Evidence map›Paper›PMID 40160533›Full record

ArticlePNAS nexus2025

Unraveling biomolecular and community grammars of RNA granules via machine learning.

Zhan Ban, Yuchen Lin, Yan Yan, Kenneth A Dawson

Abstract read
In one paragraph

Article in PNAS nexus, 2025. 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

4 authors.

Zhan BanCentre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin 4, D04 N2E5, Ireland.
Yuchen LinCentre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin 4, D04 N2E5, Ireland.
Yan YanCentre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin 4, D04 N2E5, Ireland.ORCID https://orcid.org/0000-0003-2938-4063
Kenneth A DawsonCentre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin 4, D04 N2E5, Ireland.ORCID https://orcid.org/0000-0002-0568-6588

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Membraneless RNA granules are essential for posttranscriptional gene regulation, influencing cellular functions and contributing to neurodegenerative diseases. However, a comprehensive understanding of their compositions and organization has been challenging due to their complex nature. In this study, we develop robust machine learning models to reliably identify RNA granule proteomes within the human proteome, capturing central RNA granule characteristics despite the heterogeneity across diverse in vitro conditions. Furthermore, we uncover protein-protein interaction (PPI) community grammars within the RNA granule proteome, highlighting PPIs as key stabilizers of RNA granule structure and function. Dense PPI clusters serve as stable "cores," forming key functional subunits across heterogeneous RNA granules. We introduce a state-of-the-art framework for understanding RNA granule biology and underscore the critical role of PPIs in maintaining RNA granule integrity.

Indexed as

machine learningP-bodyprotein-protein interaction networkRNA granule proteomestress granule

Identifiers

PMID40160533
PMCPMC11952899

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.