Evidence map›Paper›PMID 40836306›Full record

ArticleGenome biology2025

Highly accurate prophage island detection with PIDE.

Hongyan Gao, Bowen Li, Zihan Guo, Lei Zheng, Junnan Chen, Guanxiang Liang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026
    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

6 authors.

Hongyan Gao *Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.
Bowen Li *Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.
Zihan Guo *Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.
Lei ZhengCenter for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.
Junnan ChenCenter for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.
Guanxiang LiangCenter for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China. guanxiangliang@tsinghua.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify prophages through computational methods. Here, we introduce PIDE for identifying prophages from bacterial genomes or metagenome-assembled genomes. PIDE integrates a pre-trained protein language model and gene density clustering algorithm to distinguish prophages. Benchmarking with induced prophage sequencing datasets demonstrates that PIDE pinpoints prophages with precise boundaries. Applying PIDE to 4744 human gut representative genomes reveals 24,467 prophages with widespread functional capacity. PIDE is available at https://github.com/chyghy/PIDE , with model training code at https://zenodo.org/records/16457629 .

Indexed as

Genomic IslandsProphagesSoftwareAlgorithmsGenome, BacterialGenome, ViralHumansMetagenomeGene clusterHuman gut metagenomeProphage identificationProtein language model

Identifiers

PMID40836306
PMCPMC12366036

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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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.