Theme — virtual-cell

Items in corpus: 67

Papers

• How to build the virtual cell with AI — Bunne et al., Cell, 2024
  The canonical virtual-cell thesis — the goal everything else chases.
• From modality-specific to compositional foundation models — Theis et al., Cell Systems, 2026
  Post-reckoning forward path — stop scaling monoliths.
• Virtual Cell Challenge — a Turing test for the virtual cell — CZI / Roohani / Hsu et al., Cell, 2025
  What success is supposed to look like, operationalised.
• Human-interpretable grammar encodes multicellular systems biology — Theory in Cell (preprint/workshop), 2026
  Argues for an interpretable grammar layer to democratise virtual-cell labs.
• Cellular Intelligence — Engineering Cell Fate, towards a foundation model for cell signaling — preprint, 2026
  Reframes virtual cells as signaling-FMs rather than transcriptome-FMs.
• Virtual Cells Need Context, Not Just Scale — bioRxiv, 2026
  Names the theory: a causal-transportability problem (Pearl).
• Generative Virtual Cells — Lewis & Zueco, ICLR Gen²-workshop, 2026
  Workshop proof (<$250 compute) — joint planner + world model under validation gating.
• CellFluxRL — Biologically-Constrained Virtual Cell Modeling via RL — Wu, Su, Zhang, Sui, Lundberg, Fox, Yeung-Levy, preprint, 2026
  RL-driven virtual-cell modelling with biological constraints — Stanford/CZI/Lundberg axis.
• Lingshu-Cell — generative cellular world model for transcriptome modelling — Han Zhang, Guo-Hua Yuan, Chaohao Yuan, Tingyang Xu, Tian Bian, Hong Cheng, Wenbing Huang, Deli Zhao, Yu Rong, preprint, 2026
  Chinese-industry-led generative cellular world model for transcriptome.
• SCALE — Scalable Conditional Atlas-Level Endpoint transport for virtual-cell perturbation — preprint, 2026
  Optimal-transport / endpoint framing of perturbation prediction at atlas scale.
• 4DWCM — bringing the minimal cell to life on computer in 4D — UIUC, 2026
  UIUC 4D whole-cell model — the mech-modelling-meets-AIVC bridge.
• Beyond Alignment — Synergistic Integration for Multimodal Cell FMs — preprint, 2026
  Argues multimodal cell-FMs need synergistic (not just aligned) integration.
• AIVEVs — AI Virtual Extracellular Vesicles — Bioactive Materials, 2026
  EV-focused AIVC paper — small but exists.
• Cellular Intelligence — Engineering Cell Fate, towards a FM for cell signaling — preprint, 2026
  Reframes virtual cells as signaling-FMs.
• Towards predictive virtual embryos — Cao, Lu & Qiu, Nature Methods, 2026
  Virtual-embryo extension — integrating single-cell and spatial data into a developmental simulator.
• Digital twins of ex vivo human lungs for personalised therapeutic-efficacy evaluation — Zhou et al., Nature Biotechnology, 2026
  Virtual-organ agenda — personalised organ-scale simulation on real lungs.
• VCWorld — biological world model for virtual cell simulation — Shuangjia Zheng lab et al., arXiv, 2025
  White-box LLM-driven simulator: stepwise mechanistic reasoning, SOTA on drug-perturbation benchmarks. Anti-black-box alternative.

Reviews

• Revisiting the blueprint for an interpretable virtual cell — Nature Reviews Genetics, 2026
  Nature Reviews framing piece on what an interpretable virtual cell would even look like.
• AI virtual cell — review — Shugang Zhang, Huasen Jian et al., Briefings in Bioinformatics, 2026
  Mandarin-sphere review of the AIVC landscape.
• Flow matching in computational biology — Morehead et al., Nature Machine Intelligence, 2026
  The generative technique under generative virtual cells.

Tools

• STATE (Arc Institute) — bioRxiv, 2025
  First production virtual cell at Tahoe-100M scale.
• rBio — reasoning model trained on TranscriptFormer — CZ Biohub, 2025
  Agent that REASONS OVER a virtual cell as a verifier.
• VCHarness — autonomous virtual-cell builder — bioRxiv (BioMap), 2026
  Agent that BUILDS virtual-cell models end to end.
• ProtiCelli / ProtiCell — Emma Lundberg
  Proteomics-anchored virtual-cell project from the Lundberg lab — mostly a slide-trail.
• VCHarness (GenBio AI) — GenBio AI
  Genbio's autonomous virtual-cell builder agent — see the paper too.
• AROMA — Tencent
  Tencent-flagged virtual-cell project — name only.
• VCR-Agent
  Virtual-cell reasoning agent — name only.
• T-World
  Whispered T-World model — provenance unclear.
• AlphaCell
  AlphaCell — name only, watch for DeepMind/Isomorphic involvement.
• AetherCell
  AetherCell — name only.
• Harmony Cell
  Harmony Cell — name only.
• ConvergeCell
  ConvergeCell — name only.
• CellFluxV2
  Successor to CellFluxRL — name only.
• GigaTime
  GigaTime — name only.
• CRADLE-VAE — compositional active learning — Bunne et al.
  Closed-loop virtual-cell active learning prototype.

Benchmarks

• VCBench — arXiv
  Named benchmark for virtual cells — details still being chased down.
• CZI Virtual Cells Platform Benchmarks
  Official virtual-cell evaluation suite hosted by CZI.

Datasets

• Tahoe-100M — Roohani, Hsu et al., 2025
  First large-scale perturbation atlas framed as virtual-cell training data.

Organisations

• CZI / Biohub / Virtual Biology Initiative — Priscilla Chan
  The single largest philanthropic backer of the virtual-cell vision.
• Jian Ma's Virtual Bio Center — Carnegie Mellon
  New CMU center anchored around Jian Ma's lab as a US academic hub for virtual biology.
• Arc Institute — Patrick Hsu & Hani Goodarzi
  Largest non-DeepMind compute (~2,048× H100); built STATE, Evo2, Tahoe-100M.
• CZ Biohub — Theofanis Karaletsos, Steve Quake, Angela Pisco
  Substrate + model shipper (TranscriptFormer, rBio); breaks substrate-only stereotype.
• BioMap Research + MBZUAI — Le Song & Eric Xing
  China/Middle-East virtual-cell competitor (VCHarness, xTrimo).
• Insitro — Daphne Koller
  Applied virtual-cell case study in drug discovery.
• Latent Labs — Simon Kohl + DeepMind alumni
  DeepMind-alumni virtual-cell startup.
• Vevo / Arc
  Tahoe-100M producer — virtual-cell modelling platform.

People

• Aviv Regev — Genentech
  Agenda-setter for causal foundation models in cell biology.
• Patrick Hsu — Arc Institute
  Evo2 + STATE co-PI; Tahoe-100M architect.
• Theofanis Karaletsos — CZI
  CZI Head of AI for Science — runs the virtual-cell program.
• Hani Goodarzi — Arc Institute
  STATE co-lead.
• Le Song / Eric Xing — BioMap + MBZUAI
  VCHarness; autonomous virtual-cell direction from China.

Commentary

• Grow AI virtual cells — three data pillars and closed-loop learning — Cell Research (editorial), 2026
  Editorial framing closed-loop learning as the missing ingredient.
• From equations to agents — the AI virtual cell reshaping precision oncology — The Innovation Oncology (perspective), 2026
  Clinical-oncology framing of the AIVC story.
• Minimal life by computer — Nature Biotechnology, 2026
  Framing piece on minimal-cell simulation as the AIVC counterpoint.
• Ubiquitin Rides Again — comments on the virtual cell — Derek Lowe, Science · In the Pipeline (blog), 2026
  Pharma chemist's sceptical-pragmatist read on AIVC claims.
• CZ Biohub Data Science blog
  Blog on Tabula, CELLxGENE, virtual cells, from the inside.
• Arc Institute News
  Updates on STATE, Evo2, virtual-cell atlas.

Competition

• CZ Biohub Virtual Cell Challenge 2025
  First community virtual-cell benchmark, $50k prize.

Event

• CompuCell3D Virtual Tissue Modeling Workshop & Hackathon
  The mech-modelling crowd's annual gathering — the parallel-universe to AIVC.
• Westlake Autumn Symposium — AIVC (Tiannan Guo)
  Westlake's annual AIVC symposium — gathers the China AIVC scene.
• Virtual Cell Challenge 2025 — first round — CZI / Biohub, 2025
  The annual benchmark cycle whose 2025 launch crystallised the field.
• CZ Biohub Virtual Cell Program launch — 2024
  Multi-billion-dollar non-dilutive commitment to virtual cells.
• Arc Virtual Cell Challenge 2025
  Community benchmark with $50k prize; first formal VC evaluation.

Move

• Tahoe Therapeutics + Arc Institute + CZ Biohub collaboration — 2026
  The big three of US AIVC join up around Tahoe-100M.
• UCSD + DARPA virtual-cell programme — 2026
  DARPA money flowing to UCSD for virtual-cell work.
• Turbine raises $25M — 2026
  Validates commercial market for VC-style perturbation simulators.
• Amazon hires Stanford PhD on AIVC — 2026
  Amazon signals AIVC entry — Stanford PhD hire.

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Regenerated 2026-05-15 from a 277-item corpus by resourcelib-views.