Searching journal content for articles similar to Fabbri et al. 29 (9): 1377.

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  1. Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
    • Swann Floc'hlay,
    • Emily S. Wong,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Morgane Thomas-Chollier,
    • Denis Thieffry,
    • David A. Garfield,
    • and Eileen E.M. Furlong
    Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
    ....e., with RNA-seq signal), many promoter-proximal peaks (3907) marked by H3K4me3 with ATAC signal and/or H3K27ac show no detectable RNA signal (Fig. 1C, left upset plot). Many of these regions (approximately 850) correspond to known noncoding RNAs not captured by poly(A)+ RNA-seq libraries, suggesting...
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  2. Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    • Olga M. Sigalova,
    • Mattia Forneris,
    • Frosina Stojanovska,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Adam Rabinowitz,
    • Fayrouz Hammal,
    • Benoît Ballester,
    • Judith B. Zaugg,
    • and Eileen E.M. Furlong
    Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
    ...by 30%–50%. This fine-grained “mutagenesis” can reconstruct functionalized binding motifs for all factors. To prioritize causal variants, we trained a convolutional neural network (Basenji) to accurately predict binding from DNA sequence. The model can also predict measured allelic imbalance for strong...
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