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Prebiotic intervention changes host and microbe proteomes in plasma extracellular vesicles of Parkinson's disease.

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Paper

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The authors' code

Markdown · 30 lines · 1.1 KB · no license

  1. # Please contact us anytime for details or troubleshooting. Happy to help.
  5. This is the list of files that are part of this repo. Each file contains detailed comments/troubleshoot tips/corresponding figure/data identifier along with associated code.
  7. 1. Data Density Scatter
  8. 2. Distribution Scaling
  9. 3. Multi_range_rows
  10. 4. Dim. reduction - 3D
  11. 5. Hierarchical clustering
  12. 6. Correlation matrices for multidim. data
  13. 7. Operations_large_file
  14. 8. Testing_intergroup_variations
  15. 9. t-SNE (t-distributed stochastic neighborhood embedding)
  16. 91. test_datafits
  17. 94. k-means_clustering
  18. 95. Biological_networks_cytoscape
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  22. Technical Requirements:
  24. Softwares, Languages et al:
  26. Data Collection: Image Quant 5.2 (quantification of crosslinking timepoints), Image J 1.8.0 (quantification of western blots, in vivo bulk crosslinking)
  28. Base requirements for specific steps: Perl (Strawberry) - 5.32.0
  29. C++ with gcc 7.2 compiler, C (check your computer manual), Cygwin for Windows - 3.1, Bash - 5.0, Windows Command Prompt (check your computer manual), Tensorflow - Core v2.3.0
  30. .

README.md at commit b65e043, no license · at the source

Overview

Authors: Deepak Sharma1, Robin M Voigt2,3,4, Deborah A Hall5, Thaisa M Cantu-Jungles6, Maliha Shaikh2, Phillip A Engen2, Jeff Jones7, Shan Li8, Bruce R Hamaker6, Christopher B Forsyth2,3, Faraz Bishehsari2,9,10, Erika G Marques de Menezes11, Philip J Norris11, Christopher G Goetz5, Ali Keshavarzian2,3,4,12,13
ORCID iDs: Thaisa M Cantu-Jungles, Ali Keshavarzian
13 affiliations
  1. Bainom Inc., 750 North State Street, Chicago, IL USA
  2. Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL USA
  3. Department of Internal Medicine, Rush University Medical Center, Chicago, IL USA
  4. Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL USA
  5. Department of Neurological Sciences, Rush University Medical Center, Chicago, IL USA
  6. Whistler Cener for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN USA
  7. Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA USA
  8. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA USA
  9. Gastroenterology Research Center, Division of Gastroenterology, Hepatology & Nutrition, Department of Internal Medicine, University of Texas Houston, Houston, TX USA
  10. MD Anderson Cancer Center-UTHealth Houston Graduate School of Biomedical Sciences, University of Texas Houston, Houston, TX USA
  11. Vitalant Research Institute, San Francisco, CA USA
  12. Department of Physiology, Rush University Medical Center, Chicago, IL USA
  13. Department of Internal Medicine, Section of Gastroenterology, Rush Center of Integrated Microbiome and Chronobiology Research, 1735 W. Harrison, Suite 224, Chicago, IL 60612 USA
Institutions: Rush University Medical Center (United States); Purdue University West Lafayette (United States); California Institute of Technology (United States); The University of Texas MD Anderson Cancer Center (United States); The University of Texas Health Science Center at Houston (United States); Vitalant Research Institute (United States); Rush University (United States)
Journal: Scientific reports, volume 16, issue 1, article 20095
Dates: received 9 December 2025; accepted 23 April 2026; published online 30 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41598-026-50859-7 · PMID 42062487 · PMCID PMC13323702 · OpenAlex W7159685288
Open access: gold, a free copy (OpenAlex)
Status: empty repository
Categories: genetics / omics (modality), human (organism), Parkinson's (population)
Methods: Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing
Keywords: Biomarkers, Diseases, Microbiology, Neurology, Neuroscience
MeSH: Extracellular Vesicles*, Parkinson Disease*, Prebiotics*, Proteome*, Aged, Biomarkers, Dysbiosis, Female, Gastrointestinal Microbiome, Humans, Male, Middle Aged, Proteomics (* major topic)
Topic: Endoplasmic Reticulum Stress and Disease (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: NIH HHS (1U01DK140923-01); National Institutes of Health (1U01DK140923-01)
Citations: not cited yet (Europe PMC); 51 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.

deebratforlife/KIN-CLIP

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: b65e0436f113e7aa0f5f8d9bcb63d36632fcd78b, 7 July 2022
Size: 14 files, 0 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
1 file
At the source: github.com/deebratforlife/KIN-CLIP

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.

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
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  • 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

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Read it in the paper: doi.org/10.1038/s41598-026-50859-7.

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 5 keywords, 13 MeSH terms, 2 funders, 50 references.

Cite

This paper

Sharma, D., Voigt, R. M., Hall, D. A., Cantu-Jungles, T. M., Shaikh, M., Engen, P. A., Jones, J., Li, S., Hamaker, B. R., Forsyth, C. B., Bishehsari, F., de Menezes, E. G. M., Norris, P. J., Goetz, C. G., & Keshavarzian, A. (2026). Prebiotic intervention changes host and microbe proteomes in plasma extracellular vesicles of Parkinson's disease. Scientific reports, 16(1), 20095. https://doi.org/10.1038/s41598-026-50859-7

BibTeX

@article{sharma2026prebiotic,
author = {Sharma, Deepak and Voigt, Robin M and Hall, Deborah A and Cantu-Jungles, Thaisa M and Shaikh, Maliha and Engen, Phillip A and Jones, Jeff and Li, Shan and Hamaker, Bruce R and Forsyth, Christopher B and Bishehsari, Faraz and de Menezes, Erika G Marques and Norris, Philip J and Goetz, Christopher G and Keshavarzian, Ali},
title = {{Prebiotic intervention changes host and microbe proteomes in plasma extracellular vesicles of Parkinson's disease}},
journal = {Scientific reports},
year = {2026},
month = apr,
volume = {16},
number = {1},
pages = {20095},
publisher = {Nature Publishing Group},
issn = {2045-2322},
doi = {10.1038/s41598-026-50859-7},
url = {https://doi.org/10.1038/s41598-026-50859-7},
pmid = {42062487},
pmcid = {PMC13323702}
}

RIS

TY - JOUR
AU - Sharma, Deepak
AU - Voigt, Robin M
AU - Hall, Deborah A
AU - Cantu-Jungles, Thaisa M
AU - Shaikh, Maliha
AU - Engen, Phillip A
AU - Jones, Jeff
AU - Li, Shan
AU - Hamaker, Bruce R
AU - Forsyth, Christopher B
AU - Bishehsari, Faraz
AU - de Menezes, Erika G Marques
AU - Norris, Philip J
AU - Goetz, Christopher G
AU - Keshavarzian, Ali
TI - Prebiotic intervention changes host and microbe proteomes in plasma extracellular vesicles of Parkinson's disease
T2 - Scientific reports
J2 - Sci Rep
PY - 2026
DA - 2026/04/30
VL - 16
IS - 1
SP - 20095
SN - 2045-2322
PB - Nature Publishing Group
DO - 10.1038/s41598-026-50859-7
UR - https://doi.org/10.1038/s41598-026-50859-7
LA - en
ER -

CSL-JSON

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