Evidence map›Paper›PMID 39345479›Full record

ArticlebioRxiv : the preprint server for biology2024

An Iterative Approach to Polish the Nanopore Sequencing Basecalling for Therapeutic RNA Quality Control.

Ziyuan Wang, Mei-Juan Tu, Ziyang Liu, Katherine K Wang, Yinshan Fang, Ning Hao, Hao Helen Zhang, Jianwen Que, Xiaoxiao Sun, Ai-Ming Yu and 1 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

11 authors.

Ziyuan WangDepartment of Pharmacy Practice and Science, University of Arizona, Tucson, Arizona, USA.
Mei-Juan TuDepartment of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California, USA.
Ziyang LiuDepartment of Pharmacy Practice and Science, University of Arizona, Tucson, Arizona, USA.
Katherine K WangDepartment of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California, USA.
Yinshan FangColumbia Center for Human Development, Department of Medicine, Columbia University Medical Center, New York, New York, USA.ORCID 0000-0001-9249-4498
Ning HaoStatistics and Data Science GIDP, University of Arizona, Tucson, Arizona, USA.
Hao Helen ZhangStatistics and Data Science GIDP, University of Arizona, Tucson, Arizona, USA.
Jianwen QueColumbia Center for Human Development, Department of Medicine, Columbia University Medical Center, New York, New York, USA.
Xiaoxiao SunStatistics and Data Science GIDP, University of Arizona, Tucson, Arizona, USA.
Ai-Ming YuDepartment of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California, USA.
Hongxu DingDepartment of Pharmacy Practice and Science, University of Arizona, Tucson, Arizona, USA.

Funding

Staff InvestigatorsP30CA093373 · NCI · UNIVERSITY OF CALIFORNIA DAVIS · PI KC KENT LLOYD · 2002 to 2026
$84.9M
Novel bioengineered microRNA therapeutics for lung cancerR01CA225958 · NCI · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Aiming Yu · 2019 to 2026
$3.7M
Novel biologic RNA molecules to modulate HCC metabolismR01CA291771 · NCI · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Aiming Yu · 2024 to 2026
$2.4M
Improve Lung Regeneration Through Targeting Tuft Cells Following Viral InfectionR01HL159675 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI QUE, JIANWEN · 2021 to 2024
$2.4M
Cell Fate Regulation in Esophageal Progenitor CellsR01DK132251 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI LU, CHAO, QUE, JIANWEN · 2022 to 2025
$2.3M
Training Program in PharmacologyT32GM144303 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Donald M Bers, JOHANNES W HELL · 2022 to 2026
$2.1M
Supplement: Recombinant microRNAs in xenobiotic metabolism and dispositionR35GM140835 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI YU, AIMING · 2021 to 2025
$2.0M
VEGF/KDR Signaling in Airway Epithelial Regeneration and DiseaseR01HL152293 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI QUE, JIANWEN · 2021 to 2024
$2.0M
Recombinant microRNAs in xenobiotic and nutrient dispositionR01CA253230 · NCI · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Meijuan Tu · 2021 to 2026
$1.7M
Tuft Cells Modulate Macrophage Response Following Lung Viral InfectionR21AI163753 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI QUE, JIANWEN · 2022 to 2023
$446k
NCI NIH HHS P30 CA093373NCI NIH HHS R01 CA225958NCI NIH HHS R01 CA253230NCI NIH HHS R01 CA291771NHLBI NIH HHS R01 HL152293NHLBI NIH HHS R01 HL159675NIAID NIH HHS R21 AI163753NIDDK NIH HHS R01 DK132251NIGMS NIH HHS R35 GM140835NIGMS NIH HHS T32 GM144303
6 · The paper itself

Abstract

Nucleotide modifications deviate nanopore sequencing readouts, therefore generating artifacts during the basecalling of sequence backbones. Here, we present an iterative approach to polish modification-disturbed basecalling results. We show such an approach is able to promote the basecalling accuracy of both artificially-synthesized and real-world molecules. With demonstrated efficacy and reliability, we exploit the approach to precisely basecall therapeutic RNAs consisting of artificial or natural modifications, as the basis for quantifying the purity and integrity of vaccine mRNAs which are transcribed

Identifiers

PMID39345479
PMCPMC11429612

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.