Evidence map›Paper›PMID 40766476›Full record

ArticlebioRxiv : the preprint server for biology2025

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.

Marco Teixeira, Celia Souque, Colin J Worby, Terrance Shea, Nicoletta Commins, Joshua T Smith, Arjun M Miklos, Thomas Abeel, Ashlee M Earl, Abigail L Manson

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

10 authors.

Marco TeixeiraInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-7219-0478
Celia SouqueDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.ORCID 0000-0001-7194-4322
Colin J WorbyInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-9132-7249
Terrance SheaInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Nicoletta ComminsInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-0562-9735
Joshua T SmithInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-5511-8717
Arjun M MiklosInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0009-0000-9221-4556
Thomas AbeelInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-7205-7431
Ashlee M EarlInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-7857-9145
Abigail L MansonInfectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-3800-0714

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI EARL, ASHLEE MIRIAM · 2014 to 2024
$66.5M
Simulating the Spread and Control of Multiple MDROs Across a Network of Different Nursing HomesU19AI172725 · NIAID · UNIVERSITY OF CALIFORNIA-IRVINE · PI Bruce Y Lee · 2024 to 2026
$10.9M
NIAID NIH HHS U19 AI110818NIAID NIH HHS U19 AI172725
6 · The paper itself

Abstract

The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing plasmids easier, most (97%) of the bacterial genome assemblies in the public domain are generated from short-read data. Work to compare plasmid reconstruction tools has focused primarily on

Identifiers

PMID40766476
PMCPMC12324311

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.