Evidence map›Paper›PMID 39149337›Full record

ArticlebioRxiv : the preprint server for biology2025

Predicting the translation efficiency of messenger RNA in mammalian cells.

Dinghai Zheng, Logan Persyn, Jun Wang, Yue Liu, Fernando Ulloa Montoya, Can Cenik, Vikram Agarwal

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Dinghai ZhengmRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA.
Logan PersynDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Jun WangmRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA.
Yue LiuDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Fernando Ulloa MontoyamRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA.
Can CenikDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.ORCID 0000-0001-6370-0889
Vikram AgarwalmRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA.

Funding

Single cell quantification of translation control in early mouse developmentR35GM150667 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI Can Cenik · 2023 to 2026
$1.6M
Translational regulation of limb bud initiationR21HD110096 · NICHD · UNIVERSITY OF TEXAS AT AUSTIN · PI CENIK, CAN, VOKES, STEVEN ALEXANDER · 2022 to 2023
$436k
NICHD NIH HHS R21 HD110096NIGMS NIH HHS R35 GM150667
6 · The paper itself

Abstract

The degree to which translational control is specified by mRNA sequence is poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into a transcriptome-wide atlas of translation efficiency (TE) measurements encompassing >140 human and mouse cell types. We subsequently developed RiboNN, a multitask deep convolutional neural network, and classic machine learning models to predict TEs in hundreds of cell types from sequence-encoded mRNA features, achieving state-of-the-art performance (r=0.79 in human and r=0.78 in mouse for mean TE across cell types). While the majority of earlier models solely considered 5' UTR sequence

Indexed as

Deep learningMachine learningRibosome profilingTranslational regulationTranslation efficiency

Identifiers

PMID39149337
PMCPMC11326250

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.