Evidence map›Paper›PMID 38566187›Full record

ArticleGenome biology2024

Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

Clarence K Mah, Noorsher Ahmed, Nicole A Lopez, Dylan C Lam, Avery Pong, Alexander Monell, Colin Kern, Yuanyuan Han, Gino Prasad, Anthony J Cesnik and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.

0numbers the graph read from it
0cells of the map it votes in
38citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

38 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Topology across scales on heterogeneous cell data.PLoS computational biology · 2025
    Article
  14. Article
  15. Article
  16. Review
  17. Article
  18. Article
  19. Article
  20. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Clarence K Mah *Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Noorsher Ahmed *Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Nicole A LopezDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Dylan C LamDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Avery PongDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Alexander MonellDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Colin KernCenter for Epigenomics, University of California San Diego, La Jolla, CA, USA.
Yuanyuan HanCenter for Epigenomics, University of California San Diego, La Jolla, CA, USA.
Gino PrasadDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Anthony J CesnikDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Emma LundbergDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Quan ZhuCenter for Epigenomics, University of California San Diego, La Jolla, CA, USA.
Hannah CarterDivision of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Gene W YeoDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.ORCID http://orcid.org/0000-0002-0799-6037

Funding

Single-cell approaches to deconvolution of disease-associated signalsU19MH107367 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GOLDSTEIN, LAWRENCE S. · 2015 to 2019
$15.0M
Functional RNA elements in the human genomeR01HG004659 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Kevin Daniel Corbett, Eugene Wei-Ming Yeo · 2008 to 2026
$12.4M
Single-Cell Transcriptomic and Epigenetics CoreP01AI132122 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZUNIGA, ELINA I · 2018 to 2022
$9.8M
A Comprehensive Functional Map of Human Protein-RNA InteractionsU41HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R. · 2018 to 2021
$9.4M
Training Program in Basic Clinical GeneticsT32GM008666 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HAMILTON, BRUCE A · 1998 to 2021
$8.6M
Therapeutic strategies for microsatellite expansion diseases using RNA-targeting CRISPR/CasR01NS103172 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MAURICE SCOTT SWANSON, Eugene Wei-Ming Yeo · 2017 to 2026
$5.6M
A comprehensive binding and functional map of human RNA-binding proteinsU24HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R., YEO, EUGENE WEI-MING · 2022 to 2025
$5.5M
Using single-cell RNA-seq to interrogate host immunity to pathogensR01AI123202 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHANG, JOHN T, YEO, EUGENE WEI-MING · 2016 to 2020
$3.1M
Graduate Training Program in BioinformaticsT32GM139790 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, GAASTERLAND, THERESA · 2021 to 2025
$2.1M
Evaluating and Targeting RNA granules in neurodegenerative diseasesR56AG069098 · NIA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI YEO, EUGENE WEI-MING · 2020 to 2020
$661k
Chan Zuckerberg Initiative CZF2019-002448Knut och Alice Wallenbergs Stiftelse KAW 2021.0346National Insitute of Health MH107367National Institute of Health AG069098National Institute of Health AI132122National Science Foundation DGE-2038238NHGRI NIH HHS HG004659NHGRI NIH HHS HG009889NHGRI NIH HHS R01 HG004659NHGRI NIH HHS U24 HG009889NHGRI NIH HHS U41 HG009889NIAID NIH HHS AI123202NIAID NIH HHS P01 AI132122NIAID NIH HHS R01 AI123202NIA NIH HHS R56 AG069098NIGMS NIH HHS GM008666NIGMS NIH HHS T32 GM008666NIGMS NIH HHS T32 GM139790NIGMS NIH HHS T32GM139790NIMH NIH HHS U19 MH107367NINDS NIH HHS NS103172NINDS NIH HHS R01 NS103172
6 · The paper itself

Abstract

The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.

Indexed as

EcosystemPropanolaminesCell CommunicationGene Expression ProfilingSingle-Cell AnalysisTranscriptomebefunololPropanolamines

Identifiers

PMID38566187
PMCPMC11289963

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.