Class C3 records a modeled outcome or a certified control property. The claim reaches only as far as the model, its reachable set, and the outcome it predicts. Boundary conditions.
scREMOTE
Tran A, Yang P, Yang JYH, Ormerod JT
2022 · NAR genomics and bioinformatics
Cell reprogramming offers a potential treatment to many diseases, by regenerating specialized somatic cells.
Abstract
From the original paper, NAR genomics and bioinformatics · PubMed
Cell reprogramming offers a potential treatment to many diseases, by regenerating specialized somatic cells. Despite decades of research, discovering the transcription factors that promote cell reprogramming has largely been accomplished through trial and error, a time-consuming and costly method. A computational model for cell reprogramming, however, could guide the hypothesis formulation and experimental validation, to efficiently utilize time and resources. Current methods often cannot account for the heterogeneity observed in cell reprogramming, or they only make short-term predictions, without modelling the entire reprogramming process. Here, we present scREMOTE, a novel computational model for cell reprogramming that leverages single cell multiomics data, enabling a more holistic view of the regulatory mechanisms at cellular resolution. This is achieved by first identifying the regulatory potential of each transcription factor and gene to uncover regulatory relationships, then a regression model is built to estimate the effect of transcription factor perturbations. We show that scREMOTE successfully predicts the long-term effect of overexpressing two key transcription factors in hair follicle development by capturing higher-order gene regulations. Together, this demonstrates that integrating the multimodal processes governing gene regulation creates a more accurate model for cell reprogramming with significant potential to accelerate research in regenerative medicine.
Summary
Editorial summary pending review by the maintainer. The paper's own abstract appears above; the Atlas summary in the maintainer's voice will explain how scREMOTE relates to the inverse-design framework of the review.
Why this class
Class C3, subtype 3A, because the intervention is simulated on a learned expression map and candidates are ranked by the simulated displacement toward the target. Representation family is executable intervention model. Cited in §3.4 of the review.