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dotears: Scalable and consistent directed acyclic graph estimation using observational and interventional data
Published 2025-02-01“…Summary: New assays such as Perturb-seq link parallel CRISPR interventions to transcriptomic readouts, providing insight into gene regulatory networks. Causal regulatory networks can be represented by directed acyclic graphs (DAGs), but lack of identifiability and a combinatorial solution space complicate learning DAGs from observational data. …”
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Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk
Published 2025-01-01“…It is becoming increasingly clear that microRNAs are key players in gene regulatory networks, modulating gene expression at post-transcriptional level. …”
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The enigma of cancer polyploidy as deciphered by evolutionary cancer cell biology (ECCB)
Published 2024-06-01“…The genes, gene modules, and gene regulatory networks (GRNs) of the premetazoic cell system are preserved in the ancestral genome compartment of metazoans and humans. …”
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DyCeModel: a tool for 1D simulation for distribution of plant hormones controlling tissue patterning
Published 2023-12-01“…The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.…”
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Consensus representation of multiple cell–cell graphs from gene signaling pathways for cell type annotation
Published 2025-01-01“…Traditional annotation methods often fail to adequately address the complexity of cellular interactions and gene regulatory networks. Results We proposed scMCGraph, a comprehensive computational framework that integrates gene expression with pathway activity to accurately annotate cell types within diverse scRNA-seq datasets. …”
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