Evidence map›Paper›PMID 41279440›Full record

ArticlebioRxiv : the preprint server for biology2025

From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus.

Anton Nekrutenko, Danielle Callan, Marius Van Den Beek, Dannon Baker, David Rogers, Wolfgang Maier, Aysam Guerler, Hiram Clawson, Scott Cain, Kelsey Beavers and 3 more

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

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

13 authors.

Anton NekrutenkoDept. of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.ORCID 0000-0002-5987-8032
Danielle CallanDept. of Biology, Temple University, Philadelphia, PA, USA.
Marius Van Den BeekDept. of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Dannon BakerDept. of Biology, Johns Hopkins University, Baltimore, MD, USA.
David RogersClever Canary, LLC, Santa Cruz, CA, USA.
Wolfgang MaierDept. of Bioinformatics, Albert-Ludwigs-University Freiburg, Freiburg, Baden-Württemberg, Germany.
Aysam GuerlerDept. of Biology, Johns Hopkins University, Baltimore, MD, USA.
Hiram ClawsonBaskin School of Engineering, University of California, Santa Cruz, USA.
Scott CainDept. of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Kelsey BeaversTexas Advanced Computing Center, The University of Texas, Austin, TX, USA.
Maximilan HaeusslerBaskin School of Engineering, University of California, Santa Cruz, USA.
Bjorn GruningDept. of Bioinformatics, Albert-Ludwigs-University Freiburg, Freiburg, Baden-Württemberg, Germany.
Sergei Kosakowsky PondDept. of Biology, Temple University, Philadelphia, PA, USA.

Funding

An in integrated platform for multiomic analyses of pathogen and host data using scalable public infrastructureU24AI183870 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI Kelsey M Beavers, Maximilian Haeussler · 2024 to 2026
$10.2M
NIAID NIH HHS U24 AI183870
6 · The paper itself

Abstract

The analytical landscape of pathogen research is often fragmented, hindering transparency and reproducibility due to diverse genomic data sources, numerous software tools, and suboptimal integration methods. Here we introduce BRC-analytics, a novel browser-based environment that unifies authoritative sources of genomic data with community-curated best analysis practices on a freely accessible public computational infrastructure. We demonstrate its capabilities by analyzing the evolutionary dynamics within the P/V/C locus of the measles virus, a complex system involving overlapping coding regions and RNA editing. Our analysis, conducted entirely within BRC-analytics, reveals asymmetric evolution of the locus's reading frames under distinct selective pressures. BRC-analytics streamlines the entire research process-from data collection and primary analysis (e.g., variant calling) to interpretation (e.g., using integrated JupyterLite notebooks and LLMs) and publication-into a single web browser session. This eliminates the need for local installations and manual data transfers, implicitly tracking provenance and ensuring reproducibility. The platform's goal is to provide true data-to-publication functionality, making advanced pathogen genomics accessible to a broader research community regardless of their computational expertise or infrastructure access.

Identifiers

PMID41279440
PMCPMC12632837

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.