Evidence map›Paper›PMID 39345391›Full record

ArticlebioRxiv : the preprint server for biology2024

The Precise Basecalling of Short-Read Nanopore Sequencing.

Ziyuan Wang, Mei-Juan Tu, Chengcheng Song, Ziyang Liu, Katherine K Wang, Shuibing Chen, Ai-Ming Yu, Hongxu Ding

Abstract readPreprint
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

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

8 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.
Chengcheng SongDepartment of Surgery, Weill Cornell Medicine, New York, New York, 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.
Shuibing ChenDepartment of Surgery, Weill Cornell Medicine, New York, New York, 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
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
Recombinant microRNAs in xenobiotic and nutrient dispositionR01CA253230 · NCI · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Meijuan Tu · 2021 to 2026
$1.7M
NCI NIH HHS P30 CA093373NCI NIH HHS R01 CA225958NCI NIH HHS R01 CA253230NCI NIH HHS R01 CA291771NIGMS NIH HHS R35 GM140835NIGMS NIH HHS T32 GM144303
6 · The paper itself

Abstract

The nanopore sequencing of short sequences, whose lengths are typically less than 0.3kb therefore comparable with Illumina sequencing techniques, has recently gained wide attention. Here, we design a scheme for training nanopore basecallers that are specialized for short biomolecules. With bioengineered RNA (BioRNA) molecules as examples, we demonstrate the superior accuracy of basecallers trained by our scheme.

Identifiers

PMID39345391
PMCPMC11429927

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.