Resource library — FMs to Virtual Cells¶
Every paper, tool, org, dataset, event, and signal we've collected on the foundation-models-to-virtual-cells story — papers we've read, models named in passing, labs to watch, money moves, competitions, perspectives. Use the filters to slice by kind, topic, status, org-type, or region.
This is the FM-to-virtual-cells resource library — a landscape monitor, not a citation graph. It catalogues every paper, tool, lab, dataset, event, competition, blog, and signal we've collected, including items that are still just a name with a slide-trail attached. For the citable subgraph with relations and layout, see the paper map; for the methods next door see adjacent methods; for the one-line model index see the model glossary.
How filtering works. Each card carries faceted tags (kind / status / org / region / topic). Click any chip in the filter bar to narrow. Multiple chips in the same row are OR; rows AND together. The search box matches across name, authors, venue, and the why-it-matters line.
Source of truth. Everything here is generated from data/resource-library/fm-to-virtual-cells.yaml by scripts/resource_library_build.py. Add an item to the YAML, rerun the build, and it lands on the page with its tags wired up. The YAML is also the export point for papermap: items with kind: paper and papermap_category: set are export-eligible.
Kindbenchmarkcommentarycompetitiondataseteventmoveorgpaperpersonreviewtool
Statusannouncedfundedlaunchedname-onlypreprintpublishedrumored
Orgacademicbiotechconsortiumfoundationgov-labindustryoutlet
RegionCNEUKRUKUSglobal
Topic4d-modelingRLagentsbenchmarkcausalclinicalcompetitiondiffusiondigital-twindrug-designevalflow-matchingfoundation-modelgenerativegenomicimaginginterpretabilitylineagemass-specmech-modelingmultimodalpathologyperturb-seqperturbation-predictionproteinproteomicsscaling-lawssignalingsingle-cellspatialstate-spacevirtual-cell
Showing 277 of 277
The canonical virtual-cell thesis — the goal everything else chases.
paperpublishedacademicUSvirtual-cellfoundation-modelpapermap: position
The future of automated single-cell analysis
Regev's reference-mapping framing of the same ambition.
paperpublishedacademicUSsingle-cellfoundation-modelpapermap: position
From modality-specific to compositional foundation models
Post-reckoning forward path — stop scaling monoliths.
paperpublishedacademicEUfoundation-modelvirtual-cellpapermap: position
Virtual Cell Challenge — a Turing test for the virtual cell
What success is supposed to look like, operationalised.
paperpublishedfoundationUSvirtual-cellevalpapermap: position
Generalist biological AI — modeling the language of life
Position paper unifying the five FM families.
paperpublishedindustryUSfoundation-modelmultimodalpapermap: position
Agentic AI and in silico team science
Position paper behind the agentic-FM intersection.
paperpublishedacademicUSagentsfoundation-modelpapermap: position
Single-cell foundation models — bringing AI into cell biology
Clean mid-2025 review — the orientation read.
reviewpublishedacademicKRsingle-cellfoundation-modelpapermap: position
Revisiting the blueprint for an interpretable virtual cell
Nature Reviews framing piece on what an interpretable virtual cell would even look like.
reviewpublishedoutletglobalvirtual-cellinterpretability
via _Temp/new_paper.md
Grow AI virtual cells — three data pillars and closed-loop learning
Editorial framing closed-loop learning as the missing ingredient.
blog/newspublishedoutletglobalvirtual-cellfoundation-model
via _Temp/new_paper.md
From equations to agents — the AI virtual cell reshaping precision oncology
Clinical-oncology framing of the AIVC story.
blog/newspublishedoutletCNvirtual-cellagentsclinical
via _Temp/new_paper.md
Minimal life by computer
Framing piece on minimal-cell simulation as the AIVC counterpoint.
blog/newspublishedoutletglobalvirtual-cellmech-modeling
via _Temp/new_paper.md
Ubiquitin Rides Again — comments on the virtual cell
Pharma chemist's sceptical-pragmatist read on AIVC claims.
blog/newspublishedoutletUSvirtual-cell
via _Temp/new_paper.md
AI virtual cell — review
Mandarin-sphere review of the AIVC landscape.
reviewpublishedacademicCNvirtual-cellfoundation-model
via _Temp/new_paper.md
Human-interpretable grammar encodes multicellular systems biology
Argues for an interpretable grammar layer to democratise virtual-cell labs.
paperpreprintacademicglobalvirtual-cellinterpretabilitymech-modeling
via _Temp/new_paper.md
Cellular Intelligence — Engineering Cell Fate, towards a foundation model for cell signaling
Reframes virtual cells as signaling-FMs rather than transcriptome-FMs.
paperpreprintacademicglobalsignalingfoundation-modelvirtual-cell
via _Temp/new_paper.md
scBERT
BERT-style precursor that pre-dated the 2023 sc-FM wave.
toolpublishedacademicCNsingle-cellfoundation-modelpapermap: scfm
scGPT
Defined the category — genes + cells as tokens. The reckoning's main target.
toolpublishedacademicUSsingle-cellfoundation-modelperturbation-predictionpapermap: scfm
Geneformer / Geneformer V2
First atlas-pretrained transformer; rank-based tokenisation. V2 (Dec 2024) matched 316M at ⅓ the compute.
toolpublishedacademicUSsingle-cellfoundation-modelpapermap: scfm
Universal Cell Embedding (UCE)
Cross-species sc-FM — bridges through ESM2 protein embeddings (8 species).
toolpublishedacademicUSsingle-cellfoundation-modelpapermap: scfm
scFoundation
Read-depth-aware attention; one of the four reckoning regulars.
toolpublishedbiotechCNsingle-cellfoundation-modelperturbation-predictionpapermap: scfm
CellPLM
Cell-as-token sc-FM; beats scGPT/Geneformer on cell-typing cheaply.
toolpublishedacademicUSsingle-cellfoundation-modelpapermap: scfm
STATE (Arc Institute)
First production virtual cell at Tahoe-100M scale.
toolpreprintfoundationUSsingle-cellvirtual-cellperturbation-predictionpapermap: scfm
TranscriptFormer
First generative cross-species sc-FM; CZ Biohub flagship (112M cells, 12 species).
toolpublishedfoundationUSsingle-cellfoundation-modelpapermap: scfm
Nicheformer
Spatial-omics sc-FM with a niche-aware objective.
toolpublishedacademicEUsingle-cellspatialfoundation-modelpapermap: scfm
scMulan
Multitask single-cell language model; benchmarked in CellBench-LS.
toolpublishedacademicCNsingle-cellfoundation-model
GenePT / scELMo
NOT trained sc-FMs — frozen LLM embeddings of gene names + LR head (~$200) matching scGPT zero-shot.
toolpublishedacademicUSsingle-cellfoundation-model
CellFM
Another sc-FM from the 2025 wave.
toolpublishedacademicCNsingle-cellfoundation-model
scPRINT
50M-cell pretraining aimed at robust zero-shot gene-network inference.
toolpublishedacademicEUsingle-cellfoundation-model
scPRINT-2
Next-gen cell FM AND benchmark suite in one preprint.
toolpreprintacademicEUsingle-cellfoundation-modeleval
xVERSE — transcriptomics-native sc-FM
First evidence the architectural choice is load-bearing (+17.9% over LM-derived sc-FMs).
toolpreprintacademicUSsingle-cellfoundation-modelperturbation-predictionpapermap: arch_response
The reckoning answering itself — Wenkel co-authored both critique and response.
toolpublishedacademicEUperturbation-predictionfoundation-modelpapermap: arch_response
Zero-shot perturbation prediction for unprofiled drugs.
toolpreprintacademicglobalperturbation-predictiondrug-designpapermap: arch_response
Earliest 'linear baselines are competitive' warning
First warning shot — read it to see how early the signal was.
paperpublishedacademicUSevalsingle-cellfoundation-modelpapermap: reckoning
Showed the original scGPT split was leaky.
paperpreprintacademicEUevalperturbation-predictionpapermap: reckoning
THE canonical reckoning paper — start here.
paperpublishedacademicEUevalperturbation-predictionfoundation-modelpapermap: reckoning
Extends the result to UCE and the zero-shot setting.
paperpublishedacademicUSevalfoundation-modelsingle-cellpapermap: reckoning
Proposed the stronger baseline current FMs still don't beat.
paperpublishedacademicEUevalperturbation-predictionpapermap: reckoning
First axis-by-axis failure decomposition.
paperpublishedacademicCNevalfoundation-modelsingle-cellpapermap: reckoning
6 scFMs, cell-ontology-grounded metrics.
paperpublishedacademicCNevalfoundation-modelsingle-cellpapermap: reckoning
Strongest 'is the paradigm worth it' framing.
paperpublishedacademicUSevalfoundation-modelsingle-cellpapermap: reckoning
Cleanest post-reckoning headline; direct Ahlmann successor.
paperpreprintacademicglobalevalfoundation-modelpapermap: reckoning
Formal venue stamp on the perturbation critique.
paperpublishedacademicUSevalperturbation-predictionpapermap: reckoning
FMs lead cell-type ID; classical methods win gene-expression.
paperpreprintacademicglobalevalbenchmarksingle-cellpapermap: reckoning
Industry-authored — deployment-grade robustness gaps.
paperpreprintindustryUSevalsingle-cellclinicalpapermap: reckoning
Extends the critique to RNA-velocity / dynamics.
paperpreprintacademicglobalevalsingle-cellpapermap: reckoning
Contrarian voice — FMs DO improve with enough data.
paperpreprintacademicglobalperturbation-predictionfoundation-modelevalpapermap: contrarian_theory
Names the theory: a causal-transportability problem (Pearl).
paperpreprintacademicglobalvirtual-cellcausalfoundation-modelpapermap: contrarian_theory
Microsoft's metric for whether a multimodal FM extracts genuinely cross-modal information.
paperpreprintindustryUSevalmultimodalfoundation-modelpapermap: contrarian_theory
Protein-FM SAE paper that started the biology-FM interpretability wave.
paperpublishedacademicUSinterpretabilityproteinpapermap: interp
Mechanistic explanation of the reckoning, on Geneformer + scGPT.
paperpreprintacademicUSinterpretabilitysingle-cellfoundation-modelpapermap: interp
Independent confirmation on scGPT.
paperpreprintacademicglobalinterpretabilitysingle-cellpapermap: interp
Synthesis across families — the wave's summary read.
paperpreprintacademicglobalinterpretabilityfoundation-modelpapermap: interp
rBio — reasoning model trained on TranscriptFormer
Agent that REASONS OVER a virtual cell as a verifier.
toolpreprintfoundationUSagentsvirtual-cellfoundation-modelpapermap: agentic
VCHarness — autonomous virtual-cell builder
Agent that BUILDS virtual-cell models end to end.
toolpreprintbiotechUSagentsvirtual-cellfoundation-modelpapermap: agentic
CellVoyager — autonomous comp-bio agent
Agent that ANALYSES single-cell data with the FM as substrate.
toolpublishedacademicUSagentssingle-cellpapermap: agentic
MedAgentGym
Agentic environment / benchmark for training and evaluating medical AI agents.
toolpreprintacademicUSagentsclinicaleval
PathChat-DX
First generative-AI pathology tool with FDA Breakthrough Designation (Jan 2025).
toollaunchedacademicUSpathologyagentsclinicalmultimodal
Enformer
Pre-FM-era gene-expression-from-sequence model.
toolpublishedindustryUKgenomicfoundation-modelpapermap: other_fm
AlphaGenome
Variant-effect SOTA; replaces Enformer + Borzoi; 25/26 wins at 1-Mb context.
toolpublishedindustryUKgenomicfoundation-modelpapermap: other_fm
Evo 2
Only genomic FM with demonstrated in-context learning; 1M-token context, ~$5M training.
toolpublishedfoundationUSgenomicfoundation-modelgenerativepapermap: other_fm
Nucleotide Transformer
Early DNA FM pretrained across many genomes for variant and regulatory tasks.
toolpublishedbiotechEUgenomicfoundation-model
DNABERT-2
BPE-tokenised DNA FM; efficiency-focused DNABERT successor.
toolpublishedacademicUSgenomicfoundation-model
HyenaDNA
State-space (non-transformer) genomic FM for very long context at single-nucleotide resolution.
toolpublishedacademicUSgenomicfoundation-modelstate-space
Caduceus
Bidirectional, reverse-complement-equivariant state-space DNA FM.
toolpublishedacademicUSgenomicfoundation-modelstate-space
Borzoi
RNA-seq-coverage prediction model, Enformer successor — subsumed by AlphaGenome.
toolpublishedindustryUSgenomic
ESM-2 / ESMFold
Open protein LM; UCE's cross-species bridge; still the academic workhorse.
toolpublishedindustryUSproteinfoundation-modelpapermap: other_fm
ESM-3
98B-param multimodal protein FM; generated esmGFP de novo; cleanest compute disclosure.
toolpublishedbiotechUSproteinfoundation-modelmultimodalgenerativepapermap: other_fm
AlphaFold 3
Structure prediction extended to complexes (proteins + nucleic acids + ions + ligands).
toolpublishedindustryUKproteingenerativedrug-designpapermap: other_fm
Proteina / Proteina Complexa
Generative protein-design FMs; Complexa reports 63.5% wet-lab hit on PDGFR binders.
toolpreprintindustryUSproteingenerativedrug-design
UNI
Original Mahmood-lab pathology tile encoder.
toolpublishedacademicUSpathologyfoundation-modelmultimodalpapermap: other_fm
UNI2-h
Mahmood-stack flagship tile encoder (681M); HF-gated since Jan 2025.
toollaunchedacademicUSpathologyfoundation-model
Current pathology-FM SOTA and most hardware-transparent; 632M ViT-H/14 on ~2B tiles / ~225k patients.
toolpublishedbiotechUSpathologyfoundation-modelpapermap: other_fm
CHIEF
Pathology FM for cancer detection and prognosis across tissue types.
toolpublishedacademicUSpathologyfoundation-modelclinical
Prov-GigaPath
Whole-slide pathology FM trained on real-world clinical slides.
toolpublishedindustryUSpathologyfoundation-modelclinical
Phikon / Phikon-v2
Owkin's pathology FMs; notable as Apache-2.0 exceptions in a license-restrictive family.
toollaunchedbiotechEUpathologyfoundation-model
H-optimus-0
Open-weights pathology tile encoder; permissive-license exception.
toollaunchedbiotechEUpathologyfoundation-model
Hibou
Open pathology FM (Apache-2.0).
toollaunchedbiotechUSpathologyfoundation-model
CONCH
Contrastive vision-language pathology FM.
toolpublishedacademicUSpathologymultimodalfoundation-model
TITAN
Slide-level model on top of the UNI2-h tile encoder.
toolpublishedacademicUSpathologyfoundation-model
PathChat / PathChat-2 / PathChat-DX
Mahmood vision-language pathology assistant; DX got FDA Breakthrough.
toolpublishedacademicUSpathologyagentsmultimodalpapermap: other_fm
BioMedCLIP
Biomedical image–text contrastive model on large-scale figure–caption pairs.
toolpublishedindustryUSmultimodalimagingfoundation-model
Med-Gemini
Google's medical multimodal model family for clinical reasoning and image Q&A.
toolpublishedindustryUSmultimodalclinicalfoundation-model
Generative Virtual Cells
Workshop proof (<$250 compute) — joint planner + world model under validation gating.
paperpreprintacademicUSvirtual-cellgenerativefoundation-model
Flow matching in computational biology
The generative technique under generative virtual cells.
reviewpublishedacademicUSflow-matchinggenerativevirtual-cell
Structure-prediction breakthrough the whole protein-modelling wave builds on.
paperpublishedindustryUKproteingenerative
Diffusion-based de novo protein design exemplar.
paperpublishedacademicUSproteingenerativediffusiondrug-design
scDiffusion
Diffusion model for single-cell expression generation.
toolpreprintacademicglobalsingle-cellgenerativediffusion
CPA — Compositional Perturbation Autoencoder
Autoencoder baseline the reckoning repeatedly tests FMs against.
toolpublishedacademicEUperturbation-predictiongenerative
Graph-based perturbation-effect prediction with a gene-gene KG — the pre-FM SOTA.
toolpublishedacademicUSperturbation-prediction
PerturbFate
Perturbation screening mapping convergent regulators of melanoma drug resistance.
paperpublishedacademicUSperturb-seqdrug-designlineage
sc-FM Perturbation Adapter
Drug-conditional adapter (<1% trainable params) on a frozen FM — generalises where CPA/GEARS/scGen don't.
paperpreprintacademicUSperturbation-predictionfoundation-modeldrug-design
CINEMA-OT
Optimal-transport perturbation-effect disentanglement.
toolpublishedacademicUSperturbation-predictioncausal
Causal representation learning (Lopez/Hsu)
Causal-rep exemplar for pretraining objectives that target causality.
paperpublishedacademicUScausalsingle-cellperturbation-prediction
Replogle whole-genome Perturb-seq
Standard perturbation test set.
datasetpublishedacademicUSperturb-seqperturbation-prediction
Norman combinatorial Perturb-seq
Substrate for compositional-generalisation benchmarks.
datasetpublishedacademicUSperturb-seqperturbation-prediction
Community single-cell benchmark suite.
benchmarklaunchedconsortiumglobalevalsingle-cellbenchmark
Altos Labs perturbation-prediction benchmark.
benchmarklaunchedbiotechUKevalperturbation-prediction
Benchmark with adversarial perturbation/cell-type splits.
benchmarklaunchedacademicEUevalperturbation-prediction
First community virtual-cell benchmark, $50k prize.
competitionlaunchedfoundationUSvirtual-cellevalperturbation-prediction
Tahoe-100M
First large-scale perturbation atlas framed as virtual-cell training data.
datasetlaunchedbiotechUSperturb-seqvirtual-cell
Tabula Sapiens
Multi-organ human single-cell reference atlas.
datasetpublishedconsortiumUSsingle-cell
CELLxGENE Census
Aggregated single-cell corpus most sc-FMs pretrain on.
datasetlaunchedfoundationUSsingle-cellfoundation-model
HuBMAP
Human tissue / spatial reference atlas.
datasetpublishedconsortiumUSspatialimaging
HEST-1k
Histology-with-spatial-transcriptomics benchmark dataset.
datasetlaunchedacademicUSspatialpathologyimaging
CASP15 / CAPRI
Community structure- and complex-prediction assessments.
benchmarklaunchedconsortiumglobalproteineval
ProteinGym
Protein variant-effect benchmark.
benchmarkpublishedacademicUSproteineval
Compositional-generalisation benchmark (Hetzel et al.)
Compositional generalisation benchmark referenced in supplementary §C.3.
benchmarkpublishedacademicEUevalperturbation-prediction
Learning beyond fine-tuning
Landscape of model-adaptation paradigms past fine-tuning.
reviewpublishedacademicglobalfoundation-model
Concrete PEFT recipe for single-cell FMs (Lane 2).
paperpreprintacademicUSsingle-cellfoundation-model
Compute-optimal scaling law behind every 'under/over-trained?' judgement.
paperpreprintindustryUKscaling-laws
FLOPs ≈ 6 × params × tokens heuristic the talk's cost estimates use.
blog/newspublishedoutletglobalscaling-lawsfoundation-model
Economic backdrop for the compute-disclosure argument.
paperpreprintoutletglobalscaling-lawsfoundation-model
Genome language models
Review of transformer architectures for DNA.
reviewpublishedacademicglobalgenomicfoundation-model
Transformers vs state-space models
Transformer / recurrent / state-space crossroads.
reviewpublishedacademicglobalstate-spacefoundation-model
Protein-LM explainability
Review of interpretability methods for protein FMs.
reviewpublishedacademicEUinterpretabilityprotein
Invariant Risk Minimisation
Causal-objective method cited as basis for counterfactual pretraining.
paperpreprintindustryUScausalfoundation-model
Deep deterministic UQ
Uncertainty-quantification method for the clinical-grade-FM track.
paperpublishedacademicUKclinicaleval
Conformal prediction
Distribution-free uncertainty paired with the UQ track.
paperpublishedacademicUSevalclinical
Short framing commentary on the data-to-clinic gap.
blog/newspublishedacademicEUclinicalfoundation-model
Diffusion LM for perturbation — direct rival to State / scGPT-perturb framing.
paperpreprintacademicUSperturbation-predictiondiffusionfoundation-modelcausal
via _Temp/new_paper.md
CellFluxRL — Biologically-Constrained Virtual Cell Modeling via RL
RL-driven virtual-cell modelling with biological constraints — Stanford/CZI/Lundberg axis.
paperpreprintacademicUSvirtual-cellRLperturbation-prediction
via _Temp/new_paper.md
Lingshu-Cell — generative cellular world model for transcriptome modelling
Chinese-industry-led generative cellular world model for transcriptome.
paperpreprintindustryCNvirtual-cellgenerativefoundation-model
via _Temp/new_paper.md
SCALE — Scalable Conditional Atlas-Level Endpoint transport for virtual-cell perturbation
Optimal-transport / endpoint framing of perturbation prediction at atlas scale.
paperpreprintacademicglobalvirtual-cellperturbation-prediction
via _Temp/new_paper.md
VCBench
Named benchmark for virtual cells — details still being chased down.
benchmarkpreprintacademicglobalvirtual-cellevalbenchmark
via _Temp/new_paper.md
CZI / Biohub / Virtual Biology Initiative
The single largest philanthropic backer of the virtual-cell vision.
org/labannouncedfoundationUSvirtual-cellfoundation-model
via _Temp/new_paper.md
Jian Ma's Virtual Bio Center
New CMU center anchored around Jian Ma's lab as a US academic hub for virtual biology.
org/labannouncedacademicUSvirtual-cellsingle-cell
via _Temp/new_paper.md
ProtiCelli / ProtiCell
Proteomics-anchored virtual-cell project from the Lundberg lab — mostly a slide-trail.
toolname-onlyacademicUSproteomicsvirtual-cell
via _Temp/new_paper.md
CompuCell3D Virtual Tissue Modeling Workshop & Hackathon
The mech-modelling crowd's annual gathering — the parallel-universe to AIVC.
eventannouncedacademicUSvirtual-cellmech-modeling4d-modeling
via _Temp/new_paper.md
VCHarness (GenBio AI)
Genbio's autonomous virtual-cell builder agent — see the paper too.
toolpreprintbiotechUSagentsvirtual-cellfoundation-model
via _Temp/new_paper.md
IBS — Park Jong-eun (human digital twin)
Korean national lab investing in human-digital-twin programme around single-cell data.
org/labannouncedgov-labKRdigital-twinsingle-cellclinical
via _Temp/new_paper.md
PerturbHD
Stanford perturbation method — only a name so far.
toolname-onlyacademicUSperturbation-predictionperturb-seq
via _Temp/new_paper.md
AROMA
Tencent-flagged virtual-cell project — name only.
toolname-onlyindustryCNfoundation-modelvirtual-cell
via _Temp/new_paper.md
VCR-Agent
Virtual-cell reasoning agent — name only.
toolname-onlyacademicglobalagentsvirtual-cell
via _Temp/new_paper.md
T-World
Whispered T-World model — provenance unclear.
toolname-onlyacademicglobalvirtual-cellgenerative
via _Temp/new_paper.md
Flex v2
Broad's Flex v2 single-cell platform — currently a name.
toolname-onlyfoundationUSsingle-cellperturb-seq
via _Temp/new_paper.md
4DWCM — bringing the minimal cell to life on computer in 4D
UIUC 4D whole-cell model — the mech-modelling-meets-AIVC bridge.
paperpreprintacademicUSvirtual-cellmech-modeling4d-modeling
via _Temp/new_paper.md
Westlake Autumn Symposium — AIVC (Tiannan Guo)
Westlake's annual AIVC symposium — gathers the China AIVC scene.
eventannouncedacademicCNvirtual-cellproteomicsfoundation-model
via _Temp/new_paper.md
AlphaCell
AlphaCell — name only, watch for DeepMind/Isomorphic involvement.
toolname-onlyindustryglobalvirtual-cell
via _Temp/new_paper.md
AetherCell
AetherCell — name only.
toolname-onlybiotechglobalvirtual-cell
via _Temp/new_paper.md
Harmony Cell
Harmony Cell — name only.
toolname-onlybiotechglobalvirtual-cell
via _Temp/new_paper.md
Beyond Alignment — Synergistic Integration for Multimodal Cell FMs
Argues multimodal cell-FMs need synergistic (not just aligned) integration.
paperpreprintacademicglobalmultimodalfoundation-modelvirtual-cell
via _Temp/new_paper.md
Merck + Mayo Clinic collaboration
Feb 2026 collaboration — pharma + clinical data axis around AI models.
moveannouncedindustryUSclinicalfoundation-model
via _Temp/new_paper.md
AIVEVs — AI Virtual Extracellular Vesicles
EV-focused AIVC paper — small but exists.
paperpublishedacademicglobalvirtual-celldrug-design
via _Temp/new_paper.md
ProPer-seq
ProPer-seq assay — name only.
toolname-onlyacademicglobalperturb-seqsingle-cell
via _Temp/new_paper.md
Echoes of Silenced Genes — Myllia Biotechnology cell challenge
Biotech-run challenge focused on perturbation prediction.
competitionannouncedbiotechEUperturbation-predictionevalcompetition
via _Temp/new_paper.md
Noetik + GSK collaboration
Noetik (spatial-omics AIVC startup) lands a GSK deal.
moveannouncedbiotechUSclinicalspatialfoundation-model
via _Temp/new_paper.md
ConvergeCell
ConvergeCell — name only.
toolname-onlybiotechglobalvirtual-cell
via _Temp/new_paper.md
CellFluxV2
Successor to CellFluxRL — name only.
toolname-onlyacademicUSvirtual-cellperturbation-prediction
via _Temp/new_paper.md
Tahoe Therapeutics + Arc Institute + CZ Biohub collaboration
The big three of US AIVC join up around Tahoe-100M.
moveannouncedconsortiumUSvirtual-cellperturb-seq
via _Temp/new_paper.md
UCSD + DARPA virtual-cell programme
DARPA money flowing to UCSD for virtual-cell work.
moveannouncedgov-labUSvirtual-cellfoundation-model
via _Temp/new_paper.md
Cellular Intelligence — Engineering Cell Fate, towards a FM for cell signaling
Reframes virtual cells as signaling-FMs.
paperpreprintacademicglobalsignalingfoundation-modelvirtual-cell
via _Temp/new_paper.md
CellTRIP
CellTRIP — name only.
toolname-onlyacademicglobalsingle-cell
via _Temp/new_paper.md
GigaTime
GigaTime — name only.
toolname-onlyindustryglobalvirtual-cellgenerative
via _Temp/new_paper.md
Turbine raises $25M
Validates commercial market for VC-style perturbation simulators.
movefundedbiotechEUvirtual-cellperturbation-predictiondrug-design
via _Temp/new_paper.md
Amazon hires Stanford PhD on AIVC
Amazon signals AIVC entry — Stanford PhD hire.
moveannouncedindustryUSvirtual-cell
via _Temp/new_paper.md
AI Proteomics Competition (AIPC)
Westlake-run AI-proteomics challenge — bridges AIVC and mass-spec ML.
competitionannouncedacademicCNproteomicsevalmass-spec
via _Temp/new_paper.md
Virtual Cell Challenge 2025 — first round
The annual benchmark cycle whose 2025 launch crystallised the field.
eventlaunchedfoundationUSvirtual-cellevalcompetition
Virtual-embryo extension — integrating single-cell and spatial data into a developmental simulator.
paperpublishedacademicUSvirtual-cellspatiallineage
Virtual-organ agenda — personalised organ-scale simulation on real lungs.
paperpublishedacademicUSdigital-twinclinicalvirtual-cell
Spatial pathology FM aggregating ST + WSI signals.
toolpublishedacademicCNpathologyspatialmultimodalfoundation-model
Large-scale gigapixel pathology FM.
toolpublishedacademicCNpathologyfoundation-model
Pathology FM variant in the 2026 wave.
toolpublishedacademicglobalpathologyfoundation-model
Ensemble approach across pathology FMs.
toolpublishedacademicCNpathologyfoundation-model
PathChat-2
Successor instruction-tuned pathology assistant (>1M pairs).
toollaunchedacademicUSpathologymultimodalagents
First deployment-grade clinical FM paper (197 patients, 43% testing avoidance).
paperpublishedacademicUSpathologyclinical
Multi-task pathology benchmark for FM evaluation.
benchmarkpublishedacademicUSpathologyevalbenchmarkclinical
First genomic FM with demonstrated in-context learning (Evo2 successor).
toolpublishedfoundationUSgenomicfoundation-modelgenerative
Multimodal spatial-transcriptomics FM.
paperpreprintacademicglobalspatialmultimodalsingle-cellfoundation-model
Multimodal spatial-transcriptomics integration FM.
paperpreprintacademicglobalspatialmultimodal
Spatial + temporal context for cell language modelling.
paperpreprintacademicglobalspatialsingle-cellfoundation-model
Alternative transformer-based cell FM.
paperpublishedacademicCNsingle-cellfoundation-model
Cancer-domain-specific single-cell FM.
paperpreprintacademicglobalsingle-cellfoundation-modelclinical
LangCell / LangStem
LLM-based cell annotation tool.
toolpublishedacademicCNsingle-cellfoundation-model
GET — gene expression toolkit
sc-FM-based gene-expression analysis toolkit.
toollaunchedacademicglobalsingle-cellfoundation-model
In-browser sc-FM inference; pushes inference to where the data is.
toolpreprintacademicUSsingle-cellfoundation-model
CRADLE-VAE — compositional active learning
Closed-loop virtual-cell active learning prototype.
toolpreprintacademicUSperturbation-predictiongenerativevirtual-cell
scPoli — single-cell policy learning
Policy-based perturbation prediction; the scArches lineage.
toolpublishedacademicUKsingle-cellperturbation-prediction
Single-cell methodology reference framework underpinning much of the field.
toollaunchedacademicEUsingle-cell
scverse ecosystem (Scanpy / AnnData / squidpy / scvi-tools)
Community standards for single-cell Python tools.
toollaunchedconsortiumglobalsingle-cellspatial
signifinder — sc-FM wrapper for Bioconductor
Bioconductor interface to sc-FMs.
toollaunchedacademicEUsingle-cellfoundation-model
mia / miaTime / miaViz
Scverse-adjacent tools for single-cell analysis.
toollaunchedacademicEUsingle-cellspatial
SpatialData — unified spatial-omics data framework
Standard for spatial transcriptomics data representation.
toollaunchedacademicEUspatialsingle-cell
Graph FM bridging gene-level and patient-level AI.
paperpublishedacademicUSdrug-designfoundation-modelperturbation-prediction
Largest non-DeepMind compute (~2,048× H100); built STATE, Evo2, Tahoe-100M.
org/lablaunchedfoundationUSvirtual-cellfoundation-modelgenomic
Substrate + model shipper (TranscriptFormer, rBio); breaks substrate-only stereotype.
org/lablaunchedfoundationUSvirtual-cellfoundation-modelsingle-cell
Full pathology vertical stack: UNI → TITAN → CONCH → PathChat; PathChat-DX FDA Breakthrough.
org/lablaunchedacademicUSpathologymultimodalfoundation-model
Only sc-FM lab with full compute disclosure (NVIDIA BioNeMo).
org/lablaunchedacademicUSsingle-cellfoundation-model
Defined the sc-FM category (scGPT); agentic-AI pivot 2026 (X-Cell).
org/lablaunchedacademicUSsingle-cellfoundation-modelperturbation-prediction
Cross-species sc-FM (UCE) — 8 species via ESM2 bridge.
org/lablaunchedacademicUSsingle-cellfoundation-model
TPU-scale; closed weights + hosted API; Isomorphic Labs is the commercial arm.
org/lablaunchedindustryUKgenomicproteinfoundation-model
ESM-3 with the cleanest compute disclosure (10²⁴ FLOPs) in biology FMs.
org/lablaunchedbiotechUSproteinfoundation-model
First FDA 510(k)-cleared general-purpose pathology AI (Jan 2025); Virchow line.
org/lablaunchedbiotechUSpathologyfoundation-modelclinical
Only major industrial pathology player shipping open weights (Phikon, Apache-2.0).
org/lablaunchedbiotechEUpathologyclinicalfoundation-model
Sets compute-disclosure norm; co-marketed with Geneformer V2.
toollaunchedindustryUSfoundation-modelscaling-laws
Authored the 2025 reckoning paper; Ahlmann-Eltze now at Isomorphic Labs.
org/lablaunchedacademicEUevalsingle-cell
Methodological reference class; author of 2026 compositional-FM perspective.
org/lablaunchedacademicEUsingle-cellfoundation-modelspatial
BioMap Research + MBZUAI
China/Middle-East virtual-cell competitor (VCHarness, xTrimo).
org/lablaunchedindustryCNvirtual-cellfoundation-modelagents
Isomorphic Labs
DeepMind's commercial drug-discovery arm; bought Ahlmann-Eltze.
org/lablaunchedindustryUKdrug-designproteinfoundation-model
AI-native biotech using FMs for drug discovery.
org/lablaunchedbiotechUSimagingdrug-designfoundation-model
Applied virtual-cell case study in drug discovery.
org/lablaunchedbiotechUSdrug-designvirtual-cell
DeepMind-alumni virtual-cell startup.
org/lablaunchedbiotechUKvirtual-cellfoundation-model
Vevo / Arc
Tahoe-100M producer — virtual-cell modelling platform.
org/lablaunchedbiotechUSvirtual-cellperturb-seq
Cellarity
Cell-state engineering company.
org/lablaunchedbiotechUSdrug-designsingle-cell
BenchSci
Life-science research platform — biology-paper search agent.
toollaunchedbiotechUSagents
Tempus AI
Multimodal clinical AI; IPO June 2024.
org/lablaunchedbiotechUSmultimodalclinical
Aignostics
AI pathology vendor.
org/lablaunchedbiotechEUpathologyclinical
Proscia
Digital pathology platform.
org/lablaunchedbiotechUSpathologyclinical
Modella AI
Acquired by AstraZeneca for pathology FM stack (JPM 2026).
org/labannouncedbiotechUSpathologyfoundation-model
Roche Tissue Diagnostics
Pharma pathology AI division.
org/lablaunchedindustryEUpathologyclinical
JPM 2026 — Lilly + NVIDIA $1B AI Co-Innovation Lab
Largest pharma–AI infrastructure commitment, JPM Day 1.
moveannouncedindustryUSfoundation-modeldrug-designclinical
JPM 2026 — AstraZeneca acquires Modella AI
First big-pharma acquisition of an AI-FM firm.
moveannouncedindustryUSpathologyfoundation-model
PathChat-DX FDA Breakthrough Designation
First generative-AI pathology tool to win FDA Breakthrough.
moveannouncedacademicUSpathologyagentsclinical
Multi-billion-dollar non-dilutive commitment to virtual cells.
eventlaunchedfoundationUSvirtual-cellfoundation-model
Community benchmark with $50k prize; first formal VC evaluation.
eventlaunchedfoundationUSvirtual-cellevalcompetition
Eleven grand challenges in single-cell data science
Pre-FM landscape framing — what needed solving before the wave hit.
reviewpublishedacademicEUsingle-cell
AI builds models of biology
Accessible field overview.
blog/newspublishedoutletglobalfoundation-model
Sukumaran et al. — clinical-decision-support evaluation
Framework for clinical AI evaluation.
paperpublishedacademicUSclinicaleval
Long-form bio+ML essays — one of the better field-walkthrough writers.
blog/newslaunchedoutletUSfoundation-modeldrug-design
Weekly biotech + FM-paper digest.
blog/newslaunchedoutletUSfoundation-modeldrug-design
Blog on Tabula, CELLxGENE, virtual cells, from the inside.
blog/newslaunchedfoundationUSvirtual-cellsingle-cell
Updates on STATE, Evo2, virtual-cell atlas.
blog/newslaunchedfoundationUSvirtual-cellfoundation-modelgenomic
Weekly reading group + podcast on ML for discovery.
blog/newslaunchedoutletglobaldrug-designfoundation-model
Curated ML + science writing.
blog/newslaunchedoutletUSfoundation-model
AI podcast that books biology-FM founders.
blog/newslaunchedoutletUSfoundation-modelagents
Clinical-AI perspective from a cardiologist.
blog/newslaunchedoutletUSclinicalfoundation-model
Community preprint commentary on bio papers.
blog/newslaunchedoutletUKsingle-cellfoundation-model
Public leaderboard for drug-discovery models.
benchmarklaunchedconsortiumglobaldrug-designeval
Therapeutic ML benchmark suite.
benchmarklaunchedacademicUSdrug-designeval
Official virtual-cell evaluation suite hosted by CZI.
benchmarklaunchedfoundationUSvirtual-celleval
sc-Arena — single-cell benchmark suite
Third-party-maintained sc-FM benchmark.
benchmarklaunchedacademicUSsingle-celleval
Agent using pathology FMs inside Claude's clinical workflow — production agent-using-FM example.
toollaunchedbiotechEUpathologyagentsclinical
scones
Single-cell analysis utility.
toollaunchedacademicglobalsingle-cell
Agenda-setter for causal foundation models in cell biology.
personlaunchedindustryUSsingle-cellfoundation-modelvirtual-cell
Geneformer creator; one of the few sc-FM PIs with full compute disclosure.
personlaunchedacademicUSsingle-cellfoundation-model
scGPT PI; 2026 pivot to agentic AI (X-Cell).
personlaunchedacademicUSsingle-cellfoundation-modelagents
scArches, scPoli, CPA, CRADLE-VAE — the perturbation-and-adaptation stack.
personlaunchedacademicUKsingle-cellperturbation-prediction
Evo2 + STATE co-PI; Tahoe-100M architect.
personlaunchedfoundationUSvirtual-cellgenomicperturb-seq
UNI, CONCH, PathChat, TITAN — most complete vertical pathology stack.
personlaunchedacademicUSpathologymultimodalfoundation-model
Linear-baseline-2025 first author; recently moved to Isomorphic.
personlaunchedindustryUKevalperturbation-prediction
Bioconductor + genomics-statistics elder; co-author of the reckoning paper.
personlaunchedacademicEUsingle-celleval
CZI Head of AI for Science — runs the virtual-cell program.
personlaunchedfoundationUSvirtual-cellfoundation-model
Compositional-FM Perspective author; scvi-tools / Nicheformer.
personlaunchedacademicEUsingle-cellfoundation-model
Le Song / Eric Xing
VCHarness; autonomous virtual-cell direction from China.
personlaunchedindustryCNvirtual-cellfoundation-modelagents
TxGNN, TDC-2 creator; KG-FM-therapeutics axis.
personlaunchedacademicUSdrug-designfoundation-model
Adapter-style PEFT cuts scLLM fine-tuning to <4% params and beats zero-shot — practical answer to the reckoning.
paperpublishedacademicCNsingle-cellfoundation-model
Time-series scRNA generative model used as a virtual-disease simulator for in-silico perturbation screens.
paperpublishedacademicUSsingle-cellgenerativedrug-designclinical
Multi-agent LLM diagnosis system that outperformed physicians on rare-disease cases — the agentic-clinical proof point.
paperpublishedacademicCNagentsclinicalfoundation-modelpapermap: agentic
H&E → 40-protein spatial proteomics; +22% prognostic, +24-39% immunotherapy-response prediction across 2298 NSCLC patients.
paperpublishedacademicUSpathologyspatialproteomicsclinicalmultimodal
mCAS cohort (2019 individuals) → core-capacity / multimodal / organ-specific aging clocks; MAE 3.87y on chronological age.
paperpublishedacademicCNmultimodalclinicaldigital-twin
Knowledge-graph-conditioned pathology VLM from Shanghai Jiao Tong — Chinese answer to PathChat/Virchow.
paperpublishedacademicCNpathologyfoundation-modelmultimodalclinical
Names the metabolism-flavoured AIVC subfield (AI Virtual Metabolism) as a coherent agenda.
reviewpublishedoutletglobalsignalingmultimodalfoundation-model
Second front in the perturbation-evaluation reckoning — Wasserstein/Energy distances mislead in high-dim gene space.
paperpreprintacademicglobalevalperturbation-predictionsingle-cellpapermap: reckoning
scverse-blessed perturbation toolbox — distances, perturbation spaces, harmonisation. The canonical analysis layer.
toollaunchedacademicEUperturb-seqsingle-cellperturbation-predictioneval
Transformer pre-trained on 276M peptide precursors; +51% protein IDs vs DIA-NN. Westlake's bid for proteomics FM.
paperpublishedacademicCNproteomicsmass-specfoundation-model
Tencent AI Lab — align-free scRNA→protein generation pretrained on 2M cells + 18k bulk samples.
paperpublishedindustryCNsingle-cellmultimodalproteomicsgenerative
Structural causal model + diffusion → interpretable cellular representations with explicit cDAGs. Counter-position to black-box scLLMs.
paperpublishedacademicCNcausalsingle-cellgenerativediffusioninterpretabilitypapermap: contrarian_theory
Turns Xenium/CosMx/MERSCOPE/PhenoCycler into scalable single-cell profilers — wet-lab counterpart to virtual spatial proteomics.
paperpublishedacademicCNspatialsingle-cellimagingmultimodal
White-box LLM-driven simulator: stepwise mechanistic reasoning, SOTA on drug-perturbation benchmarks. Anti-black-box alternative.
paperpreprintacademicCNvirtual-cellperturbation-predictioninterpretabilityagentspapermap: arch_response
Computational method spotting cells with mitochondrial-transfer signatures — used as motivation in AIVM commentary.
paperpublishedacademicglobalsingle-cellsignalingclinical
CLIP for protein-molecule retrieval — zero-shot virtual screen baseline that DrugReflector and successors build on.
paperpublishedacademicCNdrug-designmultimodalfoundation-model
DrugReflector
2026 AI drug-screening foundation model picked up in industry coverage — provenance still firming up.
toollaunchedbiotechglobaldrug-designfoundation-modelagents
EvoLen
EvoLen — name only; protein/evolution model, watch the literature.
toolname-onlyacademicglobalproteinfoundation-model
scpFormer
scpFormer — name only; transformer for single-cell perturbation, no paper yet.
toolname-onlyacademicglobalsingle-cellfoundation-modelperturbation-prediction
scFOCAL
scFOCAL — name only.
toolname-onlyacademicglobalsingle-cellfoundation-model
SC-pSILAC
Single-cell pSILAC variant — Zilu Ye attribution from talk notes, not yet citable.
toolrumoredacademicCNproteomicsmass-specsingle-cell
Xlearning lab PI — multimodal-learning angle into virtual-cell territory.
personlaunchedacademicCNfoundation-modelmultimodal
scTranslator PI, AIMBE fellow — Tencent's bio-FM lead.
personlaunchedindustryCNfoundation-modelsingle-cellmultimodal
BM2 Lab — CausCell, STAMP, scPerturBench. Methods-critique + tooling powerhouse from China.
personlaunchedacademicCNsingle-cellcausalspatialeval
277 items · last built from data/resource-library/fm-to-virtual-cells.yaml.