Evidence map›Paper›PMID 41654842›Full record

ArticleGenome biology2026

PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment.

Yongxin Ji, Jiaojiao Guan, Herui Liao, Jiayu Shang, Yanni Sun

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

5 authors.

Yongxin Ji *Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR (HKG), China.
Jiaojiao Guan *Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR (HKG), China.
Herui LiaoInstitute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Jiayu ShangDepartment of Information Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR (HKG), China.
Yanni SunDepartment of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR (HKG), China. yannisun@cityu.edu.hk.ORCID http://orcid.org/0000-0003-1373-8023

Funding

CityUHK DON RMG 9229134RGC GRF CityU 11214924
6 · The paper itself

Abstract

Plasmids play a pivotal role in the emergence of multidrug-resistant and pathogenic bacteria, posing significant clinical challenges. However, the rapidly growing number of unannotated plasmids necessitates comprehensive characterization of their diverse properties. Here, we present PlasRAG, a tool that integrates multi-faceted property characterization of query plasmids and plasmid DNA retrieval based on textual queries. PlasRAG employs a bidirectional multi-modal information retrieval model that aligns DNA sequences with textual data, effectively overcoming the limitations of traditional approaches. Rigorous experiments demonstrate that PlasRAG delivers robust performance and enhanced analytical capabilities, underscoring the effectiveness of its architectural design.

Indexed as

PlasmidsSequence AlignmentSoftwareSequence Analysis, DNABiomedical language modelsMulti-modal contrastive learningRetrieval-augmented generation (RAG)Sequence-to-text plasmid characterizationText-to-sequence plasmid retrieval

Identifiers

PMID41654842
PMCPMC12977624

What OpenQuestion holds

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LicenceCC BY
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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.