ArticleStem cell reports2023
Gene regulatory network reconfiguration in direct lineage reprogramming.
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 23 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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Who cites it
23 citing papers in PubMed, 40 citations in OpenAlex.
- In Vivo Direct Reprogramming: Current Progress and Future Prospects from Mechanisms to Therapeutic Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- scGPA: an LLM-assisted workflow for directional virtual gene perturbation analysis from single-cell transcriptomes.BMC genomics · 2026Article
- Redefining cellular reprogramming with advanced genomic technologies.Nature reviews. Genetics · 2026Review
- Directing stem cell differentiation by chromatin state approximation.Nucleic acids research · 2026Article
- Single-Cell Profiling of the Developing Organ of Corti Identifies Etv4/5/1 as Key Regulators of Pillar Cell Identity.bioRxiv : the preprint server for biology · 2026Article
- Inference of Gene-Gene Interaction and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A comparison of computational methods for expression forecasting.Genome biology · 2025Article
- LogicSR: prior-guided symbolic regression for gene regulatory network inference from single-cell transcriptomics data.Briefings in bioinformatics · 2025Article
- Cell and tissue reprogramming: Unlocking a new era in medical drug discovery.Pharmacological reviews · 2025Review
- Comparative single-cell lineage tracing identifies distinct adipocyte precursor dynamics in skin and inguinal fat.Cell stem cell · 2025Article
- Developmental rewiring of the NGAL/CUC/KLU network associated with pleiotropic roles of NGAL genes.The Plant journal : for cell and molecular biology · 2025Article
- Cell identity and 5-hydroxymethylcytosine.Epigenetics & chromatin · 2025Review
- scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis.Genome biology · 2025Article
- Interplay between pioneer transcription factors and epigenetic modifiers in cell reprogramming.Regenerative therapy · 2025Review
- Inducible, virus-free direct lineage reprogramming enhances scalable generation of human inner ear hair cell-like cells.bioRxiv : the preprint server for biology · 2025Article
- A mini-review on perturbation modelling across single-cell omic modalities.Computational and structural biotechnology journal · 2024Review
- Neural crest precursors from the skin are the primary source of directly reprogrammed neurons.Stem cell reports · 2024Article
- Epigenetic Dynamics in Reprogramming to Dopaminergic Neurons for Parkinson's Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors.Bioinformatics (Oxford, England) · 2024Article
- IGFBP7 promotes endothelial cell repair in the recovery phase of acute lung injury.Clinical science (London, England : 1979) · 2024Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
In direct lineage conversion, transcription factor (TF) overexpression reconfigures gene regulatory networks (GRNs) to reprogram cell identity. We previously developed CellOracle, a computational method to infer GRNs from single-cell transcriptome and epigenome data. Using inferred GRNs, CellOracle simulates gene expression changes in response to TF perturbation, enabling in silico interrogation of network reconfiguration. Here, we combine CellOracle analysis with lineage tracing of fibroblast to induced endoderm progenitor (iEP) conversion, a prototypical direct reprogramming paradigm. By linking early network state to reprogramming outcome, we reveal distinct network configurations underlying successful and failed fate conversion. Via in silico simulation of TF perturbation, we identify new factors to coax cells into successfully converting their identity, uncovering a central role for the AP-1 subunit Fos with the Hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations, providing new mechanistic insights into lineage 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.