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Paper Citation Record · LEDGER

Single-cell spatial (scs) omics: Recent developments in data analysis

As of 20 August 2026, this Paper Citation Record lists 100 of 134 outbound references and 0 inbound Pith citation observations for arXiv:2412.13591.

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

pith.paper-citation-record.v1
2412.13591 v1

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measured 100 of 134 reference resolution

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Pith citing papers itemized under the disclosed page cap.

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Reference resolution

100 of 134 outbound references displayed

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External citation measurements

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Outbound references

Observation 91d36326-cc99-4b79-bbe2-0b49915f1ab4 · outbound

This paper cites an unresolved cited work.

Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 1

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This paper cites Alseekh et al., ‘Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Alseekh et al., ‘Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices’, Nat

Reference 2

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This paper cites Stuart et al., ‘Comprehensive Integration of Single-Cell Data’, Cell, vol.

Single-cell spatial (scs) omics: Recent developments in data analysis Stuart et al., ‘Comprehensive Integration of Single-Cell Data’, Cell, vol

Reference 3

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This paper cites Marx, ‘Method of the Year: spatially resolved transcriptomics’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Marx, ‘Method of the Year: spatially resolved transcriptomics’, Nat

Reference 4

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This paper cites Eisenstein, ‘Seven technologies to watch in 2022’, Nature, vol.

Single-cell spatial (scs) omics: Recent developments in data analysis Eisenstein, ‘Seven technologies to watch in 2022’, Nature, vol

Reference 5

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This paper cites Accessed: Apr.

Single-cell spatial (scs) omics: Recent developments in data analysis Accessed: Apr

Reference 6

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 7

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 8

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This paper cites Kleino, P.

Single-cell spatial (scs) omics: Recent developments in data analysis Kleino, P

Reference 9

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

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This paper cites Ahmed et al., ‘Spatial mapping of cancer tissues by OMICS technologies’, Biochim.

Single-cell spatial (scs) omics: Recent developments in data analysis Ahmed et al., ‘Spatial mapping of cancer tissues by OMICS technologies’, Biochim

Reference 11

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 12

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This paper cites Larsson, J.

Single-cell spatial (scs) omics: Recent developments in data analysis Larsson, J

Reference 13

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This paper cites He et al., ‘Assessing the Impact of Data Preprocessing on Analyzing Next Generation Sequencing Data’, Front.

Single-cell spatial (scs) omics: Recent developments in data analysis He et al., ‘Assessing the Impact of Data Preprocessing on Analyzing Next Generation Sequencing Data’, Front

Reference 14

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This paper cites Global Attention Mechanism: Retain Information to Enhance Channel-Spatial Interactions.

Single-cell spatial (scs) omics: Recent developments in data analysis Global Attention Mechanism: Retain Information to Enhance Channel-Spatial Interactions

Reference 15

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This paper cites Mishra, A.

Single-cell spatial (scs) omics: Recent developments in data analysis Mishra, A

Reference 16

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 17

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 18

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This paper cites Yamada, D.

Single-cell spatial (scs) omics: Recent developments in data analysis Yamada, D

Reference 19

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Single-cell spatial (scs) omics: Recent developments in data analysis Tarazona, A

Reference 20

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This paper cites Lähnemann et al., ‘Eleven grand challenges in single-cell data science’, Genome Biol., vol.

Single-cell spatial (scs) omics: Recent developments in data analysis Lähnemann et al., ‘Eleven grand challenges in single-cell data science’, Genome Biol., vol

Reference 21

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Single-cell spatial (scs) omics: Recent developments in data analysis Velten and O

Reference 22

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

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This paper cites Cao et al., ‘Microfluidics-based single cell analysis: from transcriptomics to spatiotemporal multi-omics’, TrAC Trends Anal.

Single-cell spatial (scs) omics: Recent developments in data analysis Cao et al., ‘Microfluidics-based single cell analysis: from transcriptomics to spatiotemporal multi-omics’, TrAC Trends Anal

Reference 24

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

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This paper cites Heumos et al., ‘Best practices for single-cell analysis across modalities’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Heumos et al., ‘Best practices for single-cell analysis across modalities’, Nat

Reference 26

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This paper cites Wang et al., ‘Spatial transcriptomics: Technologies, applications and experimental considerations’, Genomics, vol.

Single-cell spatial (scs) omics: Recent developments in data analysis Wang et al., ‘Spatial transcriptomics: Technologies, applications and experimental considerations’, Genomics, vol

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Single-cell spatial (scs) omics: Recent developments in data analysis Vandereyken, A

Reference 28

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Single-cell spatial (scs) omics: Recent developments in data analysis Greenstreet et al., ‘DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods’, Cell Syst., vol

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

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Single-cell spatial (scs) omics: Recent developments in data analysis Moses and L

Reference 33

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 34

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Single-cell spatial (scs) omics: Recent developments in data analysis Wang et al., ‘Three-dimensional intact-tissue sequencing of single-cell transcriptional states’, Science, vol

Reference 35

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Single-cell spatial (scs) omics: Recent developments in data analysis Jiang et al., ‘A new direction in metabolomics: Analysis of the central nervous system based on spatially resolved metabolomics’, TrAC Trends Anal

Reference 36

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

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Observation 1399cf32-b811-4698-a1ce-c42e58e2eeac · outbound

This paper cites Xing et al., ‘Next Generation of Mass Spectrometry Imaging: from Micrometer to Subcellular Resolution’, Chem.

Single-cell spatial (scs) omics: Recent developments in data analysis Xing et al., ‘Next Generation of Mass Spectrometry Imaging: from Micrometer to Subcellular Resolution’, Chem

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This paper cites Alexandrov, ‘Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence’, Annu.

Single-cell spatial (scs) omics: Recent developments in data analysis Alexandrov, ‘Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence’, Annu

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Reference 40

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Reference 41

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Reference 42

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Observation c2acd9b3-93ea-4163-bc9a-5bb4f40d7996 · outbound

This paper cites Rappez et al., ‘SpaceM reveals metabolic states of single cells’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Rappez et al., ‘SpaceM reveals metabolic states of single cells’, Nat

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Observation 5de75967-841d-48be-9e88-b4e9f41b479d · outbound

This paper cites Karrobi et al., ‘Fluorescence Lifetime Imaging Microscopy (FLIM) reveals spatial- metabolic changes in 3D breast cancer spheroids’, Sci.

Single-cell spatial (scs) omics: Recent developments in data analysis Karrobi et al., ‘Fluorescence Lifetime Imaging Microscopy (FLIM) reveals spatial- metabolic changes in 3D breast cancer spheroids’, Sci

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Reference 45

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Observation 57ff1fb2-c822-4493-ade2-f3e04c708087 · outbound

This paper cites Yue et al., ‘A guidebook of spatial transcriptomic technologies, data resources and analysis approaches’, Comput.

Single-cell spatial (scs) omics: Recent developments in data analysis Yue et al., ‘A guidebook of spatial transcriptomic technologies, data resources and analysis approaches’, Comput

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Observation 73a1ff20-91b0-4976-8fd9-f044e04318b0 · outbound

This paper cites Ràfols et al., ‘Signal preprocessing, multivariate analysis and software tools for MA(LDI)-TOF mass spectrometry imaging for biological applications’, Mass Spectrom.

Single-cell spatial (scs) omics: Recent developments in data analysis Ràfols et al., ‘Signal preprocessing, multivariate analysis and software tools for MA(LDI)-TOF mass spectrometry imaging for biological applications’, Mass Spectrom

Reference 47

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Observation ae8aec8a-9d3f-4a17-af6a-ca4fbe53d1b5 · outbound

This paper cites Baquer, L.

Single-cell spatial (scs) omics: Recent developments in data analysis Baquer, L

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Observation d33bbfa8-22ee-413f-b1cf-28976265c947 · outbound

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Reference 49

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Observation 0e3fee58-1d43-4782-93ba-b0f4f4946d19 · outbound

This paper cites Park et al., ‘Cell segmentation-free inference of cell types from in situ transcriptomics data’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Park et al., ‘Cell segmentation-free inference of cell types from in situ transcriptomics data’, Nat

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Observation 5322e37b-8cae-4262-917c-53ae742fd263 · outbound

This paper cites Hao et al., ‘Integrated analysis of multimodal single-cell data’, Cell, vol.

Single-cell spatial (scs) omics: Recent developments in data analysis Hao et al., ‘Integrated analysis of multimodal single-cell data’, Cell, vol

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Observation b3bbd467-43cd-4798-b18f-12cd8560b24d · outbound

This paper cites Palla et al., ‘Squidpy: a scalable framework for spatial omics analysis’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Palla et al., ‘Squidpy: a scalable framework for spatial omics analysis’, Nat

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Observation 73e00a82-9a5f-4fc6-b8c6-4fea4e8cda3f · outbound

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Reference 53

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Observation 46ee0cca-3cfc-4b62-a49c-9bf28a8eeae2 · outbound

This paper cites Dries et al., ‘Giotto: a toolbox for integrative analysis and visualization of spatial expression data’, Genome Biol., vol.

Single-cell spatial (scs) omics: Recent developments in data analysis Dries et al., ‘Giotto: a toolbox for integrative analysis and visualization of spatial expression data’, Genome Biol., vol

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This paper cites Hu et al., ‘Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology’, Nat.

Single-cell spatial (scs) omics: Recent developments in data analysis Hu et al., ‘Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology’, Nat

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Observation 1dad9028-250a-404d-8652-d82dc3a5689f · outbound

This paper cites STalign: Alignment of Spatial Transcriptomics Data Using Diffeomorphic Metric Mapping,.

Single-cell spatial (scs) omics: Recent developments in data analysis STalign: Alignment of Spatial Transcriptomics Data Using Diffeomorphic Metric Mapping,

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Observation db18bb80-e5fc-43a2-8034-cd0d378c29f4 · outbound

This paper cites SANTO: A Coarse-to-Fine Alignment and Stitching Method for Spatial Omics,.

Single-cell spatial (scs) omics: Recent developments in data analysis SANTO: A Coarse-to-Fine Alignment and Stitching Method for Spatial Omics,

Reference 57

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Observation 1a36c5ba-a803-4d2a-a424-a7a0c9dcfcf8 · outbound

This paper cites Cross- Modality Mapping Using Image Varifolds to Align Tissue-Scale Atlases to Molecular-Scale Measures with Application to 2D Brain Sections,.

Single-cell spatial (scs) omics: Recent developments in data analysis Cross- Modality Mapping Using Image Varifolds to Align Tissue-Scale Atlases to Molecular-Scale Measures with Application to 2D Brain Sections,

Reference 58

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Observation 69255bf2-d051-4dbe-afb6-148a49cf697e · outbound

This paper cites Search and Match across Spatial Omics Samples at Single-Cell Resolution,.

Single-cell spatial (scs) omics: Recent developments in data analysis Search and Match across Spatial Omics Samples at Single-Cell Resolution,

Reference 59

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Observation 787a9f2c-1ad8-4428-a3df-c6b6b3dc8bac · outbound

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Single-cell spatial (scs) omics: Recent developments in data analysis Koutrouli, E

Reference 60

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Observation b10d8519-2152-4f01-afe7-17480fa6f938 · outbound

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Single-cell spatial (scs) omics: Recent developments in data analysis McInnes, J

Reference 61

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Observation a3d8ec89-065e-47ce-856e-e1c6ce0cbafb · outbound

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 62

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Observation 9a8483c8-4cc9-49b9-a032-df02bf5f7161 · outbound

This paper cites Single-Cell Multi-Omic Integration Compares and Contrasts Features of Brain Cell Identity,.

Single-cell spatial (scs) omics: Recent developments in data analysis Single-Cell Multi-Omic Integration Compares and Contrasts Features of Brain Cell Identity,

Reference 63

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Single-cell spatial (scs) omics: Recent developments in data analysis Visualizing structure and transitions in high-dimensional biological data,

Reference 64

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Observation 865b3eaa-34ec-4cc1-97af-d7865ec2bdd7 · outbound

This paper cites Seamless Integration of Image and Molecular Analysis for Spatial Transcriptomics Workflows,.

Single-cell spatial (scs) omics: Recent developments in data analysis Seamless Integration of Image and Molecular Analysis for Spatial Transcriptomics Workflows,

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Observation d4ccaa07-2db0-4492-a93e-efeac7f0f95b · outbound

This paper cites Jolliffe, ‘Principal Component Analysis for Special Types of Data’, in Principal Component Analysis, in Springer Series in Statistics.

Single-cell spatial (scs) omics: Recent developments in data analysis Jolliffe, ‘Principal Component Analysis for Special Types of Data’, in Principal Component Analysis, in Springer Series in Statistics

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 67

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 68

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Observation 98d6b90a-f57a-4b2f-beda-e8f1aa0488b5 · outbound

This paper cites Barker and W.

Single-cell spatial (scs) omics: Recent developments in data analysis Barker and W

Reference 69

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 70

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Observation 9325a33f-b2b2-4bd1-b458-9f582a2d3fe3 · outbound

This paper cites Lê Cao, D.

Single-cell spatial (scs) omics: Recent developments in data analysis Lê Cao, D

Reference 71

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Observation 78d0c7cc-8baf-482b-aa6a-18d4b694bbbd · outbound

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 72

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Observation 2f184cc2-83a1-4e2b-8761-f36139ed93aa · outbound

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Single-cell spatial (scs) omics: Recent developments in data analysis Lee and H

Reference 73

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Single-cell spatial (scs) omics: Recent developments in data analysis Borg and P

Reference 74

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Observation 89fccbab-3d41-4daa-b1e6-0e84d1b1e5dc · outbound

This paper cites van der Maaten and G.

Single-cell spatial (scs) omics: Recent developments in data analysis van der Maaten and G

Reference 75

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Observation 7e87ed04-6a0e-4c60-91c2-cb1751c17d80 · outbound

This paper cites Szymańska, E.

Single-cell spatial (scs) omics: Recent developments in data analysis Szymańska, E

Reference 76

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This paper cites an unresolved cited work.

Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 77

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This paper cites an unresolved cited work.

Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 78

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Observation 7fab80e7-a748-4317-94b6-05c33e31c4da · outbound

This paper cites Kobak and P.

Single-cell spatial (scs) omics: Recent developments in data analysis Kobak and P

Reference 79

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 80

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Observation c76115d4-4fea-4218-ab11-bd88aec6453e · outbound

This paper cites Smets et al., ‘Evaluation of Distance Metrics and Spatial Autocorrelation in Uniform Manifold Approximation and Projection Applied to Mass Spectrometry Imaging Data’, Anal.

Single-cell spatial (scs) omics: Recent developments in data analysis Smets et al., ‘Evaluation of Distance Metrics and Spatial Autocorrelation in Uniform Manifold Approximation and Projection Applied to Mass Spectrometry Imaging Data’, Anal

Reference 81

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Observation 3f8bd531-596d-4507-b18a-65c8c5ef4d52 · outbound

This paper cites Sarycheva et al., ‘Structure-Preserving and Perceptually Consistent Approach for Visualization of Mass Spectrometry Imaging Datasets’, Anal.

Single-cell spatial (scs) omics: Recent developments in data analysis Sarycheva et al., ‘Structure-Preserving and Perceptually Consistent Approach for Visualization of Mass Spectrometry Imaging Datasets’, Anal

Reference 82

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 83

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Observation 76dcb72f-9cac-4503-8687-3b8bc53f01c4 · outbound

This paper cites Shang and X.

Single-cell spatial (scs) omics: Recent developments in data analysis Shang and X

Reference 84

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Observation 79049d4c-a728-455c-8f88-014ce7363ad4 · outbound

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 85

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Observation ef2cc478-f9ad-4b0a-84ef-13677e7b9d11 · outbound

This paper cites Chidester, T.

Single-cell spatial (scs) omics: Recent developments in data analysis Chidester, T

Reference 86

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This paper cites Moses et al., ‘Voyager: exploratory single-cell genomics data analysis with geospatial statistics’, bioRxiv, p.

Single-cell spatial (scs) omics: Recent developments in data analysis Moses et al., ‘Voyager: exploratory single-cell genomics data analysis with geospatial statistics’, bioRxiv, p

Reference 87

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 88

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 89

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Observation 72bb9757-c84f-4559-a4af-a48882c6d8d6 · outbound

This paper cites de Juan and R.

Single-cell spatial (scs) omics: Recent developments in data analysis de Juan and R

Reference 90

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Observation 3b28d0ba-b858-4b42-8ee1-c4acdad91442 · outbound

This paper cites Ruckebusch and L.

Single-cell spatial (scs) omics: Recent developments in data analysis Ruckebusch and L

Reference 91

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Observation 72ace907-6e4e-40b2-ad18-e9949de9014e · outbound

This paper cites Jaumot and R.

Single-cell spatial (scs) omics: Recent developments in data analysis Jaumot and R

Reference 92

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Observation a2f2bf97-910f-4f2c-8179-a51c706f6815 · outbound

This paper cites Hugelier, O.

Single-cell spatial (scs) omics: Recent developments in data analysis Hugelier, O

Reference 93

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Observation 1c82f978-9efd-463b-8599-44a4310e29cb · outbound

This paper cites Firmani, S.

Single-cell spatial (scs) omics: Recent developments in data analysis Firmani, S

Reference 94

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Observation 6b61072f-04fe-4fef-a590-440053df225f · outbound

This paper cites Vitale, S.

Single-cell spatial (scs) omics: Recent developments in data analysis Vitale, S

Reference 95

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Observation bd0fef4e-9395-478a-a8ab-969d1bb875c4 · outbound

This paper cites Li Vigni, J.

Single-cell spatial (scs) omics: Recent developments in data analysis Li Vigni, J

Reference 96

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verified exact
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Source-reported events for the cited work

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 97

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Source-reported events for the cited work

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Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 98

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Source-reported events for the cited work

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Observation 02032b3b-c547-4b77-a87b-b8ce66339256 · outbound

This paper cites an unresolved cited work.

Single-cell spatial (scs) omics: Recent developments in data analysis Unresolved cited work

Reference 99

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No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

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Observation 3c71c904-2367-401e-b46f-d396a42da6e9 · outbound

This paper cites Kircheis and D.

Single-cell spatial (scs) omics: Recent developments in data analysis Kircheis and D

Reference 100

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verified exact
doi, observed 2026-08-11T13:01:42.338264Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

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Pith citing papers

No inbound Pith citation observations are available.