Evidence map›Paper›PMID 41142120›Full record

ArticleiScience2025

Integrative multi-omics analysis

Leah P Shriver, Benjamin J Polacco, Manon Eckhardt, Max W Chang, Carles Martínez-Romero, Kayla Adkins-Travis, Celina Cahalane, Kelsey Haas, David A Stein, Slim Fourati and 24 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in iScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Review
  3. 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

34 authors.

Leah P ShriverDepartment of Chemistry, Washington University in Saint Louis, Saint Louis, MO 63130, USA.
Benjamin J PolaccoQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Manon EckhardtQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Max W ChangDepartment of Medicine, University of California, San Diego, La Jolla, CA 90293, USA.
Carles Martínez-RomeroDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kayla Adkins-TravisDepartment of Chemistry, Washington University in Saint Louis, Saint Louis, MO 63130, USA.
Celina CahalaneDepartment of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
Kelsey HaasQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
David A SteinDepartment of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA.
Slim FouratiDepartment of Pathology, Emory University, Atlanta, GA 30322, USA.
Laura Martin-SanchoDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Giorgi MetreveliDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jeffrey R JohnsonQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Raquel Muñoz-MorenoDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Billy W NewtonDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
Robyn M KaakeQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Yuan ZhouQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
David Jimenez-MoralesQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
John VonDollenQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Erik VerschuerenDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
Danielle L SwaneyQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Thong T NguyenQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Erica J StevensonQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Ethan StancliffeDepartment of Chemistry, Washington University in Saint Louis, Saint Louis, MO 63130, USA.
Gary J PattiDepartment of Chemistry, Washington University in Saint Louis, Saint Louis, MO 63130, USA.
Randy AlbrechtDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Hong M MoultonDepartment of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA.
Lars PacheInfectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Rafick P SekalyDepartment of Pathology, Emory University, Atlanta, GA 30322, USA.
Christopher BennerDepartment of Medicine, University of California, San Diego, La Jolla, CA 90293, USA.
Judd F HultquistQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
Sumit K ChandaInfectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Adolfo Garcia-SastreDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Nevan J KroganQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.

Funding

Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
Viral and Host Dynamics during Pediatric COVID-19 and Respiratory Virus Co-InfectionR01AI177498 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Bria M Coates, Judd F Hultquist · 2024 to 2026
$2.4M
NIAID NIH HHS R01 AI177498NIAID NIH HHS T32 AI060537
6 · The paper itself

Abstract

Influenza A virus (IAV) infection remodels cellular processes to support viral replication. The modulation of host factors by the virus drives pathogenesis during infection, and these factors may serve as therapeutic targets. Here, we infect mice with two IAV strains, H1N1 and H5N1, and analyze lung tissue with multi-omics. Using network propagation analysis, we identify twenty-four distinct host modules altered by infection, encompassing 2920 genes/proteins. Independently, we develop a computational pipeline, MidTOD, which integrates metabolomic data with other OMICs data-types, linking metabolites to gene/protein alterations. Combining datasets from both approaches reveals alterations in mitochondrial and peroxisomal metabolism in IAV-infected cells and identifies arginine:glycine amidinotransferase (GATM) as a host dependency factor in both human cells and mice. Knockdown of this enzyme reduces IAV-mediated pathology and host inflammatory responses after infection. Collectively, this work provides an integrated systems-level view of host changes during infection and identifies an abundance of IAV-host factors.

Indexed as

Biocomputational methodMetabolomicsModel organismProteomicsTranscriptomicsVirology

Identifiers

PMID41142120
PMCPMC12552919

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.