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Simulation-guided chemical direct reprogramming informed by temporal cellular conversion processes at the single-cell level.

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Paper

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The authors' code

Python · 1 line · 0 B · CC-BY-NC-ND-4.0

__init__.py, under CC-BY-NC-ND-4.0 · at the source

Overview

Authors: Ryoku Ito1, Momoko Hamano1, Ryota Kawasaki1, Hikaru Watanabe1, Arisa Matsuo1, Yoshihiro Yamanishi2,3
ORCID iDs: Momoko Hamano, Yoshihiro Yamanishi
  1. Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
  2. Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Japan
  3. Division of Interdisciplinary Research and Development (R&D), Aichi Cancer Center Research Institute, Nagoya, Japan
Institutions: Kyushu Institute of Technology (Japan); Aichi Cancer Center (Japan); Nagoya University (Japan)
Journal: Communications chemistry, volume 9, issue 1, article 178
Dates: received 20 June 2025; accepted 16 March 2026; published online 18 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42004-026-01991-y · PMID 42151623 · PMCID PMC13183877 · OpenAlex W7161607926
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: cellular / molecular (subfield)
Methods: Smoothing, state filtering, decompositions, Statistics, Machine learning
Keywords: Small molecules, Computational chemistry, Target identification
Topic: Pluripotent Stem Cells Research (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: MEXT | Japan Society for the Promotion of Science (JSPS) (24K21338, 21K18327, 20H05797, 18K19930); MEXT | Japan Science and Technology Agency (JST) (JPMJAX24LD); Okawa Foundation for Information and Telecommunications (The Okawa Foundation) (21-06)
Citations: not cited yet (Europe PMC); 50 references in the paper

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.

Repositories

Its files are read in the Code ↔ Paper reader above.

Zenodo 18909775

License: CC-BY-NC-ND-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (1 file), pandas (1 file), SciPy (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
6 files
At the source:

hamanolaboratory/superdirecteur

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: b001638497bb6428192cb04c822c5c7b09af8da6, 10 April 2026
Languages: Python (4)
Size: 11 files, 4 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (1 file), pandas (1 file), SciPy (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
6 files
At the source: github.com/HamanoLaboratory/superDIRECTEUR/tree/superDIRECTEUR

Code availability statement

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

  • it points to the authors' code: Zenodo 18909775

Read it in the paper: doi.org/10.1038/s42004-026-01991-y.

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 8 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability statement

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

  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1038/s42004-026-01991-y.

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 3 keywords, 3 funders, 48 references.

Cite

This paper

Ito, R., Hamano, M., Kawasaki, R., Watanabe, H., Matsuo, A., & Yamanishi, Y. (2026). Simulation-guided chemical direct reprogramming informed by temporal cellular conversion processes at the single-cell level. Communications chemistry, 9(1), 178. https://doi.org/10.1038/s42004-026-01991-y

BibTeX

@article{ito2026simulation,
author = {Ito, Ryoku and Hamano, Momoko and Kawasaki, Ryota and Watanabe, Hikaru and Matsuo, Arisa and Yamanishi, Yoshihiro},
title = {{Simulation-guided chemical direct reprogramming informed by temporal cellular conversion processes at the single-cell level}},
journal = {Communications chemistry},
year = {2026},
month = may,
volume = {9},
number = {1},
pages = {178},
publisher = {Nature Publishing Group},
issn = {2399-3669},
doi = {10.1038/s42004-026-01991-y},
url = {https://doi.org/10.1038/s42004-026-01991-y},
pmid = {42151623},
pmcid = {PMC13183877}
}

RIS

TY - JOUR
AU - Ito, Ryoku
AU - Hamano, Momoko
AU - Kawasaki, Ryota
AU - Watanabe, Hikaru
AU - Matsuo, Arisa
AU - Yamanishi, Yoshihiro
TI - Simulation-guided chemical direct reprogramming informed by temporal cellular conversion processes at the single-cell level
T2 - Communications chemistry
J2 - Commun Chem
PY - 2026
DA - 2026/05/18
VL - 9
IS - 1
SP - 178
SN - 2399-3669
PB - Nature Publishing Group
DO - 10.1038/s42004-026-01991-y
UR - https://doi.org/10.1038/s42004-026-01991-y
LA - en
ER -

CSL-JSON

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"id": "10.1038/s42004-026-01991-y",
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"title": "Simulation-guided chemical direct reprogramming informed by temporal cellular conversion processes at the single-cell level",
"container-title": "Communications chemistry",
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"DOI": "10.1038/s42004-026-01991-y",
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"PMCID": "PMC13183877",
"ISSN": "2399-3669",
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"language": "en",
"issued": {
"date-parts": [
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}
}

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