ArticleStem cell reports2022
Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.
Article in Stem cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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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.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
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- OneSC: a computational platform for recapitulating cell state transitions.Bioinformatics (Oxford, England) · 2024Article
- Integrated transcriptomics of human blood vessels defines a spatially controlled niche for early mesenchymal progenitor cells.Developmental cell · 2024Article
- OneSC: A computational platform for recapitulating cell state transitions.bioRxiv : the preprint server for biology · 2024Article
- Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells.Scientific data · 2024Article
- Analysis of the human kidney transcriptome and plasma proteome identifies markers of proximal tubule maladaptation to injury.Science translational medicine · 2023Article
- Temporally specific gene expression and chromatin remodeling programs regulate a conservedeLife · 2023Article
- RANKeLife · 2023Article
- Computational single cell oncology: state of the art.Frontiers in genetics · 2023Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Elucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. Unfortunately, existing computational gene regulatory network (GRN) reconstruction methods are imprecise, computationally burdensome, and fail to reveal dynamic regulatory topologies. Here, we present Epoch, a reconstruction tool that uses single-cell transcriptomics to accurately infer dynamic networks. We apply Epoch to identify the dynamic networks underpinning directed differentiation of mouse embryonic stem cells (ESCs) guided by multiple signaling pathways, and we demonstrate that modulating these pathways drives topological changes that bias cell fate potential. We also find that Peg3 rewires the pluripotency network to favor mesoderm specification. By integrating signaling pathways with GRNs, we trace how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively. Finally, we identify regulatory circuits of patterning and axis formation that distinguish in vitro and in vivo mesoderm specification.
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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 Socratic graph.