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Paper · 39160302

WebAtlas pipeline for integrated single-cell and spatial transcriptomic data.

Li T and 15 others. Nat Methods, 2025. Cited by 19 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. WebAtlas pipeline for integrated single-cell and spatial transcriptomic data. Papers, record 39160302. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/39160302

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title
WebAtlas pipeline for integrated single-cell and spatial transcriptomic data.
PubMed
Journal
Nat Methods
PubMed
Year
2025
PubMed
Publication types
Letter
PubMed
Citations, by iCite
19
iCite
Relative citation ratio, by iCite
4.04, provisional
iCite
Revised in PubMed
2026-10-10
PubMed

Authors16

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

OrderAuthorForenameKindORCID iD
1Li TTonghttps://orcid.org/0000-0002-8240-4476
2Horsfall DDavidhttps://orcid.org/0000-0002-8086-812X
3Basurto-Lozada DDanielahttps://orcid.org/0000-0003-3943-8424
4Roberts KKennyhttps://orcid.org/0000-0001-6155-0821
5Prete MMartinhttps://orcid.org/0000-0002-5946-821X
6Lawrence JEGJohn E G
7He PPenghttps://orcid.org/0000-0002-2457-3554
8Tuck EElisabeth
9Moore JJoshhttps://orcid.org/0000-0003-4028-811X
10Yoldas AKAybuke Kupcu

1 to 10 of 16Source PubMed

See all 16 authors

Topics0

NLM's MeSH indexing of the paper, its major topics first.

None in this release.

Grants3

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes itAgencyCountryNIH projectStated by
206194 and 220540/Z/20/AWellcome Trust (Wellcome)PubMed
221052/Z/20/Z, 221052/A/20/Z, 221052/B/20/Z, 221052/C/20/Z, and 221052/E/20/ZWellcome Trust (Wellcome)PubMed
501864659Deutsche Forschungsgemeinschaft (German Research Foundation)PubMed

Source PubMed

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References5

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

OrderPMIDTitleJournalYearIn PapersSource
137,231,260Stabilized mosaic single-cell data integration using unshared features.Nat Biotechnol2024https://conductscience.org/library/papers/37231260PubMed
237,428,210OME-Zarr: a cloud-optimized bioimaging file format with international community support.Histochem Cell Biol2023https://conductscience.org/library/papers/37428210PubMed
334,489,600Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.Nat Biotechnol2022https://conductscience.org/library/papers/34489600PubMed
435,027,729Cell2location maps fine-grained cell types in spatial transcriptomics.Nat Biotechnol2022https://conductscience.org/library/papers/35027729PubMed
535,189,131The BioImage Archive - Building a Home for Life-Sciences Microscopy Data.J Mol Biol2022https://conductscience.org/library/papers/35189131PubMed

Cited by19

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 19 citations.

PMIDTitleJournalYearIn PapersSource
42,983,086A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity.Nature2026https://conductscience.org/library/papers/42983086PubMed
42,806,090Spatially resolved multiomics of human meningeal development reveal lineage and disease dynamics.Nat Cell Biol2026https://conductscience.org/library/papers/42806090PubMed
42,706,440Spatially guided in vivo single-cell functional genomics of postnatal heart.Nat Cardiovasc Res2026https://conductscience.org/library/papers/42706440PubMed
42,555,503Computational analysis in spatial transcriptomics: methods and perspectives.Brief Bioinform2026https://conductscience.org/library/papers/42555503PubMed
42,107,049STAID: A Self-Refining Deep Learning Framework for Spatial Cell-Type Deconvolution with Biologically Informed Modeling.Adv Sci (Weinh)2026https://conductscience.org/library/papers/42107049PubMed
41,929,140Hidden immune memory niches in inflammatory skin diseases.bioRxiv2026https://conductscience.org/library/papers/41929140PubMed
41,875,135Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes.Cell Rep2026https://conductscience.org/library/papers/41875135PubMed
41,809,407The Heterogeneity and Function of Stromal Cells in the Tumor Microenvironment.Research (Wash D C)2026https://conductscience.org/library/papers/41809407PubMed
41,388,990Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.Plant Cell2026https://conductscience.org/library/papers/41388990PubMed
41,279,531A spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus.bioRxiv2025https://conductscience.org/library/papers/41279531PubMed

1 to 10 of 19

See all 19 cited by

Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed
2026-11-06
PubMed
iCite
2026-11-05
iCite
PMC's ID file
2026-11-05
PMC's ID file
NIH RePORTER's grant and paper links
2026-11-01
NIH RePORTER's grant and paper links
Trials
2026-11-12
Gene search
2026-11-11
Pipelines
2026-09-18

Sources 11

  • ChEMBL, through Open TargetsCC BY-SA 3.0
  • ClinicalTrials.govNo license stated
  • HGNCCC0
  • iCiteCC BY 4.0
  • NCBI GenePublic domain (US government)
  • NIH RePORTER's grant and paper linksPublic domain
  • Open TargetsCC0 1.0
  • PMC's ID filePublic domain (US government)
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0
Each source's terms
  • ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • ClinicalTrials.govnone stated
  • HGNCCC0: https://www.genenames.org/about/license/
  • iCiteCC BY 4.0
  • NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
  • Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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