Evidence map›Paper›PMID 40504907›Full record

ArticleScience (New York, N.Y.)2025

Pan-viral ORFs discovery using massively parallel ribosome profiling.

Shira Weingarten-Gabbay, Matthew R Bauer, Alexandra C Stanton, Yingpu Yu, Catherine A Freije, Nicole L Welch, Chloe K Boehm, Susan Klaeger, Eva K Verzani, Daniel López and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Science (New York, N.Y.), 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. Article
  2. Review
  3. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

Shira Weingarten-GabbayBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-7579-0236
Matthew R BauerHarvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA.
Alexandra C StantonBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-8355-345X
Yingpu YuLaboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.ORCID 0000-0003-4837-5744
Catherine A FreijeBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-1939-3102
Nicole L WelchBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-6225-487X
Chloe K BoehmBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-6136-3257
Susan KlaegerBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-0074-5163
Eva K VerzaniBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0004-0846-4878
Daniel LópezUnidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid), Spain.ORCID 0000-0003-0268-5878
Lisa E HensleyZoonotic and Emerging Disease Research Unit, National Bio and Agro-Defense Facility, US Department of Agriculture, Agricultural Research Service (ARS), Manhattan, KS, USA.
Karl R ClauserBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-1052-9456
Steven A CarrBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-7203-4299
Jennifer G AbelinBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-5262-7241
Charles M RiceLaboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.ORCID 0000-0003-3087-8079
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9843-1890

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI NEAFSEY, DANIEL E · 2014 to 2024
$66.5M
ProteomicsP01CA206978 · NCI · DANA-FARBER CANCER INST · PI WU, CATHERINE JU-YING · 2016 to 2025
$17.0M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3M
Proteogenomic Predictors of Recurrence in Non-small Cell Lung CancerU01CA271402 · NCI · WASHINGTON UNIVERSITY · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.0M
Structure and function of the HCV RNA replicaseR01CA057973 · NCI · WASHINGTON UNIVERSITY · PI RICE, CHARLES M · 1992 to 2013
$4.7M
Howard Hughes Medical InstituteNCI NIH HHS P01 CA206978NCI NIH HHS R01 CA057973NCI NIH HHS U01 CA271402NCI NIH HHS U24 CA270823NIAID NIH HHS U19 AI110818
6 · The paper itself

Abstract

Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively parallel ribosome profiling (MPRP) to determine open reading frames (ORFs) across tens of thousands of designed oligonucleotides. MPRP identified 4208 unannotated ORFs in 679 human-associated viral genomes. We found viral peptides originating from detected noncanonical ORFs presented on class-I human leukocyte antigen in infected cells and hundreds of upstream ORFs that likely modulate translation initiation of viral proteins. The discovery of viral ORFs across a wide range of viral families-including highly pathogenic viruses-expands the repertoire of vaccine targets and reveals potential cis-regulatory sequences.

Indexed as

Open Reading FramesRibosome ProfilingRibosomesViral ProteinsVirusesGenome, ViralHigh-Throughput Nucleotide SequencingHumansProtein BiosynthesisViral Proteins

Identifiers

PMID40504907
PMCPMC12459998

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.