Evidence map›Paper›PMID 39700255›Full record

ArticlePLoS computational biology2024

Predicting lung aging using scRNA-Seq data.

Qi Song, Alex Singh, John E McDonough, Taylor S Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J Ceulemans, Bart M Vanaudenaerde, Wim A Wuyts and 5 more

Abstract read
In one paragraph

Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–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

1 citing paper in PubMed.

  1. Article
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

15 authors.

Qi SongComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.ORCID 0000-0001-5420-4031
Alex SinghComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.
John E McDonoughFaculty of Health Sciences, McMaster University, Ontario, Canada.
Taylor S AdamsSection of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America.
Robin VosDepartment of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.ORCID 0000-0002-3468-9251
Ruben De ManSection of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America.
Greg MyersDepartment of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
Laurens J CeulemansDepartment of Respiratory Medicine, KU Leuven, Leuven, Belgium.
Bart M VanaudenaerdeDepartment of Respiratory Medicine, KU Leuven, Leuven, Belgium.
Wim A WuytsDepartment of Respiratory Medicine, KU Leuven, Leuven, Belgium.
Xiting YanSection of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America.
Jonas SchuppSection of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America.ORCID 0000-0002-7714-8076
James S HagoodDepartment of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
Naftali KaminskiSection of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America.
Ziv Bar-JosephComputational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.ORCID 0000-0003-3430-6051

Funding

Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9M
SenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1M
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
Genomic Analysis of Tissue and Cellular Heterogeneity in IPFR01HL127349 · NHLBI · YALE UNIVERSITY · PI BENOS, PANAGIOTIS V, KAMINSKI, NAFTALI · 2015 to 2025
$5.9M
Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVEOT2OD026682 · OD · CARNEGIE-MELLON UNIVERSITY · PI PATEN, BENEDICT, RUFFALO, MATTHEW · 2018 to 2021
$3.4M
Normal Aging Lung Cell Atlas (NALCA)U01HL145567 · NHLBI · YALE UNIVERSITY · PI KAMINSKI, NAFTALI · 2019 to 2022
$2.8M
Integrating single-cell based transcriptomic signatures for identifying therapeutic targets of COPDR21HL161723 · NHLBI · YALE UNIVERSITY · PI KAMINSKI, NAFTALI · 2022 to 2023
$251k
NCATS NIH HHS UL1 TR001863NCI NIH HHS U24 CA268108NHLBI NIH HHS R01 HL127349NHLBI NIH HHS R21 HL161723NHLBI NIH HHS U01 HL145567NIA NIH HHS U54 AG075931NIH HHS OT2 OD026682
6 · The paper itself

Abstract

Age prediction based on single cell RNA-Sequencing data (scRNA-Seq) can provide information for patients' susceptibility to various diseases and conditions. In addition, such analysis can be used to identify aging related genes and pathways. To enable age prediction based on scRNA-Seq data, we developed PolyEN, a new regression model which learns continuous representation for expression over time. These representations are then used by PolyEN to integrate genes to predict an age. Existing and new lung aging data we profiled demonstrated PolyEN's improved performance over existing methods for age prediction. Our results identified lung epithelial cells as the most significant predictors for non-smokers while lung endothelial cells led to the best chronological age prediction results for smokers.

Indexed as

AgingComputational BiologyLungSingle-Cell Gene Expression AnalysisEpithelial CellsHumansRNA-SeqSequence Analysis, RNA

Identifiers

PMID39700255
PMCPMC11741621

What OpenQuestion holds

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Registered trials

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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.