OSCR

Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility.

Code ↔ Paper

3 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 3 matches
  1. [1] § Methods › Gut microbial GUS gene analyses › Identification and characterization of GUS gene sequences from mouse and human fecal metagenomic data ↔ Cladogram Generation/Metagenomic GUSome Cladogram/ggtree_Endo_14_MGX_v3.r, lines 1–88 · score 0.64 · loop class, v3, ggtree, cladogram, ggplot2, Metagenomic
  2. [2] § Methods › Gut microbial GUS gene analyses › GUS gene intensity analysis ↔ sPLS-DA/mixomics_sPLS-DA_iter_export_v4.r, lines 47–91 · score 0.61 · plotIndiv, mixOmics, splsda, class
  3. [3] § Methods › Gut microbial GUS gene analyses › Identification and characterization of GUS gene sequences from mouse and human fecal metagenomic data ↔ GUS Identification/GUS Structural Class ID/GUS_Loop_ID_v3.2.py, lines 63–104 · score 0.51 · loop class, Clustal, v3, alignment, protein, GUS

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

R · 143 lines · 4.4 KB · MIT · 1 match

  1. ########################################################################################
  2. ### Cladogram - Endobiotics Cohort Metagenomic GUSome
  3. ########################################################################################
  5. ### Usage
  6. # Rscript ggtree_Endo_14_MGX_v3.r
  8. ########################################################################################
  9. ### main
  10. ########################################################################################
  12. cat("loading packages...\n")
  14. # Clean workspace
  15. rm(list=ls())
  17. # Define required packages
  18. required_packages <- c("ape", "Biostrings", "ggplot2", "ggtree",
  19. "tidyverse", "dplyr", "geiger")
  21. # Identify packages that are not installed
  22. installed <- installed.packages()[,"Package"]
  23. not_installed <- setdiff(required_packages, installed)
  25. # Install missing packages
  26. if(length(not_installed) > 0) {
  27. install.packages(not_installed, dependencies = TRUE)
  28. }
  30. # Load packages invisibly
  31. invisible(suppressPackageStartupMessages(lapply(required_packages, library, character.only = TRUE)))
  33. # Mute output other than progress updates
  34. # sink("/dev/null")
  37. # Input data and output directories
  38. cat("loading input data...\n")
  39. data.file <- "./Endo_14_MGX_GUS_100_tax.afa.treefile"
  40. tree <- read.tree(data.file)
  42. outname <- 'ggtree_Endo_14_MGX.png'
  44. loopDF_path <- "./endo_14_mgx_ggtree.csv"
  45. loopDF <- read.csv(loopDF_path)
  47. # Specify cladogram colors
  48. values <- c(
  49. "Loop_1" = "#F08080",
  50. "Loop_2" = "#7B68EE",
  51. "Mini-Loop_1" = "#8FBC8F",
  52. "Mini-Loop_2" = "#FF7F50",
  53. "Mini-Loop_1_2" = "#DEB887",
  54. "No_Loop" = "#666666",
  55. "NTL" = "#00CCCC",
  56. "CTD" = "#FFC533")
  58. cat('building plot...\n')
  60. # Plot cladogram
  61. treePlot <- ggtree(tree, aes(color=Loop_Class_Final,label=label), branch.length="none", layout="circular", size=1) %<+%
  62. loopDF +
  63. geom_tiplab(size=3, color="black",hjust=-.025,fontface='bold') + # label tips by name
  64. scale_fill_manual(na.translate=FALSE,values=values)+
  65. theme(
  66. plot.margin = margin(4,4,4,4, "cm"),
  67. panel.grid.minor = element_blank(),
  68. panel.background = element_rect(fill = "transparent",colour = NA),
  69. plot.background = element_rect(fill = "transparent",colour = NA), legend.background=element_rect(fill = alpha("white", 0)), legend.key=element_rect(fill = alpha("white", 0)),
  70. legend.position="none",
  71. )+
  73. xlim(-3.5, NA) + # modifies diam of center, changing shape of lines @ center. increase to increase diam of center
  75. scale_color_manual(
  76. values = c(
  77. "Loop_1" = "#F08080",
  78. "Loop_2" = "#7B68EE",
  79. "Mini-Loop_1" = "#8FBC8F",
  80. "Mini-Loop_2" = "#FF7F50",
  81. "Mini-Loop_1_2" = "#DEB887",
  82. "No_Loop" = "#666666",
  83. "NTL" = "#00CCCC",
  84. "CTD" = "#FFC533")
  85. )
  87. # Build plot for further edits
  88. pg <- ggplot_build(treePlot)
  90. # Change default branch coloring
  91. grey_to_smt <- function(x) {
  92. if(x=='grey50') return('#B3B3B3')
  93. else return(x)
  94. }
  96. pg$data[[2]]$colour <- sapply(pg$data[[2]]$colour, grey_to_smt)
  97. pg$data[[1]]$colour <- sapply(pg$data[[2]]$colour, grey_to_smt)
  99. cat('coloring branches...\n')
  100. for (x in pg$data[[2]]$node) {
  101. nodeLeafList1 <- tips(tree,x)
  102. str_x <- as.character(x)
  104. node_row <- pg$data[[2]] %>% filter(node == str_x)
  105. colorList <- c()
  106. if (length(nodeLeafList1)!=0){
  107. for (y in nodeLeafList1){
  108. str_y <- as.character(y)
  109. leaf_row <- pg$data[[2]] %>% filter(label == str_y)
  110. leafColor <- leaf_row$colour
  111. colorList <- c(colorList, leafColor)}
  112. uniqueColorList <- unique(colorList)
  113. colorCount <- length(uniqueColorList)
  114. if (colorCount == 1){
  115. color <- uniqueColorList[1]
  116. pg$data[[1]]$colour[x]<-color
  117. pg$data[[2]]$colour[x]<-color
  118. }}}
  120. q <- ggplot_gtable(pg)
  123. # Plot and save
  124. ggsave(outname, plot=q, device=png, height=10, width=14.5, bg = "transparent",dpi=1200)
  126. ########################################################################################
  127. ### Session Log
  128. ########################################################################################
  130. writeSessionInfo <- function(outputFilePath) {
  131. # Retrieve R, package versions
  132. rVersion <- R.version.string
  133. packageVersions <- sapply(required_packages, function(pkg) paste0(pkg, " version ", packageVersion(pkg)))
  134. # Combine log information
  135. sessionInfo <- c(rVersion, packageVersions)
  136. # Write to log
  137. writeLines(sessionInfo, outputFilePath)
  138. }
  140. # Specify output path
  141. outputFilePath <- "./session_log.txt"
  142. # Write session log
  143. writeSessionInfo(outputFilePath)

ggtree_Endo_14_MGX_v3.r at commit 2f1db57, under MIT · at the source

Overview

Authors: Valentina N Lagomarsino1, Ariel Robinson1, Perry E Mitchell1, Mira Jiang1, Lauren E Hutchinson2, Josh John Sekela2, Patrick Caron3, McKenzie K Gehris4, Kathleen I Navas1, Murillo Duarte-Silva1, Michael Netherland Jr5, Nur A Hasan5, Chantal Guillemette3, Matthew R Redinbo2, Meenakshi Rao1
ORCID iDs: Valentina N Lagomarsino, Lauren E Hutchinson, McKenzie K Gehris, Kathleen I Navas, Chantal Guillemette, Matthew R Redinbo, Meenakshi Rao
  1. Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA USA
  2. Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
  3. Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center -Université Laval, Faculty of Pharmacy, Université Laval, Quebec, Quebec Canada
  4. Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
  5. EzBiome Inc., Gaithersburg, MD USA
Institutions: Boston Children's Hospital (United States); Harvard University (United States); University of North Carolina at Chapel Hill (United States); Université Laval (Canada); Centre de recherche du CHU de Québec-Université Laval (Canada)
Journal: Nature neuroscience, volume 29, issue 8, pages 1791-1800
Dates: received 2 January 2026; accepted 27 April 2026; published online 2 June 2026; in print 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41593-026-02321-0 · PMID 42231021 · PMCID PMC13403785 · OpenAlex W7163127838
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions
Keywords: Enteric nervous system, Cellular neuroscience, Hormones, Microbiology
MeSH: Androgens*, Enteric Nervous System*, Gastrointestinal Microbiome*, Gastrointestinal Motility*, Neurons*, Animals, Glucuronidase, Humans, Male, Mice, Mice, Inbred C57BL, Nitric Oxide Synthase Type I, Receptors, Androgen, Testosterone (* major topic)
Topic: Gastrointestinal motility and disorders (Gastroenterology, Medicine), according to OpenAlex
Funding: NIDDK NIH HHS (R01 DK130836, R03 DK125636, R01 DK135707); NIGMS NIH HHS (R35 GM152079, R01 GM135218); U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (R01GM135218, R35GM152079); U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (R03DK125636, R01DK135707, R01DK130836); U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) (R01DK130836, R01DK135707, R03DK125636); U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) (R01GM135218, R35GM152079)
Citations: cited by 2 papers (Europe PMC); 59 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, with 3 matches between paragraphs and lines of code.

redinbolab/iterative_linear_fit_notebook

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: eeaa7af3521f9093f4cddad3f35723583a27050b, 1 April 2026
Languages: Jupyter (1)
Size: 2 files, 1 script
Software Heritage: not archived
Found in: the text, “In fimo analyses of GUS activity (related to Fig”
Holds: license file, 1 notebook
Not found: README, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (1 file), pandas (1 file), SciPy (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
2 files
At the source: github.com/redinbolab/iterative_linear_fit_notebook/

redinbolab/gus_endobiotics

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 2f1db57bc65c7e3354342713a4f013271cb660bd, 2 April 2024
Languages: Python (8), R (6)
Size: 82 files, 14 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (4 files), Biopython (3 files), tidyverse (3 files), NumPy (2 files), pandas (2 files), SciPy (2 files), pheatmap (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
16 files
At the source: github.com/redinbolab/GUS_Endobiotics/tree/main/GUSIdentification/

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:

Read it in the paper: doi.org/10.1038/s41593-026-02321-0.

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;
  • 15 scripts, each with its path and the digest of its content;
  • 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • 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

Data links

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:

  • it points to a dataset: NCBI

Read it in the paper: doi.org/10.1038/s41593-026-02321-0.

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 → Nature Portfolio

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 4 keywords, 14 MeSH terms, 6 funders, 58 references.

Cite

This paper

Lagomarsino, V. N., Robinson, A., Mitchell, P. E., Jiang, M., Hutchinson, L. E., Sekela, J. J., Caron, P., Gehris, M. K., Navas, K. I., Duarte-Silva, M., Netherland, M., Hasan, N. A., Guillemette, C., Redinbo, M. R., & Rao, M. (2026). Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility. Nature neuroscience, 29(8), 1791-1800. https://doi.org/10.1038/s41593-026-02321-0

BibTeX

@article{lagomarsino2026microbial,
author = {Lagomarsino, Valentina N and Robinson, Ariel and Mitchell, Perry E and Jiang, Mira and Hutchinson, Lauren E and Sekela, Josh John and Caron, Patrick and Gehris, McKenzie K and Navas, Kathleen I and Duarte-Silva, Murillo and Netherland, Michael and Hasan, Nur A and Guillemette, Chantal and Redinbo, Matthew R and Rao, Meenakshi},
title = {{Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility}},
journal = {Nature neuroscience},
year = {2026},
month = jun,
volume = {29},
number = {8},
pages = {1791--1800},
publisher = {Nature Portfolio},
issn = {1097-6256},
doi = {10.1038/s41593-026-02321-0},
url = {https://doi.org/10.1038/s41593-026-02321-0},
pmid = {42231021},
pmcid = {PMC13403785}
}

RIS

TY - JOUR
AU - Lagomarsino, Valentina N
AU - Robinson, Ariel
AU - Mitchell, Perry E
AU - Jiang, Mira
AU - Hutchinson, Lauren E
AU - Sekela, Josh John
AU - Caron, Patrick
AU - Gehris, McKenzie K
AU - Navas, Kathleen I
AU - Duarte-Silva, Murillo
AU - Netherland, Michael
AU - Hasan, Nur A
AU - Guillemette, Chantal
AU - Redinbo, Matthew R
AU - Rao, Meenakshi
TI - Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility
T2 - Nature neuroscience
J2 - Nat Neurosci
PY - 2026
DA - 2026/06/02
VL - 29
IS - 8
SP - 1791
EP - 1800
SN - 1097-6256
PB - Nature Portfolio
DO - 10.1038/s41593-026-02321-0
UR - https://doi.org/10.1038/s41593-026-02321-0
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41593-026-02321-0",
"type": "article-journal",
"title": "Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility",
"container-title": "Nature neuroscience",
"author": [
{
"family": "Lagomarsino",
"given": "Valentina N"
},
{
"family": "Robinson",
"given": "Ariel"
},
{
"family": "Mitchell",
"given": "Perry E"
},
{
"family": "Jiang",
"given": "Mira"
},
{
"family": "Hutchinson",
"given": "Lauren E"
},
{
"family": "Sekela",
"given": "Josh John"
},
{
"family": "Caron",
"given": "Patrick"
},
{
"family": "Gehris",
"given": "McKenzie K"
},
{
"family": "Navas",
"given": "Kathleen I"
},
{
"family": "Duarte-Silva",
"given": "Murillo"
},
{
"family": "Netherland",
"given": "Michael"
},
{
"family": "Hasan",
"given": "Nur A"
},
{
"family": "Guillemette",
"given": "Chantal"
},
{
"family": "Redinbo",
"given": "Matthew R"
},
{
"family": "Rao",
"given": "Meenakshi"
}
],
"container-title-short": "Nat Neurosci",
"volume": "29",
"issue": "8",
"page": "1791-1800",
"DOI": "10.1038/s41593-026-02321-0",
"PMID": "42231021",
"PMCID": "PMC13403785",
"ISSN": "1097-6256",
"publisher": "Nature Portfolio",
"URL": "https://doi.org/10.1038/s41593-026-02321-0",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
2
]
]
}
}

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:10.3389/fcimb.2026.1806356
Global research trends in enteric nervous system and gut microbiota: a bibliometric analysis (2005-2025).
Journal: Frontiers in cellular and infection microbiology
In common: cellular / molecular, 6 references
[2] doi:10.1038/s41586-026-10512-9 [code]
Astrocyte glucocorticoid receptor signalling restricts neuronal plasticity.
Journal: Nature
In common: Biopython, pheatmap, ggplot2, 4 other tools, mouse, cellular / molecular, 1 reference
[3] doi:10.1126/sciadv.aed2952 [code]
Activation of transposable elements is linked to a region- and cell type-specific interferon response in Parkinson's disease.
Journal: Science advances
In common: Biopython, pheatmap, ggplot2, 4 other tools, cellular / molecular, 1 reference
[4] doi:10.1016/j.stemcr.2026.102930 [code]
ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A.
Journal: Stem cell reports
In common: Biopython, pheatmap, ggplot2, 4 other tools, cellular / molecular, 1 reference
[5] doi:10.1038/s42003-026-10957-8 [code]
Brain defence by the extracellular matrix protein Cochlin.
Journal: Communications biology
In common: Biopython, pheatmap, ggplot2, 4 other tools, mouse, cellular / molecular
[6] doi:10.1038/s43587-026-01207-x [code]
A microprotein atlas of the human frontal cortex in Alzheimer's disease.
Journal: Nature aging
In common: Biopython, pheatmap, ggplot2, 4 other tools
[7] 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: Biopython, pheatmap, ggplot2, 4 other tools
[8] doi:10.1038/s41586-026-10490-y [code]
Lineage and organ signals sequentially build organ intrinsic nervous systems.
Journal: Nature
In common: ggplot2, tidyverse, pandas, 2 other tools, mouse, 2 references
[9] doi:10.1038/s41586-026-10629-x [code]
Whole-genome duplication shaped cell-type evolution in the vertebrate brain.
Journal: Nature
In common: pheatmap, ggplot2, tidyverse, 3 other tools, mouse, cellular / molecular, 1 reference
[10] doi:10.1038/s44318-026-00818-9 [code]
FAM134B-mediated ER-phagy degrades APP and suppresses Alzheimer's disease pathology.
Journal: The EMBO journal
In common: Biopython, ggplot2, tidyverse, 3 other tools, mouse, cellular / molecular

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.