Evidence map›Paper›PMID 40954249›Full record

ReviewNature genetics2025

Advancing biological understanding of cellular senescence with computational multiomics.

Sheng Li, Paula A Agudelo Garcia, Constantin Aliferis, Michael J Becich, Jazmin Calyeca, Benjamin D Cosgrove, Jennifer Elisseeff, Negin Farzad, Elana J Fertig, Carolyn Glass and 88 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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  16. Prosaposin in CNS health and disease, metabolic stress and exercise adaptation.Journal of molecular medicine (Berlin, Germany) · 2026
    Review
  17. Special Issue "Molecular Progression in Genome-Related Diseases".International journal of molecular sciences · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

98 authors.

Sheng LiDepartment of Cancer Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. sheng.li@med.usc.edu.ORCID http://orcid.org/0000-0002-9543-6274
Paula A Agudelo GarciaDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0002-6764-6450
Constantin AliferisMedical School and Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA.
Michael J BecichDepartment of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0001-5998-8074
Jazmin CalyecaDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.
Benjamin D CosgroveMeinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
Jennifer ElisseeffJohns Hopkins University, Baltimore, MD, USA.
Negin FarzadDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
Elana J FertigInstitute for Genome Sciences, School of Medicine, University of Maryland, College Park, MD, USA.ORCID http://orcid.org/0000-0003-3204-342X
Carolyn GlassDepartment of Pathology, Duke University, Durham, NC, USA.
Liangcai GuDepartment of Biochemistry, School of Medicine, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-8232-6025
Qianjiang HuCenter for Lung Aging and Regeneration, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0003-1069-3181
Zhicheng JiDepartment of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.ORCID http://orcid.org/0000-0002-9457-4704
Melanie KönigshoffCenter for Lung Aging and Regeneration, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Nathan K LeBrasseurRobert and Arlene Kogod Center on Aging, Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0002-2002-0418
Dongmei LiDepartment of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, USA.
Anjun MaDepartment of Biomedical Informatics, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0001-6269-398X
Qin MaDepartment of Biomedical Informatics, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0002-3264-8392
Vilas MenonCenter for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-4096-8601
Jacob T MitchellDepartment of Oncology, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-5370-9692
Ana L MoraDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.
Sushma NagarajDepartment of Oncology, Johns Hopkins University, Baltimore, MD, USA.
Andrew C NelsonDepartment of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
Laura J NiedernhoferMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0002-1074-1385
Mauricio RojasDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0001-7340-4784
Hash Brown TahaDepartment of Cancer Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0009-0007-3056-8878
Jinhua WangMasonic Cancer Center and Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA.
Siyuan WangDepartment of Genetics, Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-6550-4064
Pei-Hsun WuInstitute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-7371-2960
Jichun XieDepartment of Biostatistics and Bioinformatics, Department of Mathematics, Duke University, Durham, NC, USA.
Ming XuInstitute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0002-4477-939X
Miao YuThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-2804-6014
Xu ZhangRobert and Arlene Kogod Center on Aging, Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0002-9784-0481
Yue ZhaoThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Peter D AdamsSanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0684-1770
Cristina Aguayo-MazzucatoIslet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Boston, MA, USA.
Darren J BakerDepartment of Biochemistry and Molecular Biology, Department of Pediatrics, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0001-9006-1939
Christopher BenzBuck Institute for Research on Aging, Novato, CA, USA.ORCID http://orcid.org/0000-0001-5479-4641
David A BernlohrMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
Marta BuenoCenter for Lung Aging and Regeneration, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Jin ChenCenter for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
Bennett G ChildsDepartment of Biochemistry and Molecular Biology, Department of Pediatrics, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0001-6078-0588
Jeffrey H ChuangThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-3298-2358
Dongjun ChungDepartment of Biomedical Informatics, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0002-8072-5671
Mythili DileepanMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID http://orcid.org/0000-0003-1517-2975
Mingze DongDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7367-6819
Francesca DuncanDepartment of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Archibald EnninfulDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
William F FlynnThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0001-6533-0340
Ana Catarina FrancoRobert and Arlene Kogod Center on Aging, Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
David FurmanBuck Institute for Research on Aging, Novato, CA, USA.ORCID http://orcid.org/0000-0002-3654-9519
Vesna GarovicDivision of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
Stephanie HaleneDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-2737-9810
Allison B HermanLaboratory of Cardiovascular Science, National Institute on Aging, Baltimore, MD, USA.
Ann V HertzelMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0002-9172-7939
Kanako IwasakiIslet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Boston, MA, USA.ORCID http://orcid.org/0000-0003-1671-3980
Hyeongseon JeonDepartment of Biomedical Informatics, the Ohio State University, Columbus, OH, USA.
Jeon Woong KangLaser Biomedical Research Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
Shilpita KarmakarThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
James L KirklandDepartment of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-1676-4905
Ron KorstanjeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-2808-1610
Erich KummerfeldInstitute for Health Informatics, University of Minnesota, Minneapolis, MN, USA.
Jun Hee LeeDepartment of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
Yang LiuDepartment of Cancer Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-4433-1066
Yao LuDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
Jose Lugo-MartinezRay and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
Helene MartiniRobert and Arlene Kogod Center on Aging, Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0001-8789-4585
Simon MelovBuck Institute for Research on Aging, Novato, CA, USA.ORCID http://orcid.org/0000-0001-8554-2834
Nicolas MusiDepartment of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
João F PassosRobert and Arlene Kogod Center on Aging, Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0001-8765-1890
Samuel T PetersMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
Irfan RahmanDepartment of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, USA.
Ramalakshmi RamasamyThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Alexandra N RindoneInstitute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-2291-5933
Paul D RobbinsMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0003-1068-7099
Paul RobsonThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-0191-3958
Jhonny Rodriguez-LopezDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0009-0007-0637-8839
Lorena RosasDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.
Nadia RosenthalThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-7599-7365
Marissa J SchaferRobert and Arlene Kogod Center on Aging, Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.ORCID http://orcid.org/0000-0002-1470-1583
Birgit SchillingBuck Institute for Research on Aging, Novato, CA, USA.ORCID http://orcid.org/0000-0001-9907-2749
Elizabeth L SchmidtMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0001-8111-8382
Kevin SchneiderBuck Institute for Research on Aging, Novato, CA, USA.
Kaustav SenguptaThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Jian ShuCutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA, USA.
Peter T C SoDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Li SunDepartment of Biochemistry, School of Medicine, University of Washington, Seattle, WA, USA.
Tamar TchkoniaDepartment of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-4623-7145
Marcos G TenecheSanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4785-7987
Natalia VanegasDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0001-5135-1714
Julia WangDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Juan XieDepartment of Biomedical Informatics, the Ohio State University, Columbus, OH, USA.
Shanshan YinSanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Ke ZhangCutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA, USA.
Quan ZhuDepartment of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
Rong FanDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7805-8059
SenNet Consortium

Funding

TriState SenNET (Lung and Heart) Tissue Map and Atlas consortiumU54AG075931 · NIA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI TOREN FINKEL, Melanie Koenigshoff · 2021 to 2026
$14.0M
The KAPP-Sen Tissue Mapping Center CollaborativeU54AG075941 · NIA · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GAROVIC, VESNA D, KUCHEL, GEORGE A · 2021 to 2025
$13.8M
The Duke Senescent Cell Evaluations in Normal Tissues (SCENT) Mapping CenterU54AG075936 · NIA · DUKE UNIVERSITY · PI LEE, PATTY J · 2021 to 2025
$12.7M
Senescent cell mapping, identification and validation for human somatic and reproductive tissuesU54AG075932 · NIA · BUCK INSTITUTE FOR RESEARCH ON AGING · PI Simon Melov, Birgit Schilling · 2021 to 2026
$12.5M
Midwest Murine-Tissue Mapping Center (MM-TMC)U54AG079754 · NIA · UNIVERSITY OF MINNESOTA · PI GR Scott Budinger, Sundeep Khosla · 2022 to 2026
$11.5M
The Jackson Laboratory Senescence Tissue Mapping Center (JAX-Sen TMC) - Data Analysis CoreU54AG079753 · NIA · JACKSON LABORATORY · PI KORSTANJE, RONNY, ROBSON, PAUL · 2022 to 2025
$11.0M
Minnesota Tissue Mapping Center for Senescent CellsU54AG076041 · NIA · UNIVERSITY OF MINNESOTA · PI Constantin F. Aliferis, LAURA Jane NIEDERNHOFER · 2021 to 2026
$10.5M
WU-SN-TMC Data Analysis CoreU54AG075934 · NIA · WASHINGTON UNIVERSITY · PI FENG CHEN, Li Ding · 2021 to 2026
$8.0M
Effect of Aging on Preadipocyte DifferentiationR37AG013925 · NIA · MAYO CLINIC ROCHESTER · PI KIRKLAND, JAMES L. · 2016 to 2025
$6.6M
JHU-Mayo-NIA Murine Senescence Mapping Program (JMN-MSMP)U54AG079779 · NIA · JOHNS HOPKINS UNIVERSITY · PI JENNIFER H ELISSEEFF · 2022 to 2026
$6.4M
Translational Geroscience NetworkR33AG061456 · NIA · MAYO CLINIC ROCHESTER · PI JAMES L. KIRKLAND, STEPHEN B. KRITCHEVSKY · 2019 to 2026
$6.2M
Single-cell label-free identification of senescence by Raman microscopy and spatial genomicsUH3CA275687 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Jeon Woong Kang, Jian Shu · 2024 to 2026
$2.3M
NCI NIH HHS UG3 CA268103NCI NIH HHS UG3 CA275669NCI NIH HHS UG3 CA275681NCI NIH HHS UH3 CA268091NCI NIH HHS UH3 CA268202NCI NIH HHS UH3 CA275681NCI NIH HHS UH3 CA275687NIA NIH HHS R01 AG068048NIA NIH HHS R01 AG082708NIA NIH HHS R33 AG061456NIA NIH HHS R37 AG013925NIA NIH HHS U54 AG075931NIA NIH HHS U54 AG075932NIA NIH HHS U54 AG075934NIA NIH HHS U54 AG075936NIA NIH HHS U54 AG075941NIA NIH HHS U54 AG076041NIA NIH HHS U54 AG079753NIA NIH HHS U54 AG079754NIA NIH HHS U54 AG079779
6 · The paper itself

Abstract

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.

Indexed as

Cellular SenescenceComputational BiologyGenomicsAgingAnimalsHumansMultiomicsProteomics

Identifiers

PMID40954249
PMCPMC12916282

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.