ArticlePLoS computational biology2021
Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 55 citations in OpenAlex.
- Using human induced pluripotent stem cell-derived cardiomyocytes to understand the mechanisms driving cardiomyocyte maturation.Frontiers in cardiovascular medicine · 2022Pooled it
- CMAC: A deep learning framework for absolute cardiomyocyte transcriptional age estimation.bioRxiv : the preprint server for biology · 2026Article
- Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution.Biology open · 2026Article
- Decoding Cardiac Development and Maturation at Single-Cell and Spatial Transcriptomic Resolution.Circulation research · 2026Review
- Article
- Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment.Stem cell reports · 2025Article
- Deciphering normal and cancer stem cell niches by spatial transcriptomics: opportunities and challenges.Genes & development · 2025Review
- Article
- Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics.Nature reviews. Molecular cell biology · 2025Review
- Single-cell Technology in Stem Cell Research.Current stem cell research & therapy · 2025Review
- Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation.Genome biology · 2024Article
- Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments.PLoS computational biology · 2024Article
- A transcriptional enhancer regulates cardiac maturation.Nature cardiovascular research · 2024Article
- Estimating Transcriptome Diversity and Specialization inPlants (Basel, Switzerland) · 2024Article
- Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments.bioRxiv : the preprint server for biology · 2024Article
- Pediatric dilated cardiomyopathy: a review of current clinical approaches and pathogenesis.Frontiers in pediatrics · 2024Review
- Defining the Role of Metastasis-Initiating Cells in Promoting Carcinogenesis in Ovarian Cancer.Biology · 2023Review
- Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics.Stem cell research & therapy · 2023Article
- Immune Infiltration in Tumor and Adjacent Non-Neoplastic Regions Codetermines Patient Clinical Outcomes in Early-Stage Lung Cancer.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2023Article
- Adapting to a new environment: postnatal maturation of the human cardiomyocyte.The Journal of physiology · 2023Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The immaturity of pluripotent stem cell (PSC)-derived tissues has emerged as a universal problem for their biomedical applications. While efforts have been made to generate adult-like cells from PSCs, direct benchmarking of PSC-derived tissues against in vivo development has not been established. Thus, maturation status is often assessed on an ad-hoc basis. Single cell RNA-sequencing (scRNA-seq) offers a promising solution, though cross-study comparison is limited by dataset-specific batch effects. Here, we developed a novel approach to quantify PSC-derived cardiomyocyte (CM) maturation through transcriptomic entropy. Transcriptomic entropy is robust across datasets regardless of differences in isolation protocols, library preparation, and other potential batch effects. With this new model, we analyzed over 45 scRNA-seq datasets and over 52,000 CMs, and established a cross-study, cross-species CM maturation reference. This reference enabled us to directly compare PSC-CMs with the in vivo developmental trajectory and thereby to quantify PSC-CM maturation status. We further found that our entropy-based approach can be used for other cell types, including pancreatic beta cells and hepatocytes. Our study presents a biologically relevant and interpretable metric for quantifying PSC-derived tissue maturation, and is extensible to numerous tissue engineering contexts.
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Registered trials
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.