Evidence map›Paper›PMID 34043326›Full record

ArticleAnalytical chemistry2021

Agnostic Framework for the Classification/Identification of Organisms Based on RNA Post-Transcriptional Modifications.

William D McIntyre, Reza Nemati, Mehraveh Salehi, Colin C Aldrich, Molly FitzGibbon, Limin Deng, Manuel A Pazos, Rebecca E Rose, Botros Toro, Rachel E Netzband and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Analytical chemistry, 2021. 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

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

15 authors.

William D McIntyreDepartment of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States.
Reza NematiDepartment of Chemistry, University at Albany (SUNY), Albany, New York 12222, United States.
Mehraveh SalehiDepartment of Electrical Engineering, Yale University, New Haven, Connecticut 06520, United States.
Colin C AldrichDepartment of Chemistry, University at Albany (SUNY), Albany, New York 12222, United States.
Molly FitzGibbonDepartment of Biological Sciences, University at Albany, Albany, New York 12222, United States.
Limin DengDepartment of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States.
Manuel A PazosDepartment of Biological Sciences, University at Albany, Albany, New York 12222, United States.
Rebecca E RoseDepartment of Chemistry, University at Albany (SUNY), Albany, New York 12222, United States.
Botros ToroDepartment of Biological Sciences, University at Albany, Albany, New York 12222, United States.
Rachel E NetzbandDepartment of Biological Sciences, University at Albany, Albany, New York 12222, United States.
Cara T PagerDepartment of Biological Sciences, University at Albany, Albany, New York 12222, United States.
Ingrid P RobinsonDepartment of Biological Sciences, University at Albany, Albany, New York 12222, United States.
Sean M BialosukniaSchool of Public Health, University at Albany, Albany, New York 12222, United States.
Alexander T CiotaSchool of Public Health, University at Albany, Albany, New York 12222, United States.
Daniele FabrisDepartment of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States.ORCID 0000-0003-0786-1578

Funding

Modulation of RNA modifications by RNA virusesR01GM123050 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI FABRIS, DANIELE, PAGER, CARA THERESIA · 2018 to 2021
$1.9M
RNA post-transcriptional modifications as possible communication hubs between substances of abuse and HIV-1 replication processesR01DA046113 · NIDA · UNIVERSITY OF CONNECTICUT STORRS · PI FABRIS, DANIELE · 2018 to 2022
$1.9M
Characterization of ncRNAs' post-transcriptional modifications by antisense affinity capture and MS analysisR01GM121844 · NIGMS · UNIVERSITY OF CONNECTICUT STORRS · PI FABRIS, DANIELE · 2017 to 2021
$1.6M
Role of Post-transcription RNA Modifications on Zika Virus Gene ExpressionR21AI133617 · NIAID · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI FABRIS, DANIELE, PAGER, CARA THERESIA · 2017 to 2018
$486k
NIAID NIH HHS R21 AI133617NIDA NIH HHS R01 DA046113NIGMS NIH HHS R01 GM121844NIGMS NIH HHS R01 GM123050
6 · The paper itself

Abstract

We propose a novel approach for building a classification/identification framework based on the full complement of RNA post-transcriptional modifications (rPTMs) expressed by an organism at basal conditions. The approach relies on advanced mass spectrometry techniques to characterize the products of exonuclease digestion of total RNA extracts. Sample profiles comprising identities and relative abundances of all detected rPTM were used to train and test the capabilities of different machine learning (ML) algorithms. Each algorithm proved capable of identifying rigorous decision rules for differentiating closely related classes and correctly assigning unlabeled samples. The ML classifiers resolved different members of the

Indexed as

AlgorithmsRNACluster AnalysisHumansSaccharomyces cerevisiaeRNA

Identifiers

PMID34043326
PMCPMC8351319

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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.