Evidence map›Paper›PMID 41724754›Full record

ArticleBMC genomics2026

ModSeqR: an R package for efficient analysis of modified nucleotide data.

Hailey E Zimmerman, Jordan L Moore, Ryan H Miller, Isaac Stirland, Andrew Jenkins, Erin Saito, Tim Jenkins, Jonathon T Hill

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes.bioRxiv : the preprint server for biology · 2026
    Article
  3. 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

8 authors.

Hailey E ZimmermanWasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA.
Jordan L MooreWasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA.
Ryan H MillerWasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA.
Isaac StirlandWasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA.
Andrew JenkinsWasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA.
Erin SaitoWasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA.
Tim Jenkins *Wasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA. tim_jenkins@byu.edu.
Jonathon T Hill *Wasatch BioLabs, 2315 West 700 South, Suite R, Pleasant Grove, UT, 84062, USA. jhill@byu.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

DNA methylation regulates a wide range of biological processes, including gene expression, disease progression, and cell identity. Long-read technologies now enable more comprehensive and accurate methylome analyses than ever before, but they are hindered by the computational resources needed to analyze the massive datasets. Here, we present the CH3 file format, which aids data storage and transfer by reducing file sizes by more than 95%, and the ModSeqR R package, which builds on the CH3 format and a database backend to enable a broad range of epigenetic analyses. Together, these tools enable high-throughput methylation analysis while minimizing computational resource requirements.

Indexed as

Computational BiologyDNA MethylationNucleotidesSoftwareEpigenesis, GeneticHigh-Throughput Nucleotide SequencingHumansNucleotides5-hydroxymethylcytosine5-methylcytosineDifferential methylation analysesDNA methylationIllumina methylation microarrayOxford Nanopore sequencingR

Identifiers

PMID41724754
PMCPMC13032569

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.