Searching journal content for articles similar to Roy and Sridharan 27 (7): 1250.

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  1. Method: Dynamic regulatory module networks for inference of cell type–specific transcriptional networks
    • Alireza Fotuhi Siahpirani,
    • Sara Knaack,
    • Deborah Chasman,
    • Morten Seirup,
    • Rupa Sridharan,
    • Ron Stewart,
    • James Thomson,
    • and Sushmita Roy
    Genome Res. July 2022 32: 1367-1384; Published in Advance June 15, 2022, doi:10.1101/gr.276542.121
    ...module networks (DRMNs), a novel approach to infer cell type–specific cis-regulatory networks and their dynamics. DRMN integrates expression, chromatin state, and accessibility to predict cis-regulators of context-specific expression, where context can be cell type, developmental stage, or time point...
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  2. Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
    • Howard J. Womersley,
    • Daniel Muliaditan,
    • Ramanuj DasGupta,
    • and Lih Feng Cheow
    Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
    ...are dynamic and heterogeneous, reflecting the diversity of epigenetic changes during tumor progression. These results further corroborated our previous findings that global changes in the epi could lead to change in gene expression, highlighting the need for considering chromatin state changes when exploring...
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  3. Perspective: Defining cell types and states with single-cell genomics
    • Cole Trapnell
    Genome Res. October 2015 25: 1491-1498; doi:10.1101/gr.190595.115
    .... RNA-seq is only one of several aspects of cell state to be measured with single-cell genomics. Peter Fraser and colleagues adapted Hi-C, a technique for measuring chromatin conformation (Lieberman-Aiden et al. 2009) to work in single cells (Nagano et al. 2013). Hi-C measures physical proximity between...
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  4. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M. Riley,
    • Randa Elsayed,
    • Mark D. Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C. Nelson
    Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...genes showing strongest fold enrichment in sox17E over sox17N at 28 hpf.ATAC-seq analysis revealed thousands of differentially accessible regions (DARs) distinguishing the three sorted populations both within and between time points (Fig. 2A,B; Supplemental Tables 2, 3). Chromatin accessibility profiles...
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