Theme — single-cell

Items in corpus: 87

Papers

• The future of automated single-cell analysis — Rood, Regev et al., Cell, 2024
  Regev's reference-mapping framing of the same ambition.
• Earliest 'linear baselines are competitive' warning — Boiarsky et al., NeurIPS workshop, 2023
  First warning shot — read it to see how early the signal was.
• Limits of zero-shot foundation models in single-cell biology — Kedzierska et al., Genome Biology, 2025
  Extends the result to UCE and the zero-shot setting.
• 27 methods × 29 datasets × 6 metrics — Wu et al., Nature Methods, 2026
  First axis-by-axis failure decomposition.
• No single scFM consistently outperforms — Wu et al., Genome Biology, 2025
  6 scFMs, cell-ontology-grounded metrics.
• scEval — challenges the necessity of sc-FMs — Liu et al., Advanced Science, 2026
  Strongest 'is the paradigm worth it' framing.
• CellBench-LS — stratified low-supervision benchmark — bioRxiv, 2026
  FMs lead cell-type ID; classical methods win gene-expression.
• Real-world RNA-seq integration — Han et al., bioRxiv, 2026
  Industry-authored — deployment-grade robustness gaps.
• Zero-shot scFMs fail to recover cellular dynamics — bioRxiv, 2026
  Extends the critique to RNA-velocity / dynamics.
• SAEs reveal organized biology but minimal regulatory logic — Simon & Zou, arXiv, 2026
  Mechanistic explanation of the reckoning, on Geneformer + scGPT.
• SAEs reveal interpretable features in single-cell FMs — bioRxiv, 2025
  Independent confirmation on scGPT.
• Causal representation learning (Lopez/Hsu) — Nature Methods, 2025
  Causal-rep exemplar for pretraining objectives that target causality.
• PEFT / LoRA recipe for sc-FMs — Hossain et al., arXiv 2412.13478, 2024
  Concrete PEFT recipe for single-cell FMs (Lane 2).
• OmniCell — multimodal spatial FM — bioRxiv, 2025
  Multimodal spatial-transcriptomics FM.
• CLM-X — spatial-temporal cell-language model — bioRxiv, 2026
  Spatial + temporal context for cell language modelling.
• CELLama — cell language model — Advanced Science, 2026
  Alternative transformer-based cell FM.
• CancerFoundation — bioRxiv, 2024
  Cancer-domain-specific single-cell FM.
• scPEFT — parameter-efficient fine-tuning for single-cell LLMs — He et al., Nature Machine Intelligence, 2025
  Adapter-style PEFT cuts scLLM fine-tuning to <4% params and beats zero-shot — practical answer to the reckoning.
• UNAGI — generative model for cellular dynamics + in-silico drug discovery — Ding lab et al., Nature Biomedical Engineering, 2025
  Time-series scRNA generative model used as a virtual-disease simulator for in-silico perturbation screens.
• Evaluating single-cell perturbation response models is far from straightforward — Heidari, Karimpour, Srivatsa & Montazeri, bioRxiv, 2026
  Second front in the perturbation-evaluation reckoning — Wasserstein/Energy distances mislead in high-dim gene space.
• scTranslator — transcriptome→proteome generative model — Jianhua Yao et al., Nature Biomedical Engineering, 2025
  Tencent AI Lab — align-free scRNA→protein generation pretrained on 2M cells + 18k bulk samples.
• CausCell — causal disentanglement + counterfactual single-cell generation — Qi Liu lab (Tongji) et al., Nature Communications, 2025
  Structural causal model + diffusion → interpretable cellular representations with explicit cDAGs. Counter-position to black-box scLLMs.
• STAMP — single-cell transcriptomics + multimodal profiling through imaging — Qi Liu lab et al., Cell, 2025
  Turns Xenium/CosMx/MERSCOPE/PhenoCycler into scalable single-cell profilers — wet-lab counterpart to virtual spatial proteomics.
• MERCI — mitochondrial-receiver cell detection in tumours — Cell Metabolism
  Computational method spotting cells with mitochondrial-transfer signatures — used as motivation in AIVM commentary.

Reviews

• Single-cell foundation models — bringing AI into cell biology — Singh et al., Experimental & Molecular Medicine, 2025
  Clean mid-2025 review — the orientation read.
• Eleven grand challenges in single-cell data science — Lähnemann et al., Genome Biology, 2020
  Pre-FM landscape framing — what needed solving before the wave hit.

Tools

• scBERT — Yang et al., Nature Machine Intelligence, 2022
  BERT-style precursor that pre-dated the 2023 sc-FM wave.
• scGPT — Cui et al., Nature Methods, 2024
  Defined the category — genes + cells as tokens. The reckoning's main target.
• Geneformer / Geneformer V2 — Theodoris et al., Nature, 2023
  First atlas-pretrained transformer; rank-based tokenisation. V2 (Dec 2024) matched 316M at ⅓ the compute.
• Universal Cell Embedding (UCE) — Rosen et al., Nature Methods, 2024
  Cross-species sc-FM — bridges through ESM2 protein embeddings (8 species).
• scFoundation — Hao et al., Nature Methods, 2024
  Read-depth-aware attention; one of the four reckoning regulars.
• CellPLM — Wen et al., ICLR, 2024
  Cell-as-token sc-FM; beats scGPT/Geneformer on cell-typing cheaply.
• STATE (Arc Institute) — bioRxiv, 2025
  First production virtual cell at Tahoe-100M scale.
• TranscriptFormer — Pearce et al., Science, 2025
  First generative cross-species sc-FM; CZ Biohub flagship (112M cells, 12 species).
• Nicheformer — Theis lab, Nature Methods, 2025
  Spatial-omics sc-FM with a niche-aware objective.
• scMulan
  Multitask single-cell language model; benchmarked in CellBench-LS.
• GenePT / scELMo
  NOT trained sc-FMs — frozen LLM embeddings of gene names + LR head (~$200) matching scGPT zero-shot.
• CellFM — Zhang et al., Nature Communications, 2025
  Another sc-FM from the 2025 wave.
• scPRINT — Kalfon et al., Nature Communications, 2025
  50M-cell pretraining aimed at robust zero-shot gene-network inference.
• scPRINT-2 — Kalfon, Peyré & Cantini, bioRxiv, 2025
  Next-gen cell FM AND benchmark suite in one preprint.
• xVERSE — transcriptomics-native sc-FM — bioRxiv, 2026
  First evidence the architectural choice is load-bearing (+17.9% over LM-derived sc-FMs).
• CellVoyager — autonomous comp-bio agent — Nature Methods, 2026
  Agent that ANALYSES single-cell data with the FM as substrate.
• scDiffusion
  Diffusion model for single-cell expression generation.
• Flex v2 — Broad Institute
  Broad's Flex v2 single-cell platform — currently a name.
• ProPer-seq
  ProPer-seq assay — name only.
• CellTRIP
  CellTRIP — name only.
• LangCell / LangStem
  LLM-based cell annotation tool.
• GET — gene expression toolkit
  sc-FM-based gene-expression analysis toolkit.
• CytoVerse — browser-native sc-FM via ONNX — bioRxiv, 2026
  In-browser sc-FM inference; pushes inference to where the data is.
• scPoli — single-cell policy learning — Lotfollahi et al.
  Policy-based perturbation prediction; the scArches lineage.
• scvi-tools — Theis Lab
  Single-cell methodology reference framework underpinning much of the field.
• scverse ecosystem (Scanpy / AnnData / squidpy / scvi-tools)
  Community standards for single-cell Python tools.
• signifinder — sc-FM wrapper for Bioconductor — Calura lab, U Padua
  Bioconductor interface to sc-FMs.
• mia / miaTime / miaViz — Borman, U Turku
  Scverse-adjacent tools for single-cell analysis.
• SpatialData — unified spatial-omics data framework — Marconato, Palla et al. (Theis + Stegle)
  Standard for spatial transcriptomics data representation.
• scones
  Single-cell analysis utility.
• Pertpy — end-to-end framework for perturbation analysis — Heumos, Ji, May, Theis et al., Nature Methods, 2025
  scverse-blessed perturbation toolbox — distances, perturbation spaces, harmonisation. The canonical analysis layer.
• scpFormer
  scpFormer — name only; transformer for single-cell perturbation, no paper yet.
• scFOCAL
  scFOCAL — name only.
• SC-pSILAC — Zilu Ye
  Single-cell pSILAC variant — Zilu Ye attribution from talk notes, not yet citable.

Benchmarks

• Open Problems v2
  Community single-cell benchmark suite.
• sc-Arena — single-cell benchmark suite
  Third-party-maintained sc-FM benchmark.

Datasets

• Tabula Sapiens — Science, 2022
  Multi-organ human single-cell reference atlas.
• CELLxGENE Census
  Aggregated single-cell corpus most sc-FMs pretrain on.

Organisations

• 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.
• IBS — Park Jong-eun (human digital twin) — Institute for Basic Science, Korea
  Korean national lab investing in human-digital-twin programme around single-cell data.
• CZ Biohub — Theofanis Karaletsos, Steve Quake, Angela Pisco
  Substrate + model shipper (TranscriptFormer, rBio); breaks substrate-only stereotype.
• Theodoris Lab (Gladstone / UCSF) — Christina Theodoris
  Only sc-FM lab with full compute disclosure (NVIDIA BioNeMo).
• Bo Wang Lab (U. Toronto / Vector / UHN) — Bo Wang
  Defined the sc-FM category (scGPT); agentic-AI pivot 2026 (X-Cell).
• Leskovec + Quake (Stanford / SNAP) — Jure Leskovec & Steve Quake
  Cross-species sc-FM (UCE) — 8 species via ESM2 bridge.
• Ahlmann-Eltze / Huber (EMBL Heidelberg)
  Authored the 2025 reckoning paper; Ahlmann-Eltze now at Isomorphic Labs.
• Theis Lab (Helmholtz Munich) — Fabian Theis
  Methodological reference class; author of 2026 compositional-FM perspective.
• Cellarity
  Cell-state engineering company.

People

• Aviv Regev — Genentech
  Agenda-setter for causal foundation models in cell biology.
• Christina Theodoris — Gladstone Institutes
  Geneformer creator; one of the few sc-FM PIs with full compute disclosure.
• Bo Wang — U. Toronto / Vector
  scGPT PI; 2026 pivot to agentic AI (X-Cell).
• Mohammad Lotfollahi — Wellcome Sanger
  scArches, scPoli, CPA, CRADLE-VAE — the perturbation-and-adaptation stack.
• Jure Leskovec — Stanford
  UCE co-PI; graph + sc-FM bridge.
• Sara Mostafavi — UW Allen School
  Gene-expression modelling expert.
• Wolfgang Huber — EMBL
  Bioconductor + genomics-statistics elder; co-author of the reckoning paper.
• Kasia Z. Kedzierska — Oxford / MSR
  Zero-shot-critique first author.
• Hani Goodarzi — Arc Institute
  STATE co-lead.
• Fabian Theis — Helmholtz Munich
  Compositional-FM Perspective author; scvi-tools / Nicheformer.
• Jianhua Yao — Tencent AI Lab
  scTranslator PI, AIMBE fellow — Tencent's bio-FM lead.
• Qi Liu — Tongji University
  BM2 Lab — CausCell, STAMP, scPerturBench. Methods-critique + tooling powerhouse from China.

Commentary

• CZ Biohub Data Science blog
  Blog on Tabula, CELLxGENE, virtual cells, from the inside.
• preLights — preprint commentary — Company of Biologists
  Community preprint commentary on bio papers.

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