Optimal Transport (Nature Methods 2023) [paper] [code] [ask deepwiki]
[tGPT] [Foundation Model] Generative Pretraining from Large-Scale Transcriptomes for Single-Cell Deciphering (iScience 2023) [paper] [code] [ask deepwiki]
[Virtual Cell] Building the Next Generation of Virtual Cells to Understand Cellular Biology (Biophysical Journal 2023) [paper]
[Research Highlight] [Virtual Cell] Simulating a Whole Cell (Nature Methods 2022) [paper]
[Comment] Personalized Medicine: Time for One-Person Trials (Nature Comment 2015) [paper]
[Theory] [Virtual Cell] A Whole-Cell Computational Model Predicts Phenotype from Genotype (Cell 2012) [paper]
[Virtual Cell] The Virtual Cell - A Candidate Co-Ordinator for "Middle-Out" Modelling of Biological Systems (BIB 2009) [paper]
[VCell 7.7] [Virtual Cell] Virtual Cell Modelling and Simulation Software Environment (IET Systems Biology 2008) [paper] [software]
Quantitative Cell Biology with the Virtual Cell (Trends in Cell Biology 2003) [paper]
[Review] The Virtual Cell: A Software Environment for Computational Cell Biology (Trends in Biotechnology 2001) [paper]
[Opinion] Whole-Cell Simulation: A Grand Challenge of the 21st Century (Trends in Biotechnology 2001) [paper]

Related Resources

[Virtual Cell Challenge] Official challenge site for evaluation and community updates [homepage]
[Arc Virtual Cell Atlas] Large-scale perturbation atlas and codebase from Arc Institute [repo]
[VCell Software] Long-running software environment for computational cell biology [site]
[Noetik OCTO-vc] Technical report and demo for virtual cells in tissue [report] [demo]

Contributing

If you want to suggest a paper, dataset, benchmark, blog, or project, open an Issue or Pull Request. Please follow CONTRIBUTING.md for the submission format and quality bar.

Name		Name	Last commit message	Last commit date
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.github/workflows		.github/workflows
Awesome-Scientific-Figures		Awesome-Scientific-Figures
config		config
docs		docs
scripts		scripts
skills		skills
tests		tests
CONTRIBUTING.md		CONTRIBUTING.md
README.md		README.md
auto_update_summary.md		auto_update_summary.md

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Awesome Virtual Cell

Contents

Scope

Inclusion Rules

Overview Papers

Research Papers

2026

2025

2024

2024