ArticlebioRxiv : the preprint server for biology2026
SenNet Portal: Build, Optimization and Usage.
Katy Börner, Philip D Blood, Jonathan C Silverstein, Matthew Ruffalo, Rahul Satija, Nils Gehlenborg, Brendan Honick, Andreas Bueckle, Yashvardhan Jain, Danial Qaurooni and 18 more
Abstract readPreprint
In one paragraphArticle in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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 registryThe 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 literatureWho cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
4 · The recordCorrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
5 · Who and what moneyAuthors and funding
28 authors.
Jonathan C SilversteinDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0000-0002-9252-6039 Matthew RuffaloRay and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.ORCID 0000-0003-2222-6169 Andreas BueckleDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0000-0002-8977-498X Yashvardhan JainDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0000-0002-6300-5568 Danial QaurooniDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0000-0001-6190-073X Kay MétisDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
Joe BisciottiDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0009-0007-8276-1477 Richard S MorganDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
Morgan L TurnerDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
So-Jin KimDivision of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID 0000-0003-2413-2609 Patty J LeeDivision of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID 0000-0001-9906-1628 Josh BartzMasonic Institute on the Biology of Aging and Metabolism, Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.ORCID 0000-0003-2347-3663 Samuel T PetersMasonic Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.ORCID 0000-0003-1479-8087 Negin FarzadDepartment of Biomedical Engineering, Yale University, New Haven, CT, USA.
SenNet Team
Bruce W HerrDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0000-0002-6703-7647 Funding
Center for Integrated Cellular Analysis - Valeria A. Sanchez EstradaRM1HG011014 · NHGRI · NEW YORK GENOME CENTER · PI LANDAU, DAN, SATIJA, RAHUL · 2020 to 2025
$22.1MSenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1MConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI KRETZLER, MATTHIAS · 2017 to 2021
$21.0MFlexible Hybrid Cloud Infrastructure for Seamless Integration and Use of Human Biomolecular Data and Reference Maps [1 of 5]OT2OD033759 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., SILVERSTEIN, JONATHAN C. · 2022 to 2025
$20.4MSpatiotemporal Tumor Analytics for Guiding Sequential Targeted-Inhibitor: Immunotherapy Combinations (ST-Analytics)U54CA274509 · NCI · INSTITUTE FOR SYSTEMS BIOLOGY · PI Rong Fan · 2022 to 2026
$15.6MThe KAPP-Sen Tissue Mapping Center CollaborativeU54AG075941 · NIA · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GAROVIC, VESNA D, KUCHEL, GEORGE A · 2021 to 2025
$13.8MThe Duke Senescent Cell Evaluations in Normal Tissues (SCENT) Mapping CenterU54AG075936 · NIA · DUKE UNIVERSITY · PI LEE, PATTY J · 2021 to 2025
$12.7MMidwest Murine-Tissue Mapping Center (MM-TMC)U54AG079754 · NIA · UNIVERSITY OF MINNESOTA · PI GR Scott Budinger, Sundeep Khosla · 2022 to 2026
$11.5MMinnesota Tissue Mapping Center for Senescent CellsU54AG076041 · NIA · UNIVERSITY OF MINNESOTA · PI Constantin F. Aliferis, LAURA Jane NIEDERNHOFER · 2021 to 2026
$10.5MKPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4MTech Core 2U54CA268083 · NCI · JOHNS HOPKINS UNIVERSITY · PI Pei-Hsun wu · 2022 to 2026
$10.2MFlexible Hybrid Cloud Infrastructure for Seamless Management of HuBMAP Resources, Including Consortium-Wide and External EngagementOT2OD026675 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., SILVERSTEIN, JONATHAN C. · 2018 to 2021
$8.9MNCI NIH HHS R01 CA245313NCI NIH HHS U01 CA294514NCI NIH HHS U24 CA268108NCI NIH HHS U54 CA268083NCI NIH HHS U54 CA274509NCI NIH HHS UH3 CA257393NHGRI NIH HHS RM1 HG011014NIA NIH HHS U54 AG075936NIA NIH HHS U54 AG075941NIA NIH HHS U54 AG076041NIA NIH HHS U54 AG076043NIA NIH HHS U54 AG079754NIA NIH HHS U54 AG079759NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIH HHS OT2 OD026671NIH HHS OT2 OD026675NIH HHS OT2 OD026682NIH HHS OT2 OD030545NIH HHS OT2 OD033756NIH HHS OT2 OD033759NIH HHS OT2 OD033760NIH HHS OT2 OD033761NIH HHS R03 OD039970NIMH NIH HHS RF1 MH128876NIMH NIH HHS RM1 MH132648
6 · The paper itselfAbstract
Cellular senescence is a hallmark of aging and a driver of functional decline across tissues, yet its heterogeneity and context dependence have limited systematic study. The Common Fund's Cellular Senescence Network (SenNet) Program addresses this challenge by generating multimodal, multi-tissue datasets that profile senescent cells across the human lifespan and complementary mouse models. The SenNet Data Portal (https://data.sennetconsortium.org) serves as the public gateway to these resources, providing open access to harmonized single-cell, spatial, imaging, transcriptomic, and proteomic data; senescence biomarker catalogs; and standardized protocols that can be used to comprehensively identify and characterize senescent cells in mouse and human tissue. As of January 2026, the portal hosts 1,753 publicly available human and mouse datasets across 15 organs using 6 general assay types. Experts from 13 Tissue Mapping Centers (TMCs) and 12 Technology Development and Application (TDAs) components contribute tissue data, analyze data, identify senescent biomarkers, and agree on panels for cross-tissue antibody harmonization. They also register human tissue data into the Human Reference Atlas (HRA) and develop user interfaces for the multiscale and multimodal exploration of this data. Built on a scalable hybrid cloud microservices architecture by the Consortium Organization and Data Coordinating Center (CODCC), the Portal enables data submission, management, integrated analysis, spatial context mapping, and cross-species senescence mapping critical for aging research. This paper presents user needs, the Portal's architecture, data processing workflows, and senescence-focused analytical tools. The paper also presents usage scenarios illustrating applications in biomarker discovery, quality benchmarking, hypothesis generation, spatial analysis, cost-efficient profiling, and cell distance distribution analysis. Current limitations and planned extensions-including expanded spatial-omics releases and improved tools for senotype characterization-are discussed. SenNet protocols, code, and user interfaces are freely available on https://docs.sennetconsortium.org/apis.
Identifiers
PMID41727059
PMCPMC12918883
What Socratic holds
Textmetadata
LicenceCC BY
Read underepoch 390