Searching journal content for articles similar to Mendoza-Parra et al. 26 (11): 1505.

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  1. Research: Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
    • Hong-Bing Yu,
    • Rory Johnson,
    • Galih Kunarso,
    • and Lawrence W. Stanton
    Genome Res. August 2011 21: 1284-1293; Published in Advance June 1, 2011, doi:10.1101/gr.114488.110
    .... [Supplemental material is available for this article.] The pluripotent state of embryonic stem cells (ESC) is maintained by a highly interconnected network of regulatory transcription factors (TF). These factors serve as a DNA sequence-specific platform for the recruitment of various positively and negatively...
  2. Research: Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons
    • Jiaxu Wang,
    • Piroon Jenjaroenpun,
    • Akshay Bhinge,
    • Vladimir Espinosa Angarica,
    • Antonio Del Sol,
    • Intawat Nookaew,
    • Vladimir A. Kuznetsov,
    • and Lawrence W. Stanton
    Genome Res. November 2017 27: 1783-1794; Published in Advance October 13, 2017, doi:10.1101/gr.223313.117
    ...the course of maturation revealed biological insights with regard to key regulatory transcription factors and lincRNAs that control cellular programs in the identified neuronal subpopulations. [Supplemental material is available for this article.] Given their defining characteristics to self-renewand give...
  3. Method: Reconstructing differentiation networks and their regulation from time series single-cell expression data
    • Jun Ding,
    • Bruce J. Aronow,
    • Naftali Kaminski,
    • Joseph Kitzmiller,
    • Jeffrey A. Whitsett,
    • and Ziv Bar-Joseph
    Genome Res. March 2018 28: 383-395; Published in Advance January 9, 2018, doi:10.1101/gr.225979.117
    ...factors (TFs) that are active during advancing stages of organogenesis. To enable such modeling, we have developed a method that learns a probabilistic model that integrates expression similarity with regulatory information to reconstruct the dynamic developmental cell trajectories. When applied to mouse...
  4. Review: Advancements in prospective single-cell lineage barcoding and their applications in research
    • Xiaoli Zhang,
    • Yirui Huang,
    • Yajing Yang,
    • Qi-En Wang,
    • and Lang Li
    Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
    ...study (Fig. 1B; Biddy et al. 2018). In this case, a multilayer clonal tree can be reconstructed, and the subclonal relationships from different cell types can be revealed by analyzing the clonal trees based on the number of barcodes (Chen et al. 2022).Since its first publication (Lu et al. 2011...
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  5. Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
    • Matthew A. Lalli,
    • Denis Avey,
    • Joseph D. Dougherty,
    • Jeffrey Milbrandt,
    • and Robi D. Mitra
    Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
    ...or aberrations in region-specific gene regulatory networks will not be captured by this system. However, as core transcriptional programs that control neuronal differentiation and maturation are largely conserved across neuronal subtypes (Li et al. 2018), we can model these critical disease-relevant processes...
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