ArticleThe EMBO journal2019
A common molecular logic determines embryonic stem cell self-renewal and reprogramming.
Article in The EMBO journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data.PLoS computational biology · 2026Article
- KLF7 is a general inducer of human pluripotency.EMBO reports · 2025Article
- Insights into Noncanonical and Diversified Functions of ABCF1: From Health to Disease.Journal of molecular biology · 2025Review
- Deep exploration of logical models of cell differentiation in human preimplantation embryos.NPJ systems biology and applications · 2025Article
- Construction of a proximity labeling vector to identify protein-protein interactions in human stem cells.PloS one · 2025Article
- OneSC: a computational platform for recapitulating cell state transitions.Bioinformatics (Oxford, England) · 2024Article
- Canalizing kernel for cell fate determination.Briefings in bioinformatics · 2024Article
- Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers.Journal of animal science and biotechnology · 2024Article
- OneSC: A computational platform for recapitulating cell state transitions.bioRxiv : the preprint server for biology · 2024Article
- MiR-290 Family Maintains Pluripotency and Self-Renewal by Regulating MAPK Signaling Pathway in Intermediate Pluripotent Stem Cells.International journal of molecular sciences · 2024Article
- KLF2 controls proliferation and apoptosis of human spermatogonial stem cells via targeting GJA1.iScience · 2024Article
- Modeling unveils sex differences of signaling networks in mouse embryonic stem cells.Molecular systems biology · 2023Article
- Rat post-implantation epiblast-derived pluripotent stem cells produce functional germ cells.Cell reports methods · 2023Article
- Esrrb guides naive pluripotent cells through the formative transcriptional programme.Nature cell biology · 2023Article
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- Towards AI-driven longevity research: An overview.Frontiers in aging · 2023Review
- NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity.Genome biology · 2022Article
- Design and Fabrication of Artificial Stem Cell Microenvironments.Bioengineering (Basel, Switzerland) · 2022Article
- CELLoGeNe - An energy landscape framework for logical networks controlling cell decisions.iScience · 2022Article
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5 authors.
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Abstract
During differentiation and reprogramming, new cell identities are generated by reconfiguration of gene regulatory networks. Here, we combined automated formal reasoning with experimentation to expose the logic of network activation during induction of naïve pluripotency. We find that a Boolean network architecture defined for maintenance of naïve state embryonic stem cells (ESC) also explains transcription factor behaviour and potency during resetting from primed pluripotency. Computationally identified gene activation trajectories were experimentally substantiated at single-cell resolution by RT-qPCR Contingency of factor availability explains the counterintuitive observation that Klf2, which is dispensable for ESC maintenance, is required during resetting. We tested 124 predictions formulated by the dynamic network, finding a predictive accuracy of 77.4%. Finally, we show that this network explains and predicts experimental observations of somatic cell reprogramming. We conclude that a common deterministic program of gene regulation is sufficient to govern maintenance and induction of naïve pluripotency. The tools exemplified here could be broadly applied to delineate dynamic networks underlying cell fate transitions.
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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.