Evidence map›Paper›PMID 40992925›Full record

ArticleLife science alliance2025

Predicting nonsense-mediated mRNA decay from splicing events in sepsis using RNA-sequencing data.

Jaewook Shin, Alger M Fredericks, Brandon E Armstead, Alfred Ayala, Maya Cohen, William G Fairbrother, Mitchell M Levy, Kwesi K Lillard, Emanuele Raggi, Gerard J Nau and 1 more

Abstract read
In one paragraph

Article in Life science alliance, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Jaewook ShinDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.ORCID 0000-0003-0445-546X
Alger M FredericksDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Brandon E ArmsteadDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Alfred AyalaDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Maya CohenDivision of Pulmonary, Critical Care, and Sleep Medicine, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
William G FairbrotherDepartment of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
Mitchell M LevyDivision of Pulmonary, Critical Care, and Sleep Medicine, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Kwesi K LillardDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Emanuele RaggiDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Gerard J NauDivision of Infectious Diseases, Department of Medicine, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA.
Sean F MonaghanDivision of Surgical Research, Department of Surgery, Rhode Island Hospital/Alpert Medical School of Brown University, Providence, RI, USA sean_monaghan@brown.edu.ORCID 0000-0003-1490-3043

Funding

Using Genomic Epidemiology to Identify Transmission Patterns and Inform Intervention Strategies for Antibiotic-Resistant N. GonorrhoeaeP20GM121344 · NIGMS · MIRIAM HOSPITAL · PI FREDERICKS, ALGER M · 2018 to 2022
$9.4M
Mechanisms of Immune Dysfunction and Morbid Outcome in Response to Shock/SepsisR35GM118097 · NIGMS · RHODE ISLAND HOSPITAL · PI AYALA, ALFRED · 2016 to 2025
$6.3M
Discovering Splicing Defects in Human GenesR01GM127472 · NIGMS · BROWN UNIVERSITY · PI William G Fairbrother · 2018 to 2026
$5.9M
Brown Respiratory Research Training ProgramT32HL134625 · NHLBI · BROWN UNIVERSITY · PI Elizabeth O Harrington, Sharon Irene Smith Rounds · 2017 to 2026
$5.1M
Effects of DHEA in Pulmonary Hypertension (DiPH)R01HL141268 · NHLBI · RHODE ISLAND HOSPITAL · PI VENTETUOLO, COREY E · 2018 to 2022
$3.7M
Assessment of Implementation Methods in Sepsis and Respiratory FailureR01HL162954 · NHLBI · RHODE ISLAND HOSPITAL · PI Mitchell M Levy · 2022 to 2026
$3.4M
Trauma and Inflammation Research TrainingT32GM065085 · NIGMS · RHODE ISLAND HOSPITAL · PI Alfred Ayala · 2004 to 2026
$3.2M
Improving Sepsis Care with Deep RNA Sequencing DataR35GM142638 · NIGMS · RHODE ISLAND HOSPITAL · PI Sean Farrell Monaghan · 2021 to 2026
$2.6M
Pulmonary Artery Endothelial Cell Endotypes and the Role of Anoikis Resistance in Pulmonary HypertensionR01HL174007 · NHLBI · RHODE ISLAND HOSPITAL · PI Olin D. Liang, Corey E Ventetuolo · 2025 to 2026
$1.3M
NHLBI NIH HHS R01 HL141268NHLBI NIH HHS R01 HL162954NHLBI NIH HHS R01 HL174007NHLBI NIH HHS T32 HL134625NIGMS NIH HHS P20 GM121344NIGMS NIH HHS R01 GM127472NIGMS NIH HHS R35 GM118097NIGMS NIH HHS R35 GM142638NIGMS NIH HHS T32 GM065085
6 · The paper itself

Abstract

Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are highly conserved cellular mechanisms that modulate gene expression. Here, we introduce the NMD pipeline that computes how splicing events introduce premature termination codons to mRNA transcripts via frameshift, then predicts the rate of premature termination codon-dependent NMD. We use whole-blood, deep RNA-sequencing data from critically ill patients to study gene expression in sepsis. Statistical significance was determined as adjusted

Indexed as

Alternative SplicingNonsense Mediated mRNA DecayRNA SplicingSepsisCodon, NonsenseCritical IllnessFemaleGene Expression ProfilingHumansMaleMiddle AgedRNA, MessengerSequence Analysis, RNACodon, NonsenseRNA, Messenger

Identifiers

PMID40992925
PMCPMC12461151

What OpenQuestion holds

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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.