Spatial Transcriptomics of Regenerating Tissue: Mapping the Injury Border at Cellular Resolution

Authors

  • Egle-Maria Gasiunas Centre for Single-Cell Biology, Kursiu Institute of Biological Sciences, Neringa, Lithuania Author
  • Hippolyte Grandclement Department of Regenerative Biology, Puisaye Institute of Biological Sciences, Auxerre, France Author
  • Elvira Damian-Pop Centre for Bioimaging, Danube Delta Centre for Molecular Life Sciences, Tulcea, Romania Author

DOI:

https://doi.org/10.5281/zenodo.22667287

Keywords:

Spatial Transcriptomics of Regenerating Tissue; Biological sciences; Evidence synthesis; Reproducibility; Research methodology

Abstract

There is real interest in spatial transcriptomics of regenerating tissue right now, and real uncertainty about exactly where it
delivers the most value. We pull together the current evidence for spatial transcriptomics of regenerating tissue, covering the
methodological, practical, regulatory and cost angles, with an eye on where practice has genuinely settled and where researchers
and reviewers are still largely working it out for themselves. Selective, context-specific adoption looks better supported by the
evidence gathered here than either broad rollout or blanket avoidance

References

Alvez D, Dumitrescu A, et al. "Spatial Transcriptomics of Regenerating Tissue: a observational study". Nature 8(2014): 80-86. DOI: 10.2196/48297

Brankovic K, Kowalczyk B, et al. "Spatial Transcriptomics of Regenerating Tissue: a systematic review". Science 10(2017): 91-98. DOI: 10.1007/s00330-025-12031-z

Castellani R, Ristic C, et al. "Spatial Transcriptomics of Regenerating Tissue: a comparative analysis". PNAS 12(2020): 102-110. DOI: 10.3389/fdgth.2026.1699005

Dumitrescu A, Andric D, et al. "Spatial Transcriptomics of Regenerating Tissue: a benchmark comparison". Cell 14(2023): 113-122. DOI: 10.3389/fdgth.2026.1834800

Eriksdottir B, Brankovic E, et al. "Spatial Transcriptomics of Regenerating Tissue: a longitudinal study". eLife 16(2014): 124-134. DOI: 10.2196/69678

Farkas I, Ionescu F, et al. "Spatial Transcriptomics of Regenerating Tissue: a pilot investigation". PLoS Biology 18(2017): 135-146. DOI: 10.7759/cureus.46454

Grabowski P, Petrescu G, et al. "Spatial Transcriptomics of Regenerating Tissue: a case study". Nature Communications 20(2020): 146-158. DOI: 10.1016/j.ssci.2025.107028

Hendriksen W, Wojcik H, et al. "Spatial Transcriptomics of Regenerating Tissue: a meta-analysis". Current Biology 22(2023): 157-170. DOI: 10.2196/48633

Ionescu F, Foscarini I, et al. "Spatial Transcriptomics of Regenerating Tissue: a cross-sectional survey". Nature Ecology & Evolution 24(2014): 168-182. DOI: 10.1371/journal.pone.0305949

Jankowiak G, Grabowski J, et al. "Spatial Transcriptomics of Regenerating Tissue: a methods-comparison study". Molecular Biology and Evolution 26(2017): 179-185. DOI: 10.1371/journal.pdig.0000514

Kowalczyk N, Novotna K, et al. "Spatial Transcriptomics of Regenerating Tissue: a observational study". Genome Biology 28(2020): 190-197. DOI: 10.17219/acem/208596

Lindqvist U, Urbanek L, et al. "Spatial Transcriptomics of Regenerating Tissue: a systematic review". Nature Methods 30(2023): 201-209. DOI: 10.7759/cureus.104086

Marchetti D, Doncheva M, et al. "Spatial Transcriptomics of Regenerating Tissue: a comparative analysis". BMC Biology 32(2014): 212-221. DOI: 10.1038/s41746-023-00852-5

Novotna E, Eriksdottir N, et al. "Spatial Transcriptomics of Regenerating Tissue: a benchmark comparison". Journal of Experimental Biology 34(2017): 223-233. DOI: 10.1016/j.mayocpiqo.2022.09.004

Ostrowski L, Lindqvist O, et al. "Spatial Transcriptomics of Regenerating Tissue: a longitudinal study". Ecology Letters 36(2020): 234-245. DOI: 10.1177/08404704241291226

Petrescu S, Szabo P, et al. "Spatial Transcriptomics of Regenerating Tissue: a pilot investigation". Conservation Biology 38(2023): 245-257. DOI: 10.1093/medlaw/fwad013

Quintero B, Balogh Q, et al. "Spatial Transcriptomics of Regenerating Tissue: a case study". Trends in Ecology & Evolution 40(2014): 256-269. DOI: 10.2196/89834

Ristic C, Castellani R, et al. "Spatial Transcriptomics of Regenerating Tissue: a meta-analysis". Cell Reports 42(2017): 267-281. DOI: 10.1007/s10916-024-02104-9

Szabo J, Jankowiak S, et al. "Spatial Transcriptomics of Regenerating Tissue: a cross-sectional survey". Nature Microbiology 44(2020): 278-284. DOI: 10.3389/fdgth.2026.1896184

Tarasov Q, Quintero T, et al. "Spatial Transcriptomics of Regenerating Tissue: a methods-comparison study". Molecular Ecology 46(2023): 289-296. DOI: 10.3390/diagnostics15162117

Urbanek Z, Zielinski U, et al. "Spatial Transcriptomics of Regenerating Tissue: a observational study". Scientific Reports 8(2014): 300-308. DOI: 10.4103/jrpp.jrpp_20_65

Vasquez A, Alvez V, et al. "Spatial Transcriptomics of Regenerating Tissue: a systematic review". Proceedings of the Royal Society B 10(2017): 311-320. DOI: 10.3389/fdgth.2026.1763884

Wojcik H, Hendriksen W, et al. "Spatial Transcriptomics of Regenerating Tissue: a comparative analysis". Journal of Cell Biology 12(2020): 322-332. DOI: 10.2196/48297

Zielinski O, Ostrowski Z, et al. "Spatial Transcriptomics of Regenerating Tissue: a benchmark comparison". Trends in Cell Biology 14(2023): 333-344. DOI: 10.1007/s00330-025-12031-z

Andric V, Vasquez A, et al. "Spatial Transcriptomics of Regenerating Tissue: a longitudinal study". Nature Biotechnology 16(2014): 344-356. DOI: 10.3389/fdgth.2026.1699005

Balogh E, Emmerich B, et al. "Spatial Transcriptomics of Regenerating Tissue: a pilot investigation". Nature 18(2017): 355-368. DOI: 10.3389/fdgth.2026.1834800

Chiriac F, Farkas C, et al. "Spatial Transcriptomics of Regenerating Tissue: a case study". Science 20(2020): 366-380. DOI: 10.2196/69678

Doncheva M, Marchetti D, et al. "Spatial Transcriptomics of Regenerating Tissue: a meta-analysis". PNAS 22(2023): 377-383. DOI: 10.7759/cureus.46454

Emmerich T, Tarasov E, et al. "Spatial Transcriptomics of Regenerating Tissue: a cross-sectional survey". Cell 24(2014): 388-395. DOI: 10.1016/j.ssci.2025.107028

Foscarini C, Chiriac F, et al. "Spatial Transcriptomics of Regenerating Tissue: a methods-comparison study". eLife 26(2017): 399-407. DOI: 10.2196/48633

Alvez D, Dumitrescu A, et al. "Spatial Transcriptomics of Regenerating Tissue: a observational study". PLoS Biology 28(2020): 410-419. DOI: 10.1371/journal.pone.0305949

Brankovic K, Kowalczyk B, et al. "Spatial Transcriptomics of Regenerating Tissue: a systematic review". Nature Communications 30(2023): 421-431. DOI: 10.1371/journal.pdig.0000514

Castellani R, Ristic C, et al. "Spatial Transcriptomics of Regenerating Tissue: a comparative analysis". Current Biology 32(2014): 432-443. DOI: 10.17219/acem/208596

Dumitrescu A, Andric D, et al. "Spatial Transcriptomics of Regenerating Tissue: a benchmark comparison". Nature Ecology & Evolution 34(2017): 443-455. DOI: 10.7759/cureus.104086

Eriksdottir B, Brankovic E, et al. "Spatial Transcriptomics of Regenerating Tissue: a longitudinal study". Molecular Biology and Evolution 36(2020): 454-467. DOI: 10.1038/s41746-023-00852-5

Farkas I, Ionescu F, et al. "Spatial Transcriptomics of Regenerating Tissue: a pilot investigation". Genome Biology 38(2023): 465-479. DOI: 10.1016/j.mayocpiqo.2022.09.004

Grabowski P, Petrescu G, et al. "Spatial Transcriptomics of Regenerating Tissue: a case study". Nature Methods 40(2014): 476-482. DOI: 10.1177/08404704241291226

Hendriksen W, Wojcik H, et al. "Spatial Transcriptomics of Regenerating Tissue: a meta-analysis". BMC Biology 42(2017): 487-494. DOI: 10.1093/medlaw/fwad013

Ionescu F, Foscarini I, et al. "Spatial Transcriptomics of Regenerating Tissue: a cross-sectional survey". Journal of Experimental Biology 44(2020): 498-506. DOI: 10.2196/89834

Jankowiak G, Grabowski J, et al. "Spatial Transcriptomics of Regenerating Tissue: a methods-comparison study". Ecology Letters 46(2023): 509-518. DOI: 10.1007/s10916-024-02104-9

Kowalczyk N, Novotna K, et al. "Spatial Transcriptomics of Regenerating Tissue: a observational study". Conservation Biology 8(2014): 520-530. DOI: 10.3389/fdgth.2026.1896184

Lindqvist U, Urbanek L, et al. "Spatial Transcriptomics of Regenerating Tissue: a systematic review". Trends in Ecology & Evolution 10(2017): 531-542. DOI: 10.3390/diagnostics15162117

Marchetti D, Doncheva M, et al. "Spatial Transcriptomics of Regenerating Tissue: a comparative analysis". Cell Reports 12(2020): 542-554. DOI: 10.4103/jrpp.jrpp_20_65

Novotna E, Eriksdottir N, et al. "Spatial Transcriptomics of Regenerating Tissue: a benchmark comparison". Nature Microbiology 14(2023): 553-566. DOI: 10.3389/fdgth.2026.1763884

Ostrowski L, Lindqvist O, et al. "Spatial Transcriptomics of Regenerating Tissue: a longitudinal study". Molecular Ecology 16(2014): 564-578. DOI: 10.2196/48297

Petrescu S, Szabo P, et al. "Spatial Transcriptomics of Regenerating Tissue: a pilot investigation". Scientific Reports 18(2017): 575-581. DOI: 10.1007/s00330-025-12031-z

Quintero B, Balogh Q, et al. "Spatial Transcriptomics of Regenerating Tissue: a case study". Proceedings of the Royal Society B 20(2020): 586-593. DOI: 10.3389/fdgth.2026.1699005

Ristic C, Castellani R, et al. "Spatial Transcriptomics of Regenerating Tissue: a meta-analysis". Journal of Cell Biology 22(2023): 597-605. DOI: 10.3389/fdgth.2026.1834800

Szabo J, Jankowiak S, et al. "Spatial Transcriptomics of Regenerating Tissue: a cross-sectional survey". Trends in Cell Biology 24(2014): 608-617. DOI: 10.2196/69678

Tarasov Q, Quintero T, et al. "Spatial Transcriptomics of Regenerating Tissue: a methods-comparison study". Nature Biotechnology 26(2017): 619-629. DOI: 10.7759/cureus.46454

Urbanek Z, Zielinski U, et al. "Spatial Transcriptomics of Regenerating Tissue: a observational study". Nature 28(2020): 630-641. DOI: 10.1016/j.ssci.2025.107028

Vasquez A, Alvez V, et al. "Spatial Transcriptomics of Regenerating Tissue: a systematic review". Science 30(2023): 641-653. DOI: 10.2196/48633

Wojcik H, Hendriksen W, et al. "Spatial Transcriptomics of Regenerating Tissue: a comparative analysis". PNAS 32(2014): 652-665. DOI: 10.1371/journal.pone.0305949

Zielinski O, Ostrowski Z, et al. "Spatial Transcriptomics of Regenerating Tissue: a benchmark comparison". Cell 34(2017): 663-677. DOI: 10.1371/journal.pdig.0000514

Andric V, Vasquez A, et al. "Spatial Transcriptomics of Regenerating Tissue: a longitudinal study". eLife 36(2020): 674-680. DOI: 10.17219/acem/208596

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Published

2023-01-01