ArticleStem cell reports2023
Entropy sorting of single-cell RNA sequencing data reveals the inner cell mass in the human pre-implantation embryo.
Article in Stem cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- A Deep Learning Approach to Assessing Cell Identity in Stem Cell-Based Embryo Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst.Nature communications · 2025Article
- Uncovering candidate Nanog-Helper genes in early mouse embryo differentiation using differential entropy and network inference.Scientific reports · 2025Article
- Pluripotent cell states and fates in human embryo models.Development (Cambridge, England) · 2025Review
- The guinea pig serves as an alternative model to study human preimplantation development.Nature cell biology · 2025Article
- An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast.Development (Cambridge, England) · 2025Article
- A comprehensive human embryo reference tool using single-cell RNA-sequencing data.Nature methods · 2025Article
- Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing.Nature methods · 2025Article
- Article
- Propagating pluripotency - The conundrum of self-renewal.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- Profiling the transcriptomic age of single-cells in humans.Communications biology · 2024Article
- Early human development and stem cell-based human embryo models.Cell stem cell · 2024Review
- Revisiting trophectoderm-inner cell mass lineage segregation in the mammalian preimplantation embryo.Human reproduction (Oxford, England) · 2024Review
- Branching topology of the human embryo transcriptome revealed by Entropy Sort Feature Weighting.Development (Cambridge, England) · 2024Article
- Self-renewing human naïve pluripotent stem cells dedifferentiate in 3D culture and form blastoids spontaneously.Nature communications · 2024Article
- A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass.PLoS biology · 2023Article
- The human embryo selection arena is associated with transposable element activity.PLoS biology · 2023Article
- Evidence implicating sequential commitment of the founder lineages in the human blastocyst by order of hypoblast gene activation.Development (Cambridge, England) · 2023Article
- Generating human blastoids modeling blastocyst-stage embryos and implantation.Nature protocols · 2023Review
- Accessing the human trophoblast stem cell state from pluripotent and somatic cells.Cellular and molecular life sciences : CMLS · 2022Review
Corrections and comments
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5 authors.
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Abstract
A major challenge in single-cell gene expression analysis is to discern meaningful cellular heterogeneity from technical or biological noise. To address this challenge, we present entropy sorting (ES), a mathematical framework that distinguishes genes indicative of cell identity. ES achieves this in an unsupervised manner by quantifying if observed correlations between features are more likely to have occurred due to random chance versus a dependent relationship, without the need for any user-defined significance threshold. On synthetic data, we demonstrate the removal of noisy signals to reveal a higher resolution of gene expression patterns than commonly used feature selection methods. We then apply ES to human pre-implantation embryo single-cell RNA sequencing (scRNA-seq) data. Previous studies failed to unambiguously identify early inner cell mass (ICM), suggesting that the human embryo may diverge from the mouse paradigm. In contrast, ES resolves the ICM and reveals sequential lineage bifurcations as in the classical model. ES thus provides a powerful approach for maximizing information extraction from high-dimensional datasets such as scRNA-seq data.
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