Evidence map›Paper›PMID 39763808›Full record

ArticlebioRxiv : the preprint server for biology2025

Linkage-based ortholog refinement in bacterial pangenomes with CLARC.

Indra González Ojeda, Samantha G Palace, Pamela P Martinez, Taj Azarian, Lindsay R Grant, Laura L Hammitt, William P Hanage, Marc Lipsitch

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

8 authors.

Indra González OjedaCenter for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.ORCID 0000-0003-2040-956X
Samantha G PalaceCenter for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.ORCID 0000-0002-7849-8078
Pamela P MartinezDepartment of Microbiology, University of Illinois Urbana-Champaign, Champaign, Illinois, USA.ORCID 0000-0002-3607-0938
Taj AzarianBurnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA.ORCID 0000-0002-8611-5241
Lindsay R GrantDepartment of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
Laura L HammittDepartment of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.ORCID 0000-0001-6051-1484
William P HanageCenter for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.
Marc LipsitchCenter for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.ORCID 0000-0003-1504-9213

Funding

MOLECULAR BIOPHYSICS TRAINING GRANTT32GM008313 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI MURTHY, VENKATESH N · 1989 to 2023
$14.6M
NIGMS NIH HHS T32 GM008313
6 · The paper itself

Abstract

Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) [https://github.com/IndraGonz/CLARC] improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8,000+

Indexed as

Accessory genesBacteriaClusteringOrthologPangenomePipelineRoaryS. pneumonia

Identifiers

PMID39763808
PMCPMC11702680

What OpenQuestion holds

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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.