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Advancing biological understanding of cellular senescence with computational multiomics.

Publication ,  Journal Article
Li, S; Agudelo Garcia, PA; Aliferis, C; Becich, MJ; Calyeca, J; Cosgrove, BD; Elisseeff, J; Farzad, N; Fertig, EJ; Glass, C; Gu, L; Hu, Q ...
Published in: Nat Genet
October 2025

Cellular senescence is a complex biological process that plays a pathophysiological role in aging and age-related diseases. The biological understanding of senescence at the cellular and tissue levels remains incomplete due to the lack of specific biomarkers as well as the relative rarity of senescent cells, their phenotypic heterogeneity and dynamic features. This Review provides a comprehensive overview of multiomic approaches for the characterization and biological understanding of cellular senescence. The technical capability and challenges of each approach are discussed, and practical guidelines are provided for selecting tools for identifying, characterizing and spatially mapping senescent cells. The importance of computational analyses in multiomics research, including senescent cell identification, signature detection and interactions of senescent cells with microenvironments, is highlighted. Moreover, tissue-specific case studies and experimental design considerations for individual organs are presented. Finally, future directions and the potential impact of multiomic approaches on the biological understanding of cellular senescence are discussed.

Duke Scholars

Published In

Nat Genet

DOI

EISSN

1546-1718

Publication Date

October 2025

Volume

57

Issue

10

Start / End Page

2381 / 2394

Location

United States

Related Subject Headings

  • Proteomics
  • Multiomics
  • Humans
  • Genomics
  • Developmental Biology
  • Computational Biology
  • Cellular Senescence
  • Animals
  • Aging
  • 3105 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
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Li, S., Agudelo Garcia, P. A., Aliferis, C., Becich, M. J., Calyeca, J., Cosgrove, B. D., … SenNet Consortium. (2025). Advancing biological understanding of cellular senescence with computational multiomics. Nat Genet, 57(10), 2381–2394. https://doi.org/10.1038/s41588-025-02314-y
Li, Sheng, Paula A. Agudelo Garcia, Constantin Aliferis, Michael J. Becich, Jazmin Calyeca, Benjamin D. Cosgrove, Jennifer Elisseeff, et al. “Advancing biological understanding of cellular senescence with computational multiomics.Nat Genet 57, no. 10 (October 2025): 2381–94. https://doi.org/10.1038/s41588-025-02314-y.
Li S, Agudelo Garcia PA, Aliferis C, Becich MJ, Calyeca J, Cosgrove BD, et al. Advancing biological understanding of cellular senescence with computational multiomics. Nat Genet. 2025 Oct;57(10):2381–94.
Li, Sheng, et al. “Advancing biological understanding of cellular senescence with computational multiomics.Nat Genet, vol. 57, no. 10, Oct. 2025, pp. 2381–94. Pubmed, doi:10.1038/s41588-025-02314-y.
Li S, Agudelo Garcia PA, Aliferis C, Becich MJ, Calyeca J, Cosgrove BD, Elisseeff J, Farzad N, Fertig EJ, Glass C, Gu L, Hu Q, Ji Z, Königshoff M, LeBrasseur NK, Li D, Ma A, Ma Q, Menon V, Mitchell JT, Mora AL, Nagaraj S, Nelson AC, Niedernhofer LJ, Rojas M, Taha HB, Wang J, Wang S, Wu P-H, Xie J, Xu M, Yu M, Zhang X, Zhao Y, Adams PD, Aguayo-Mazzucato C, Baker DJ, Benz C, Bernlohr DA, Bueno M, Chen J, Childs BG, Chuang JH, Chung D, Dileepan M, Ding L, Dong M, Duncan F, Enninful A, Flynn WF, Franco AC, Furman D, Garovic V, Halene S, Herman AB, Hertzel AV, Iwasaki K, Jeon H, Kang JW, Karmakar S, Kirkland JL, Korstanje R, Kummerfeld E, Lee JH, Liu Y, Lu Y, Lugo-Martinez J, Martini H, Melov S, Musi N, Passos JF, Peters ST, Rahman I, Ramasamy R, Rindone AN, Robbins PD, Robson P, Rodriguez-Lopez J, Rosas L, Rosenthal N, Schafer MJ, Schilling B, Schmidt EL, Schneider K, Sengupta K, Shu J, So PTC, Sun L, Tchkonia T, Teneche MG, Vanegas N, Yin S, Zhang K, Zhu Q, Fan R, SenNet Consortium. Advancing biological understanding of cellular senescence with computational multiomics. Nat Genet. 2025 Oct;57(10):2381–2394.

Published In

Nat Genet

DOI

EISSN

1546-1718

Publication Date

October 2025

Volume

57

Issue

10

Start / End Page

2381 / 2394

Location

United States

Related Subject Headings

  • Proteomics
  • Multiomics
  • Humans
  • Genomics
  • Developmental Biology
  • Computational Biology
  • Cellular Senescence
  • Animals
  • Aging
  • 3105 Genetics