Evidence map›Paper›PMID 33274189›Full record

ArticleFrontiers in physics2020

Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks.

Sirajul Salekin, Milad Mostavi, Yu-Chiao Chiu, Yidong Chen, Jianqiu Michelle Zhang, Yufei Huang

Abstract read
In one paragraph

Article in Frontiers in physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Review
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  9. AI applications in functional genomics.Computational and structural biotechnology journal · 2021
    Review
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

6 authors.

Sirajul SalekinDepartment of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX, 78207, USA.
Milad MostaviDepartment of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX, 78207, USA.
Yu-Chiao ChiuGreehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
Yidong ChenGreehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
Jianqiu Michelle ZhangDepartment of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX, 78207, USA.
Yufei HuangDepartment of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX, 78207, USA.

Funding

TISSUE CULTURE---COREP30CA054174 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Robin Jean Leach · 1991 to 2026
$59.1M
INSTITUTE FOR INTEGRATION OF MEDICINE & SCIENCE: A PARTNERSHIP TO IMPROVE HEALTHUL1RR025767 · NCRR · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI CLARK, ROBERT A · 2008 to 2011
$23.8M
Institute for Integration of Medicine & Science: A Partnership to Improve HealthUM1TR004538 · NCATS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI ROBERT A CLARK, Kenneth M Hargreaves · 2023 to 2026
$22.3M
Institute for Integration of Medicine & Science: A Partnership to Improve HealthUL1TR002645 · NCATS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI CLARK, ROBERT A, HARGREAVES, KENNETH M · 2018 to 2022
$20.4M
Collaborative Research:Graphical models for characterizing global RNA methylationR01GM113245 · NIGMS · UNIVERSITY OF TEXAS SAN ANTONIO · PI HUANG, YUFEI · 2014 to 2016
$1.1M
Deep learning of drug sensitivity and genetic dependency of pediatric cancer cellsK99CA248944 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI CHIU, YU-CHIAO · 2020 to 2021
$212k
NCATS NIH HHS UL1 TR002645NCATS NIH HHS UM1 TR004538NCI NIH HHS K99 CA248944NCI NIH HHS P30 CA054174NCRR NIH HHS UL1 RR025767NIGMS NIH HHS R01 GM113245
6 · The paper itself

Abstract

Epitranscriptome is an exciting area that studies different types of modifications in transcripts and the prediction of such modification sites from the transcript sequence is of significant interest. However, the scarcity of positive sites for most modifications imposes critical challenges for training robust algorithms. To circumvent this problem, we propose MR-GAN, a generative adversarial network (GAN) based model, which is trained in an unsupervised fashion on the entire pre-mRNA sequences to learn a low dimensional embedding of transcriptomic sequences. MR-GAN was then applied to extract embeddings of the sequences in a training dataset we created for eight epitranscriptome modifications, including m

Indexed as

epitranscriptomegenerative adversarial networks (GAN)methylated RNA immunoprecipitation sequencing (MeRIP-Seq)N6-methyladenosine (m6A)RNA modification site predictionunsupervised representation learning

Identifiers

PMID33274189
PMCPMC7710330

What OpenQuestion holds

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Registered trials

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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.