ArticlePhysical biology2017
Cellular reprogramming dynamics follow a simple 1D reaction coordinate.
Article in Physical biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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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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Who cites it
12 citing papers in PubMed.
- Article
- Finding signatures of low-dimensional geometric landscapes in high-dimensional cell fate transitions.ArXiv · 2025Article
- Finding signatures of low-dimensional geometric landscapes in high-dimensional cell fate transitions.bioRxiv : the preprint server for biology · 2025Article
- EnhancerNet: a predictive model of cell identity dynamics through enhancer selection.Development (Cambridge, England) · 2024Article
- scTOP: physics-inspired order parameters for cellular identification and visualization.Development (Cambridge, England) · 2023Article
- scTOP: physics-inspired order parameters for cellular identification and visualization.bioRxiv : the preprint server for biology · 2023Article
- Multipotent Embryonic Lung Progenitors: Foundational Units of In Vitro and In Vivo Lung Organogenesis.Advances in experimental medicine and biology · 2023Article
- Derivation of Thyroid Follicular Cells From Pluripotent Stem Cells: Insights From Development and Implications for Regenerative Medicine.Frontiers in endocrinology · 2021Review
- Article
- Learning dynamical information from static protein and sequencing data.Nature communications · 2019Article
- Modeling disease progression in Multiple Myeloma with Hopfield networks and single-cell RNA-seq.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2019Article
- Thyroid Progenitors Are Robustly Derived from Embryonic Stem Cells through Transient, Developmental Stage-Specific Overexpression of Nkx2-1.Stem cell reports · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used. Using Monte-Carlo simulations, we show that such a reaction coordinate emerges from epigenetic landscape models where cellular reprogramming is viewed as a 'barrier-crossing' process between cell fates. Overall, our analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an 'optimal path' in gene expression space for reprogramming.
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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.