OSCR

Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Jupyter notebook · 92 lines · 2.7 KB · BSD-2-Clause

  1. # %%
  2. import os
  3. import pandas as pd
  4. from pathlib import Path
  6. from abc_atlas_access.abc_atlas_cache.abc_project_cache import AbcProjectCache
  8. # %%
  9. version = '20250531'
  10. download_base = Path('../../../data/abc_atlas')
  11. abc_cache = AbcProjectCache.from_s3_cache(download_base)
  12. abc_cache.load_manifest(f'releases/{version}/manifest.json')
  14. # %%
  15. abbreviation_term = abc_cache.get_metadata_dataframe(
  16. directory='HMBA-BG-taxonomy-CCN20250428',
  17. file_name='abbreviation_term',
  18. )
  19. abbreviation_term
  21. # %% [markdown]
  22. # Helper functions to format a clickable ontology id link to identifiers.
  24. # %%
  25. def create_clickable_ident_org_link(id):
  26. url_template = '''<a href="https://identifiers.org/{id}" target="_blank">{id}</a>'''.format(id=id)
  27. return url_template
  29. def create_clickable_dhba_link(id):
  30. _, id_num = id.split(':')
  32. # Don't link to the DHBA if the id_num starts with 'AA'
  33. if id_num.startswith('AA'):
  34. url_template = id
  35. else:
  36. url_template = '''<a href="https://atlas.brain-map.org/atlas?atlas=265297126&structure={id_num}" target="_blank">{id}</a>'''.format(id_num=id_num, id=id)
  37. return url_template
  39. def parse_abbreviation_term(id_val):
  40. if pd.isna(id_val):
  41. return ""
  42. elif id_val.startswith('DHBA'):
  43. return create_clickable_dhba_link(id_val)
  44. else:
  45. return create_clickable_ident_org_link(id_val)
  47. # %% [markdown]
  48. # Helper function to create a gene list
  50. # %%
  51. def create_output_html(df, file, title) :
  53. df['primary_identifier'] = df['primary_identifier'].apply(parse_abbreviation_term)
  54. df['secondary_identifier'] = df['secondary_identifier'].apply(parse_abbreviation_term)
  55. formatter = {'abbreviation_term': lambda x: '<b>' + x + '</b>'}
  56. output = df.to_html(index=False, na_rep='',
  57. render_links=True,escape=False,
  58. classes="mystyle",formatters=formatter)
  60. html_string = '''
  61. <html>
  62. <head><title>%s</title></head>
  63. <link rel="stylesheet" type="text/css" href="../../_static/simple_style.css"/>
  64. <body>
  65. {table}
  66. </body>
  67. </html>.
  68. ''' % title
  70. # OUTPUT AN HTML FILE
  71. with open(file, 'w') as f:
  72. f.write(html_string.format(table=output))
  75. # %% [markdown]
  76. # Create gene list html for HMBA-BG
  78. # %%
  79. terms = abc_cache.get_metadata_dataframe(
  80. directory='HMBA-BG-taxonomy-CCN20250428',
  81. file_name='abbreviation_term',
  82. )
  83. terms.sort_values('abbreviation_term', inplace=True)
  84. print(len(terms))
  86. output_directory = 'HMBA-BG-taxonomy-CCN20250428'
  87. os.makedirs(output_directory, exist_ok=True)
  88. output_file = os.path.join( output_directory, 'abbreviation_list.html')
  89. create_output_html(terms, output_file, 'HMBA-BG-taxonomy-CCN20250428: abbreviation list')
  91. # %%

create_abbreviation_terms_list_html.ipynb at commit b16ee22, under BSD-2-Clause · at the source

Overview

Authors: Petar N Grozdanov1, Laura B Ferguson2, Brent R Kisby1, Clinton C MacDonald3, Robert O Messing4, Igor Ponomarev1
  1. Department of Pharmacology and Neuroscience, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 USA
  2. Bowles Center for Alcohol Studies, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599 USA
  3. Department of Cell Biology and Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430 USA
  4. Waggoner Center for Alcohol and Addiction Research, Department of Neuroscience, University of Texas at Austin, Austin, TX 78712 USA
Institutions: Texas Tech University (United States); Texas Tech University Health Sciences Center (United States); University of North Carolina at Chapel Hill (United States); The University of Texas at Austin (United States)
Journal: Molecular neurobiology, volume 63, issue 1, article 833
Dates: received 28 March 2026; accepted 4 August 2026; published online 13 August 2026; in print 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1007/s12035-026-06122-1 · PMID 42595924 · PMCID PMC13473237 · OpenAlex W7202363448
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, Machine learning, Preprocessing, Connectivity
Keywords: Alcohol use disorder, Synaptic plasticity, Alternative polyadenylation, Chronic intermittent ethanol exposure procedure, Gene expression
Topic: Amyotrophic Lateral Sclerosis Research (Neurology, Medicine), according to OpenAlex
Funding: Texas Tech University Health Sciences Center; National Institutes of Health
Citations: not cited yet (OpenAlex); 77 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.

Repository

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

alleninstitute/abc_atlas_access

License: BSD-2-Clause
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: b16ee223d3466a57b30066973413ccc948c2e983, 8 July 2026
Languages: Jupyter (51), Python (19), Shell (1)
Size: 246 files, 71 scripts
Software Heritage: not archived
Found in: the text, “Datasets”
Holds: README, license file, environment (pyproject.toml), tests, continuous integration, documentation, 51 notebooks
Not found: CITATION.cff
Tools: pandas (22 files), anndata (19 files), Matplotlib (19 files), NumPy (18 files), Pillow (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
24 files
At the source: github.com/AllenInstitute/abc_atlas_access/blob/main/descriptions/WMB-10X.md

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;
  • 22 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/10.1007/s12035-026-06122-1.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

  • Publisher: n/a → Springer Science+Business Media
  • Funding: added Texas Tech University Health Sciences Center; National Institutes of Health

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 5 keywords, 76 references.

Cite

This paper

Grozdanov, P. N., Ferguson, L. B., Kisby, B. R., MacDonald, C. C., Messing, R. O., & Ponomarev, I. (2026). Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner. Molecular neurobiology, 63(1), 833. https://doi.org/10.1007/s12035-026-06122-1

BibTeX

@article{grozdanov2026alternative,
author = {Grozdanov, Petar N and Ferguson, Laura B and Kisby, Brent R and MacDonald, Clinton C and Messing, Robert O and Ponomarev, Igor},
title = {{Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner}},
journal = {Molecular neurobiology},
year = {2026},
month = aug,
volume = {63},
number = {1},
pages = {833},
publisher = {Springer Science+Business Media},
doi = {10.1007/s12035-026-06122-1},
url = {https://doi.org/10.1007/s12035-026-06122-1},
pmid = {42595924},
pmcid = {PMC13473237}
}

RIS

TY - JOUR
AU - Grozdanov, Petar N
AU - Ferguson, Laura B
AU - Kisby, Brent R
AU - MacDonald, Clinton C
AU - Messing, Robert O
AU - Ponomarev, Igor
TI - Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner
T2 - Molecular neurobiology
PY - 2026
DA - 2026/08/13
VL - 63
IS - 1
SP - 833
PB - Springer Science+Business Media
DO - 10.1007/s12035-026-06122-1
UR - https://doi.org/10.1007/s12035-026-06122-1
LA - en
ER -

CSL-JSON

{
"id": "10.1007/s12035-026-06122-1",
"type": "article-journal",
"title": "Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner",
"container-title": "Molecular neurobiology",
"author": [
{
"family": "Grozdanov",
"given": "Petar N"
},
{
"family": "Ferguson",
"given": "Laura B"
},
{
"family": "Kisby",
"given": "Brent R"
},
{
"family": "MacDonald",
"given": "Clinton C"
},
{
"family": "Messing",
"given": "Robert O"
},
{
"family": "Ponomarev",
"given": "Igor"
}
],
"volume": "63",
"issue": "1",
"page": "833",
"DOI": "10.1007/s12035-026-06122-1",
"PMID": "42595924",
"PMCID": "PMC13473237",
"publisher": "Springer Science+Business Media",
"URL": "https://doi.org/10.1007/s12035-026-06122-1",
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
13
]
]
}
}

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

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1186/s12974-026-03868-2
Translational evidence for increased central amygdala IL-6 activity in alcohol dependence.
Journal: Journal of neuroinflammation
In common: other condition, mouse, 6 references
[2] doi:10.1186/s13059-026-04177-w [code]
Genomic sequence evolution underlying human neocortical interareal diversification.
Journal: Genome biology
In common: anndata, Pillow, pandas, 2 other tools, mouse, cellular / molecular, 2 references
[3] doi:10.1038/s41467-026-71803-3 [code]
Charting the transition from in vitro gliogenesis to the in vivo maturation of human glial progenitor cells transplanted into the hypomyelinated mouse brain.
Journal: Nature communications
In common: anndata, pandas, Matplotlib, 1 other tool, mouse, cellular / molecular, 3 references
[4] doi:10.1038/s41586-026-10629-x [code]
Whole-genome duplication shaped cell-type evolution in the vertebrate brain.
Journal: Nature
In common: anndata, pandas, Matplotlib, 1 other tool, mouse, cellular / molecular, 3 references
[5] doi:10.1038/s41467-026-76675-1 [code]
Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.
Journal: Nature communications
In common: anndata, pandas, Matplotlib, 1 other tool, 3 references
[6] doi:10.1038/s41592-026-03057-2 [code]
CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.
Journal: Nature methods
In common: anndata, Pillow, pandas, 2 other tools, mouse, 1 reference
[7] doi:10.1016/j.xgen.2026.101278 [code]
Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.
Journal: Cell genomics
In common: pandas, NumPy, 5 references
[8] doi:10.1126/sciadv.adq6577 [code]
Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency.
Journal: Science advances
In common: anndata, pandas, Matplotlib, 1 other tool, mouse, 2 references
[9] doi:10.1038/s41467-026-73796-5 [code]
Cross-species transcriptomic analysis of rodent model fidelity to human mesial temporal lobe epilepsy.
Journal: Nature communications
In common: anndata, pandas, Matplotlib, 1 other tool, mouse, cellular / molecular, 2 references
[10] doi:10.1038/s41597-026-07173-8 [code]
The Cell Ontology in the age of single-cell omics.
Journal: Scientific data
In common: anndata, pandas, Matplotlib, 1 other tool, cellular / molecular, 2 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.