Evidence map›Paper›PMID 32091578›Full record

ArticleBioinformatics (Oxford, England)2020

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics.

Zaki Hasnain, Andrew K Fraser, Dan Georgess, Alex Choi, Paul Macklin, Joel S Bader, Shelly R Peyton, Andrew J Ewald, Paul K Newton

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Review
  6. Mammary Organoids and 3D Cell Cultures: Old Dogs with New Tricks.Journal of mammary gland biology and neoplasia · 2020
    Review
  7. Multi-Aperture Transformers for 3D (MAT3D) Segmentation of Clinical and Microscopic Images.IEEE Winter Conference on Applications of Computer Vision. IEEE Winter Conference on Applications of Computer Vision
    Article
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

9 authors.

Zaki HasnainDepartment of Aerospace & Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA.
Andrew K FraserDepartment of Cell Biology and Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21218, USA.
Dan GeorgessDepartment of Cell Biology and Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21218, USA.
Alex ChoiDepartment of Cell Biology and Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21218, USA.
Paul MacklinIntelligent Systems Engineering, Indiana University, Bloomington, IN 47408, USA.
Joel S BaderDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Shelly R PeytonDepartment of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
Andrew J EwaldDepartment of Cell Biology and Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21218, USA.
Paul K NewtonDepartment of Aerospace & Mechanical Engineering, University of Southern California, Los Angeles, CA 90089, USA.

Funding

MEDICAL SCIENTIST TRAINING PROGRAMT32GM007309 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI COX, ANDREA L · 1985 to 2019
$43.2M
The Role of Physical Cues in Collective Cell InvasionU54CA210173 · NCI · JOHNS HOPKINS UNIVERSITY · PI SUN, SEAN X · 2016 to 2020
$9.9M
Pathway Discovery and Target Validation for Outgrowth of Breast Cancer MetastasesU01CA217846 · NCI · JOHNS HOPKINS UNIVERSITY · PI BADER, JOEL S., EWALD, ANDREW JOSEF · 2017 to 2021
$4.8M
NCI NIH HHS U01 CA217846NCI NIH HHS U54 CA210173NIGMS NIH HHS T32 GM007309
6 · The paper itself

Abstract

summaryOrganoid model systems recapitulate key features of mammalian tissues and enable high throughput experiments. However, the impact of these experiments may be limited by manual, non-standardized, static or qualitative phenotypic analysis. OrgDyn is an open-source and modular pipeline to quantify organoid shape dynamics using a combination of feature- and model-based approaches on time series of 2D organoid contour images. Our pipeline consists of (i) geometrical and signal processing feature extraction, (ii) dimensionality reduction to differentiate dynamical paths, (iii) time series clustering to identify coherent groups of organoids and (iv) dynamical modeling using point distribution models to explain temporal shape variation. OrgDyn can characterize, cluster and model differences among unique dynamical paths that define diverse final shapes, thus enabling quantitative analysis of the molecular basis of tissue development and disease. AVAILABILITY AND IMPLEMENTATION: https://github.com/zakih/organoidDynamics (BSD 3-Clause License). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

OrganoidsSoftwareAnimalsCluster Analysis

Identifiers

PMID32091578
PMCPMC7214016

What OpenQuestion holds

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Registered trials

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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.