OSCR

GPU-accelerated modeling of biological regulatory networks.

A correction to this paper has been published: the notice, 42697917, from Europe PMC.

Overview

Authors: Joyce Reimer1, Pranta Saha1, Chris Chen1, Neeraj Dhar1, Brook Byrns2, Steven Rayan3,4, Gordon Broderick1,3,4
  1. Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK Canada
  2. Information and Communications Technology, University of Saskatchewan, Saskatoon, SK Canada
  3. Centre for Quantum Topology and Its Applications (quanTA), University of Saskatchewan, Saskatoon, SK Canada
  4. Dep. of Mathematics and Statistics, College of Arts and Science, University of Saskatchewan, Saskatoon, SK Canada
Institutions: University of Saskatchewan (Canada); Vaccine and Infectious Disease Organization (Canada)
Journal: Scientific reports, volume 16, issue 1, article 17599
Dates: received 24 December 2025; accepted 9 April 2026; published online 15 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41598-026-48748-0 · PMID 41986459 · PMCID PMC13243530 · OpenAlex W4416059725
Open access: gold, a free copy (OpenAlex)
Preprint: arxiv:2506.19866
Status: dead link
Categories: computational modeling (no new data) (modality), none (in silico) (organism), computational (subfield)
Keywords: regulatory networks, logical modeling, constraint satisfaction, global optimization, GPU, simulated annealing, Computational biology and bioinformatics, Mathematics and computing
MeSH: Computer Graphics*, Gene Regulatory Networks*, Models, Biological*, Algorithms, Animals, Computer Simulation (* major topic)
Topic: Gene Regulatory Network Analysis (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Prairies Economic Development Canada (Regional Innovation Ecosystems (RIE)); Canada Foundation for Innovation (Major Science Initiatives Fund, CFI John R. Evans Leaders Fund); Ministry of Agriculture - Saskatchewan; Innovation Saskatchewan
Citations: not cited yet (Europe PMC); 47 references in the paper
Notices: A correction to this paper has been published (42697917, from Europe PMC)

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Code

No file of the authors' code could be read here: it is described below, and read at its source.

miilusaskvido/scientificreports-codes](https:

License: none: the authors keep all their rights
State: the link is dead, verified on 29 September 2026
Evidence: found in the paper
Software Heritage: not archived
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 29 September 2026: the link is dead
  • 29 September 2026: the link is dead
At the source: github.com/MIILUsaskVIDO/scientificReports-codes](https:/github.com/MIILUsaskVIDO/scientificReports-codes)

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 0 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41598-026-48748-0.

Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 8 keywords, 6 MeSH terms, 4 funders, 46 references, 1 integrity notice.

Cite

This paper

Reimer, J., Saha, P., Chen, C., Dhar, N., Byrns, B., Rayan, S., & Broderick, G. (2026). GPU-accelerated modeling of biological regulatory networks. Scientific reports, 16(1), 17599. https://doi.org/10.1038/s41598-026-48748-0

BibTeX

@article{reimer2026gpu,
author = {Reimer, Joyce and Saha, Pranta and Chen, Chris and Dhar, Neeraj and Byrns, Brook and Rayan, Steven and Broderick, Gordon},
title = {{GPU-accelerated modeling of biological regulatory networks}},
journal = {Scientific reports},
year = {2026},
month = apr,
volume = {16},
number = {1},
pages = {17599},
publisher = {Nature Publishing Group},
issn = {2045-2322},
doi = {10.1038/s41598-026-48748-0},
url = {https://doi.org/10.1038/s41598-026-48748-0},
pmid = {41986459},
pmcid = {PMC13243530}
}

RIS

TY - JOUR
AU - Reimer, Joyce
AU - Saha, Pranta
AU - Chen, Chris
AU - Dhar, Neeraj
AU - Byrns, Brook
AU - Rayan, Steven
AU - Broderick, Gordon
TI - GPU-accelerated modeling of biological regulatory networks
T2 - Scientific reports
J2 - Sci Rep
PY - 2026
DA - 2026/04/15
VL - 16
IS - 1
SP - 17599
SN - 2045-2322
PB - Nature Publishing Group
DO - 10.1038/s41598-026-48748-0
UR - https://doi.org/10.1038/s41598-026-48748-0
LA - en
ER -

CSL-JSON

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{
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"ISSN": "2045-2322",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41598-026-48748-0",
"language": "en",
"issued": {
"date-parts": [
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]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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