3D epithelial cell topology tunes signaling range to promote precise patterning.
Paper
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The authors' code
Python · 31 lines · 661 B · MIT
- from datetime import datetime
- import os
- import sys
- sys.path.insert(0, os.path.abspath("../../src"))
- project = "MultiLayer-NotchDelta"
- author = "Francisco Berkemeier"
- copyright = f"{datetime.now().year}, {author}"
- release = "0.1.0"
- extensions = [
- "sphinx.ext.autodoc",
- "sphinx.ext.napoleon",
- "sphinx.ext.viewcode",
- "sphinx_copybutton",
- "myst_parser",
- ]
- templates_path = ["_templates"]
- exclude_patterns = [".ipynb_checkpoints", "**/.ipynb_checkpoints"]
- html_theme = "sphinx_rtd_theme"
- html_static_path = ["_static"]
- html_theme_options = {
- "version_selector": False,
- "language_selector": False,
- "flyout_display": "hidden",
- }
conf.py at commit 3b57131, under MIT · at the source
Overview
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- Department of Mathematics, University College London, London WC1E 6BT, United Kingdom
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 19385318
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
- 28 September 2026: the link answers (HTTP 200)
1 file
- README.txt, Text, 36 lines
fberkemeier/MultiLayer-NotchDelta
3b57131a149ff4723dbdf43e401c0ee2cbb141af, 8 May 2026Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
6 files
- docs/
source/ , Python, 31 linesconf.py - notebooks/
msm_notebook.ipynb , Jupyter, 376 lines - src/
__init__.py , Python, 1 line - src/
msm_model.py , Python, 1,071 lines - LICENSE, License, 21 lines
- README.md, Text, 153 lines
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:
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- 4 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
- biostudies:S-BIAD3120, at BioStudies; found in the references
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:
- it points to the authors' code: fberkemeier/
MultiLayer-NotchDelta , Zenodo 19385318
Read it in the paper: doi.org/10.1073/pnas.2522727123.
Versions
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Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 5 keywords, 13 MeSH terms, 5 funders, 32 references.
Cite
This paper
Paci, G., Berkemeier, F., Baum, B., Page, K. M., & Mao, Y. (2026). 3D epithelial cell topology tunes signaling range to promote precise patterning. Proceedings of the National Academy of Sciences of the United States of America, 123(19), e2522727123. https://
BibTeX
@article{paci20263d,
author = {Paci, Giulia and Berkemeier, Francisco and Baum, Buzz and Page, Karen M and Mao, Yanlan},
title = {{3D epithelial cell topology tunes signaling range to promote precise patterning}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = may,
volume = {123},
number = {19},
pages = {e2522727123},
publisher = {National Academy of Sciences},
issn = {0027-8424},
doi = {10.1073/
url = {https://
pmid = {42090248},
pmcid = {PMC13167770}
}
RIS
TY - JOUR
AU - Paci, Giulia
AU - Berkemeier, Francisco
AU - Baum, Buzz
AU - Page, Karen M
AU - Mao, Yanlan
TI - 3D epithelial cell topology tunes signaling range to promote precise patterning
T2 - Proceedings of the National Academy of Sciences of the United States of America
J2 - Proc Natl Acad Sci U S A
PY - 2026
DA - 2026/
VL - 123
IS - 19
SP - e2522727123
SN - 0027-8424
PB - National Academy of Sciences
DO - 10.1073/
UR - https://
LA - en
ER -
CSL-JSON
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}
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