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Paper Citation Record · LEDGER

Benchmarking virtual cell models for in-the-wild perturbation response

As of 5 August 2026, this Paper Citation Record lists 61 of 61 outbound references and 1 inbound Pith citation observation for arXiv:2604.27646.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2604.27646 v1

Coverage vector

measured 61 of 61 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-05-07T04:58:32.817486Z

measured 62 of 62 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-05T06:32:48.257954+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-01T21:34:46.133993Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

61 of 61 outbound references displayed

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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 2ef9d8de-fecc-40ea-8b3f-bb4ac0173d8d · outbound

This paper cites Perturb-seq: dissecting molecular circuits with scalable single-cell rna profiling of pooled genetic screens.cell, 167(7): 1853–1866.

Benchmarking virtual cell models for in-the-wild perturbation response Perturb-seq: dissecting molecular circuits with scalable single-cell rna profiling of pooled genetic screens.cell, 167(7): 1853–1866

Reference 1

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Observation 34b0bd84-359f-4f58-b025-df176315ea3e · outbound

This paper cites A multiplexed single- cell crispr screening platform enables systematic dissection of the unfolded protein response.

Benchmarking virtual cell models for in-the-wild perturbation response A multiplexed single- cell crispr screening platform enables systematic dissection of the unfolded protein response

Reference 2

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 26b24f1c-cf1e-48cd-a839-d72e489ba4a7 · outbound

This paper cites Pooled crispr screening with single-cell transcriptome readout.Nature methods, 14(3):297–301.

Benchmarking virtual cell models for in-the-wild perturbation response Pooled crispr screening with single-cell transcriptome readout.Nature methods, 14(3):297–301

Reference 3

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Source-reported events for the cited work

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Observation a256c030-66f0-4cb7-9f57-48c15f02681f · outbound

This paper cites Massively multiplex chemical transcriptomics at single-cell resolution.Science, 367(6473): 45–51.

Benchmarking virtual cell models for in-the-wild perturbation response Massively multiplex chemical transcriptomics at single-cell resolution.Science, 367(6473): 45–51

Reference 4

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 58d58495-66c8-4be8-8780-ae1f3d92ff47 · outbound

This paper cites Genome-scale crispr-cas9 knockout screening in human cells.Science, 343(6166):84–87.

Benchmarking virtual cell models for in-the-wild perturbation response Genome-scale crispr-cas9 knockout screening in human cells.Science, 343(6166):84–87

Reference 5

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation a7a05456-3b1c-4c95-88d5-9f32d4cfd055 · outbound

This paper cites High-content crispr screening.Nature Reviews Methods Primers, 2(1):8.

Benchmarking virtual cell models for in-the-wild perturbation response High-content crispr screening.Nature Reviews Methods Primers, 2(1):8

Reference 6

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Source-reported events for the cited work

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Observation ceb215ac-1778-4b8a-a963-54e311df3d4f · outbound

This paper cites Machine learning and statistical methods for clustering single-cell rna-sequencing data.Briefings in bioinformatics, 21(4):1209–1223.

Benchmarking virtual cell models for in-the-wild perturbation response Machine learning and statistical methods for clustering single-cell rna-sequencing data.Briefings in bioinformatics, 21(4):1209–1223

Reference 7

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation e212dd6e-b7da-451c-8633-efb81e592ab1 · outbound

This paper cites Dissecting cell identity via network inference and in silico gene perturbation.Nature, 614(7949):742–751.

Benchmarking virtual cell models for in-the-wild perturbation response Dissecting cell identity via network inference and in silico gene perturbation.Nature, 614(7949):742–751

Reference 8

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 28998c38-bfe3-452e-980c-7e1b7f78d729 · outbound

This paper cites Applications of single-cell rna sequencing in drug discovery and development.Nature Reviews Drug Discovery, 22(6):496–520.

Benchmarking virtual cell models for in-the-wild perturbation response Applications of single-cell rna sequencing in drug discovery and development.Nature Reviews Drug Discovery, 22(6):496–520

Reference 9

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Source-reported events for the cited work

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Observation 794644fa-1fb5-4f03-9ced-c85d5bd6fdf7 · outbound

This paper cites The chemical space project.Accounts of Chemical Research, 48(3):722–730.

Benchmarking virtual cell models for in-the-wild perturbation response The chemical space project.Accounts of Chemical Research, 48(3):722–730

Reference 10

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 3684f451-2a57-4cf5-8fd0-1aed5d555ab1 · outbound

This paper cites Mapping information-rich genotype-phenotype landscapes with genome-scale perturb-seq.

Benchmarking virtual cell models for in-the-wild perturbation response Mapping information-rich genotype-phenotype landscapes with genome-scale perturb-seq

Reference 11

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No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 97597a60-a38b-4bbb-9161-29a6f0741771 · outbound

This paper cites A mini-review on perturbation modelling across single-cell omic modalities.Computational and Structural Biotechnology Journal, 23:1886–1896.

Benchmarking virtual cell models for in-the-wild perturbation response A mini-review on perturbation modelling across single-cell omic modalities.Computational and Structural Biotechnology Journal, 23:1886–1896

Reference 12

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Source-reported events for the cited work

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Observation c53e103c-f6cc-450d-8ad3-1f9211e16f37 · outbound

This paper cites Toward a foundation model of causal cell and tissue biology with a perturbation cell and tissue atlas.Cell, 187(17):4520–4545.

Benchmarking virtual cell models for in-the-wild perturbation response Toward a foundation model of causal cell and tissue biology with a perturbation cell and tissue atlas.Cell, 187(17):4520–4545

Reference 13

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation bada9e2d-dc01-4022-83f9-a2fb08e16b27 · outbound

This paper cites Benchmarking algorithms for generalizable single-cell perturbation response prediction.Nature Methods, 23(2):451–464.

Benchmarking virtual cell models for in-the-wild perturbation response Benchmarking algorithms for generalizable single-cell perturbation response prediction.Nature Methods, 23(2):451–464

Reference 14

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 6b4dc4e5-f4d9-4629-99ed-d130e7c5f559 · outbound

This paper cites Perturbench: Benchmarking machine learning models for cellular perturbation analysis.arXiv preprint arXiv:2408.10609.

Benchmarking virtual cell models for in-the-wild perturbation response Perturbench: Benchmarking machine learning models for cellular perturbation analysis.arXiv preprint arXiv:2408.10609

Reference 15

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Source-reported events for the cited work

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Observation 832587ee-4f16-497e-bd7b-cf246ab67790 · outbound

This paper cites Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.Nature Methods, 22:1657–1661.

Benchmarking virtual cell models for in-the-wild perturbation response Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.Nature Methods, 22:1657–1661

Reference 16

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Observation 7902a129-3bc0-4230-bdd1-fd2d4b6c4d52 · outbound

This paper cites Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations.

Benchmarking virtual cell models for in-the-wild perturbation response Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations

Reference 17

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Observation e5b457ff-c084-4c93-b9b7-f28f80ee4996 · outbound

This paper cites scgen predicts single-cell pertur- bation responses.Nature methods, 16(8):715–721.

Benchmarking virtual cell models for in-the-wild perturbation response scgen predicts single-cell pertur- bation responses.Nature methods, 16(8):715–721

Reference 18

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Observation d772491a-decd-45d3-95e9-f40d7d847bea · outbound

This paper cites Deep generative modeling for single-cell transcriptomics.Nature methods, 15(12):1053–1058.

Benchmarking virtual cell models for in-the-wild perturbation response Deep generative modeling for single-cell transcriptomics.Nature methods, 15(12):1053–1058

Reference 19

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No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 8b7dc846-a14c-4435-a126-66c410a8126f · outbound

This paper cites Condi- tional out-of-distribution generation for unpaired data using transfer vae.Bioinformatics, 36 (Supplement_2):i610–i617.

Benchmarking virtual cell models for in-the-wild perturbation response Condi- tional out-of-distribution generation for unpaired data using transfer vae.Bioinformatics, 36 (Supplement_2):i610–i617

Reference 20

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 739182af-2059-47a9-b931-ee7e6d926996 · outbound

This paper cites Predicting cellular responses to complex perturbations in high-throughput screens.Molecular systems biology, 19(6):MSB202211517.

Benchmarking virtual cell models for in-the-wild perturbation response Predicting cellular responses to complex perturbations in high-throughput screens.Molecular systems biology, 19(6):MSB202211517

Reference 21

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No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation a9949e7e-a132-4b14-842e-3221c7980edb · outbound

This paper cites Learning single-cell perturbation responses using neural optimal transport.Nature Methods, 20(11):1759–1768.

Benchmarking virtual cell models for in-the-wild perturbation response Learning single-cell perturbation responses using neural optimal transport.Nature Methods, 20(11):1759–1768

Reference 22

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation fa0d6c7a-480b-4f8d-b6ff-002e880be894 · outbound

This paper cites Cellflow enables generative single-cell phenotype modeling with flow matching.

Benchmarking virtual cell models for in-the-wild perturbation response Cellflow enables generative single-cell phenotype modeling with flow matching

Reference 23

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 4c8c1890-58ec-450c-b077-ee801f10f445 · outbound

This paper cites Predicting transcriptional outcomes of novel multigene perturbations with gears.Nature Biotechnology, 42(6):927–935.

Benchmarking virtual cell models for in-the-wild perturbation response Predicting transcriptional outcomes of novel multigene perturbations with gears.Nature Biotechnology, 42(6):927–935

Reference 24

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation d697c71e-c980-4685-97e9-9c56c0d00eef · outbound

This paper cites Squidiff: predicting cellular development and responses to perturbations using a diffusion model.Nature Methods, 23(1):65–77.

Benchmarking virtual cell models for in-the-wild perturbation response Squidiff: predicting cellular development and responses to perturbations using a diffusion model.Nature Methods, 23(1):65–77

Reference 25

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation bd082de2-7dd6-4416-8b9d-f8a785c185fe · outbound

This paper cites scgpt: toward building a foundation model for single-cell multi-omics using generative ai.Nature methods, 21(8):1470–1480.

Benchmarking virtual cell models for in-the-wild perturbation response scgpt: toward building a foundation model for single-cell multi-omics using generative ai.Nature methods, 21(8):1470–1480

Reference 26

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation d1dd5c93-240e-4c7b-8e77-f5b46a945c61 · outbound

This paper cites Large-scale foundation model on single-cell tran- scriptomics.Nature Methods, 21(8):1481–1491.

Benchmarking virtual cell models for in-the-wild perturbation response Large-scale foundation model on single-cell tran- scriptomics.Nature Methods, 21(8):1481–1491

Reference 27

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation f8979093-5bc8-40f3-ae2f-15087a421157 · outbound

This paper cites Transfer learning enables predictions in network biology.Nature, 618(7965):616–624.

Benchmarking virtual cell models for in-the-wild perturbation response Transfer learning enables predictions in network biology.Nature, 618(7965):616–624

Reference 28

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation c282184e-d638-4908-abe8-d1cca7031c3b · outbound

This paper cites scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data.Nature Machine Intelligence, 4(10):852–866.

Benchmarking virtual cell models for in-the-wild perturbation response scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data.Nature Machine Intelligence, 4(10):852–866

Reference 29

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation a7f0a8ab-93c2-4f40-9c21-bba27f4882ab · outbound

This paper cites Benchmarking foundation cell models for post-perturbation rna-seq prediction.BMC genomics, 26(1):393.

Benchmarking virtual cell models for in-the-wild perturbation response Benchmarking foundation cell models for post-perturbation rna-seq prediction.BMC genomics, 26(1):393

Reference 30

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

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Observation 0750f3a4-5c85-4da1-952e-54e754f65ce9 · outbound

This paper cites Perteval-scfm: bench- markingsingle-cellfoundationmodelsforperturbationeffectprediction.BioRxiv, pages2024–10.

Benchmarking virtual cell models for in-the-wild perturbation response Perteval-scfm: bench- markingsingle-cellfoundationmodelsforperturbationeffectprediction.BioRxiv, pages2024–10

Reference 31

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raw_fallback, observed 2026-05-27T10:53:59.588248Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:ad7b4a0de7955c303e445fc38d35f811844ff6fac7540e907d2a92a0c3e80e73

Observation fbe4fee5-f601-404a-9ff7-8fc1847eb1c3 · outbound

This paper cites A systematic comparison of computational methods for expression forecasting.bioRxiv.

Benchmarking virtual cell models for in-the-wild perturbation response A systematic comparison of computational methods for expression forecasting.bioRxiv

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verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.526410Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:9b73597f9a6de5793e5d3721753b04338bc66b8cae130f64f7eb677a75b42c38

Observation d1b4d2a1-d7e4-422d-90c8-c0b7bfc14da1 · outbound

This paper cites Single-cell perturbation prediction: generalizing experimental interventions to unseen contexts.

Benchmarking virtual cell models for in-the-wild perturbation response Single-cell perturbation prediction: generalizing experimental interventions to unseen contexts

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.671290Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:bf91196d6ce489f6138397725c04f1440f87c53ff8c91bf8c8ba28481bf0e8d5

Observation 00a0890d-8eda-425b-b138-afe9403c55f4 · outbound

This paper cites Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all.

Benchmarking virtual cell models for in-the-wild perturbation response Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all

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Resolution
verified exact
arxiv_id, observed 2026-05-12T10:41:29.570635Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:ebfb3ad11a7d57794c2cd08a47f8918eb71dc56ef9fca3781dd2f0990cff046a

Observation b8590b29-5e75-44e4-b8b8-6a7dc216d5c8 · outbound

This paper cites scperturb: harmonizedsingle-cell perturbation data.Nature Methods, 21(3):531–540.

Benchmarking virtual cell models for in-the-wild perturbation response scperturb: harmonizedsingle-cell perturbation data.Nature Methods, 21(3):531–540

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.540805Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:96258fc8b3fe36b5753dcb9252cbcb77501084b75338e80a83e369e5d8c759e0

Observation 8022a2d6-2fde-4e02-a1c2-d1d341b305e8 · outbound

This paper cites Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action.Nature communications, 11(1):4296.

Benchmarking virtual cell models for in-the-wild perturbation response Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action.Nature communications, 11(1):4296

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.544539Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:4b6ead28bb7664d6842695f38008f18513ae6119db45f1e7b6e8b97cac503823

Observation 50851bfd-6688-4c71-95e5-23a8e7406240 · outbound

This paper cites Multiplexed droplet single-cell rna-sequencing using natural genetic variation.Nature biotechnology, 36(1): 89–94.

Benchmarking virtual cell models for in-the-wild perturbation response Multiplexed droplet single-cell rna-sequencing using natural genetic variation.Nature biotechnology, 36(1): 89–94

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.577274Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:ac886e9aac4446f8da19896ee49a69080d3c3be3fd1edeed8bd30216d24a4702

Observation 2a507706-4e0a-4fd6-bcbe-4f54133247ef · outbound

This paper cites Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.Science, 365(6455):786–793.

Benchmarking virtual cell models for in-the-wild perturbation response Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.Science, 365(6455):786–793

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.655732Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:dbb22be8bbd1874dcb98dec9e8ba05202eab59648e6a91422f6daabda8722b97

Observation 6e77cabb-9dc5-47ea-9f07-f2f57e11e7f9 · outbound

This paper cites A kernel two-sample test.Journal of Machine Learning Research, 13(25):723–773.

Benchmarking virtual cell models for in-the-wild perturbation response A kernel two-sample test.Journal of Machine Learning Research, 13(25):723–773

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.519745Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:74016042c0aa560b2bc9c519c8efdcdfe4e3c7fa8cc282821af05d3c92f3fb34

Observation ec785251-39d5-4b90-822e-fcfe3f381c6a · outbound

This paper cites Energy statistics: A class of statistics based on distances.

Benchmarking virtual cell models for in-the-wild perturbation response Energy statistics: A class of statistics based on distances

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.664710Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:bae84acf8cec63b70c26bd0e32565f1bc9eca1883dc64afff6839f7769c54060

Observation 55064dcf-b69e-4394-a452-6499a6a256c0 · outbound

This paper cites Optimal distance metrics for single-cell rna-seq populations.

Benchmarking virtual cell models for in-the-wild perturbation response Optimal distance metrics for single-cell rna-seq populations

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.645796Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:7a70422919e475cd8b5e56807c56f48f2c4b9a1c9dbbe4ab48fdf3428b54f1af

Observation 674f5607-717a-428b-a09a-e9526db82469 · outbound

This paper cites scpram accurately predicts single- cell gene expression perturbation response based on attention mechanism.Bioinformatics, 40 (5):btae265.

Benchmarking virtual cell models for in-the-wild perturbation response scpram accurately predicts single- cell gene expression perturbation response based on attention mechanism.Bioinformatics, 40 (5):btae265

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.533138Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:e6fe790d4842e47718506af659bd079564739ab054c3c0e3acf55d24b8e920ab

Observation 1a12ef0f-7bde-460b-a97b-4aff85a55cc2 · outbound

This paper cites Benchmarking atlas-level data integration in single-cell genomics.Nature Methods, 19(1):41–50.

Benchmarking virtual cell models for in-the-wild perturbation response Benchmarking atlas-level data integration in single-cell genomics.Nature Methods, 19(1):41–50

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.550647Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:2e78c8a4cb491b7a44363287e611fda4883184db8054019d09cfbca1f1ef7969

Observation a9f530c2-ce57-495c-9d6d-71bca3f05265 · outbound

This paper cites Scaling Laws for Neural Language Models.

Benchmarking virtual cell models for in-the-wild perturbation response Scaling Laws for Neural Language Models

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Resolution
verified exact
local_arxiv, observed 2026-05-12T10:41:29.564244Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:72baabc4d55af6ec4668371363a194f56dde4303e6ae79b921d02d4e0a2890a7

Observation e92b4b57-8912-4922-a599-2bcf009e8c77 · outbound

This paper cites Predicting cellular responses to novel drug perturbations at a single-cell resolution.Advances in Neural Information Processing Systems, 35:26711–26722.

Benchmarking virtual cell models for in-the-wild perturbation response Predicting cellular responses to novel drug perturbations at a single-cell resolution.Advances in Neural Information Processing Systems, 35:26711–26722

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.652285Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:8cdfa43f4c5327b0ab50250a71d950424c7438bd1a0e000731e6f2341f57eb3b

Observation 10ccc375-1948-420c-b59a-1a648319eceb · outbound

This paper cites Comprehensive integra- tion of single-cell data.cell, 177(7):1888–1902.

Benchmarking virtual cell models for in-the-wild perturbation response Comprehensive integra- tion of single-cell data.cell, 177(7):1888–1902

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.573251Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:e082336f2f0b39e0f52f71657dd68b9953b1f76b1d5a43e42befac0abf34be72

Observation 6fcece42-cb93-479c-8ed1-8b7600bd5607 · outbound

This paper cites Tahoe-100m: A giga-scale single-cell perturbation atlas for context-dependent gene function and cellular modeling.bioRxiv.

Benchmarking virtual cell models for in-the-wild perturbation response Tahoe-100m: A giga-scale single-cell perturbation atlas for context-dependent gene function and cellular modeling.bioRxiv

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.625385Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:a89dcb492b120a4050dbb3d16b7cb05c427262cbcfe89418aa2c77e6b008ff9c

Observation aa659bc7-2123-46a6-8804-8354f867c9dc · outbound

This paper cites X-atlas/orion: Genome-wide perturb-seq datasets via a scalable fix- cryopreserve platform for training dose-dependent biological foundation models.bioRxiv.

Benchmarking virtual cell models for in-the-wild perturbation response X-atlas/orion: Genome-wide perturb-seq datasets via a scalable fix- cryopreserve platform for training dose-dependent biological foundation models.bioRxiv

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.557602Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:066aa48324dd52b18e469249cae631498664aa4cb0173faf0ca277864bd53069

Observation 9b89bca7-8e28-4320-b40e-9a25fbbc5b04 · outbound

This paper cites an unresolved cited work.

Benchmarking virtual cell models for in-the-wild perturbation response Unresolved cited work

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Resolution
unresolved
raw_fallback, observed 2026-05-27T10:53:59.668013Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:5ec4c16bf194badc2b95e614bf07eead4445b5aa42d32337fcc5b8cc587c7610

Observation 1e0780f2-8b25-4ab8-9fab-5536aed3bf96 · outbound

This paper cites Scanpy: large-scale single-cell gene expression data analysis.Genome biology, 19(1):15.

Benchmarking virtual cell models for in-the-wild perturbation response Scanpy: large-scale single-cell gene expression data analysis.Genome biology, 19(1):15

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.639167Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:bea1206797714e5637f468e01c93fa73213c02f001ba9bad665f117f10a1df8a

Observation 1e70ec3f-e671-4870-8804-e498d2d93a5c · outbound

This paper cites anndata: Annotated data.BioRxiv, pages 2021–12.

Benchmarking virtual cell models for in-the-wild perturbation response anndata: Annotated data.BioRxiv, pages 2021–12

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.635648Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:9f5ec8851702bf37a3dacb674248b92bfe288a401ffad3f23e35f4fe82577913

Observation 676cfd1a-edf3-4bb0-88bc-f4daa05b8cf4 · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379(6637):1123–1130.

Benchmarking virtual cell models for in-the-wild perturbation response Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379(6637):1123–1130

Reference 52

Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.584461Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:50089b6db507227ac2740b0694eff546db1ba00e5696c13e16897256b88915e5

Observation 6557a3ff-b9b8-4c03-bdbd-332c91b9cd68 · outbound

This paper cites Extended-connectivity fingerprints.Journal of chemical information and modeling, 50(5):742–754.

Benchmarking virtual cell models for in-the-wild perturbation response Extended-connectivity fingerprints.Journal of chemical information and modeling, 50(5):742–754

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.642654Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:df108e794cf51f5c86c57f19fa3581e2eff73c657fa5d3d4bc54fda716e4026f

Observation c025ae0a-ce9d-4350-aa35-c4e70b075243 · outbound

This paper cites Disentanglement of single-cell data with biolord.Nature Biotechnology, 42(11):1678–1683.

Benchmarking virtual cell models for in-the-wild perturbation response Disentanglement of single-cell data with biolord.Nature Biotechnology, 42(11):1678–1683

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.661804Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:ab588185bcbb557071cd7231bb8a1e8c7f2d10d91457446c9cd1b0e761a7a7f6

Observation aee63897-82da-4474-98b4-35bda09b047f · outbound

This paper cites Modelling cellular perturbations with the sparse additive mechanism shift variational autoencoder.Advances in Neural Information Processing Systems, 36:1–12.

Benchmarking virtual cell models for in-the-wild perturbation response Modelling cellular perturbations with the sparse additive mechanism shift variational autoencoder.Advances in Neural Information Processing Systems, 36:1–12

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.628824Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:b48dfeee8042dfbc6eea2ac098ce94639337aef6fdbedf882cc162e22c7245a4

Observation 50137cab-29dd-4774-a58f-e0ce0ffd4322 · outbound

This paper cites Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery.

Benchmarking virtual cell models for in-the-wild perturbation response Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.615723Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:abd0135f9676c452f3e79a5f40bfd1a564e07f119cf101a53ec5670faba4d976

Observation f32a15c1-10a0-416e-8124-b0177dce256c · outbound

This paper cites Modeling and predicting single-cell multi-gene perturbation responses with sclambda.bioRxiv.

Benchmarking virtual cell models for in-the-wild perturbation response Modeling and predicting single-cell multi-gene perturbation responses with sclambda.bioRxiv

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.537451Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:6d143e3f168936213d04b1d3961f3a2c7464e676242dee09a42325b503cb7a15

Observation 824d7c0e-fbe9-49ea-befd-cbef7c1f03fa · outbound

This paper cites Genepert: Leveraging genept embeddings for gene perturbation prediction.bioRxiv.

Benchmarking virtual cell models for in-the-wild perturbation response Genepert: Leveraging genept embeddings for gene perturbation prediction.bioRxiv

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.570331Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:7a4a3bdbdce6d96b8b4264d5a74db1928c53fa2125503a91b9be06a1a361ce10

Observation 3d191ba9-3737-42b1-8c50-63d2fdf30bc1 · outbound

This paper cites Predicting cellular responses to perturbation across diverse contexts with state.bioRxiv.

Benchmarking virtual cell models for in-the-wild perturbation response Predicting cellular responses to perturbation across diverse contexts with state.bioRxiv

Reference 59

Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.529801Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:aaaa98694aa8bf47a88969350b527cb4b2ef7ed83b8d6f9c97bedc8c300cfa32

Observation 2a1f1ae2-a795-4001-a731-665d5a62dd7d · outbound

This paper cites Sinkhorn distances: Lightspeed computation of optimal transport.Advances in neural information processing systems, 26.

Benchmarking virtual cell models for in-the-wild perturbation response Sinkhorn distances: Lightspeed computation of optimal transport.Advances in neural information processing systems, 26

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Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.509372Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:9697276e16963aae68b851dd99f71d9b27603afdd6dea4b562810ed00be08b2b

Observation 3bf9203c-daaf-47c3-bfea-73140fbf9531 · outbound

This paper cites Interpolating between optimal transport and mmd using sinkhorn divergences.

Benchmarking virtual cell models for in-the-wild perturbation response Interpolating between optimal transport and mmd using sinkhorn divergences

Reference 61

Resolution
verified fuzzy
raw_fallback, observed 2026-05-27T10:53:59.497713Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

source=pdf_text observed=2026-05-07T04:58:32.817486Z digest=sha256:a8816fecda5a5ee78de8427a7a386ccc6bb01f5542d099b6a483b2493c3aaf3e

Pith citing papers

Observation 07c228fe-2244-4469-a7a8-5166f67339ab · inbound

SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery cites this paper.

SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery Benchmarking virtual cell models for in-the-wild perturbation response

Reference 64

Resolution
unresolved
no resolver link, observed 2026-08-01T21:34:46.133993Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-01T21:34:46.133993Z digest=sha256:c481e2bde88697a8110496f48aadac911065f6e74e0b7484dfc6d1f381a8d250