Evidence map›Paper›PMID 36423582›Full record

ArticleCell2022

Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding.

Weixiang Fang, Claire M Bell, Abel Sapirstein, Soichiro Asami, Kathleen Leeper, Donald J Zack, Hongkai Ji, Reza Kalhor

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
6.3field-weighted citation impact, top 4% of its field
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

23 citing papers in PubMed, 31 citations in OpenAlex.

  1. Review
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  10. Inferring Cell Differentiation Dynamics with Unobserved Progenitors.bioRxiv : the preprint server for biology · 2025
    Article
  11. Article
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  14. The lives of cells, recorded.Nature reviews. Genetics · 2025
    Review
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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

8 authors at 2 institutions in 1 country.

Weixiang FangDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Claire M BellDepartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Abel SapirsteinDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Soichiro AsamiDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Kathleen LeeperDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Donald J ZackDepartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Hongkai JiDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. Electronic address: hji@jhu.edu.
Reza KalhorDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: kalhor@jhu.edu.
Johns Hopkins University · USGeorgia Institute of Technology · US

Funding

Wilmer Core Grant for Vision ResearchP30EY001765 · NEI · JOHNS HOPKINS UNIVERSITY · PI Jiang Qian · 1985 to 2026
$22.1M
Dynamics of lineage-specific genome reorganization in gastrulation and their response to disease-associated epigenetic perturbationsU01HL156056 · NHLBI · JOHNS HOPKINS UNIVERSITY · PI KALHOR, REZA · 2020 to 2024
$3.1M
Mapping the dynamics of mouse neurogenesis in autism models using high-resolution genomic barcoding technologiesR01HG012357 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI KALHOR, REZA · 2022 to 2025
$2.1M
Big Data Methods for Decoding Gene RegulationR01HG009518 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI JI, HONGKAI · 2018 to 2021
$1.7M
Computational tools for regulome mapping using single-cell genomic dataR01HG010889 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI JI, HONGKAI · 2019 to 2022
$1.6M
Simultaneous Single-cell Lineage Tracing and Transcriptome Analysis for Mapping Human and Mouse Retinal DevelopmentF31EY030769 · NEI · JOHNS HOPKINS UNIVERSITY · PI BELL, CLAIRE · 2020 to 2022
$112k
NEI NIH HHS F31 EY030769NEI NIH HHS P30 EY001765NHGRI NIH HHS R01 HG009518NHGRI NIH HHS R01 HG010889NHGRI NIH HHS R01 HG012357NHLBI NIH HHS U01 HL156056
6 · The paper itself

Abstract

Natural and induced somatic mutations that accumulate in the genome during development record the phylogenetic relationships of cells; whether these lineage barcodes capture the complex dynamics of progenitor states remains unclear. We introduce quantitative fate mapping, an approach to reconstruct the hierarchy, commitment times, population sizes, and commitment biases of intermediate progenitor states during development based on a time-scaled phylogeny of their descendants. To reconstruct time-scaled phylogenies from lineage barcodes, we introduce Phylotime, a scalable maximum likelihood clustering approach based on a general barcoding mutagenesis model. We validate these approaches using realistic in silico and in vitro barcoding experiments. We further establish criteria for the number of cells that must be analyzed for robust quantitative fate mapping and a progenitor state coverage statistic to assess the robustness. This work demonstrates how lineage barcodes, natural or synthetic, enable analyzing progenitor fate and dynamics long after embryonic development in any organism.

Indexed as

Embryonic DevelopmentCell LineageMutagenesisPhylogenyRetrospective Studiesclonal dynamicscoalescent theoryhoming CRISPR MARC1 barcodingICE-FASEphylogenetic inferencePhylotimeprogenitor field dynamicssingle cell ineage tracingsomatic mutationstime-scaled cell phylogeny

Identifiers

PMID36423582
PMCPMC9708097
OpenAlexW4310074701

What OpenQuestion holds

Textmetadata
LicenceTDM
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.