Searching journal content for articles similar to Teng and Irizarry 27 (11): 1930.

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  1. 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
    ...during embryogenesis or even between tissues (Pollex et al. 2024), and we therefore profiled one representative time point at mid-embryogenesis (6–8 h) overlapping Mef2 and Biniou time points.When mapping ChIP-seq reads from different genetic backgrounds, mapping biases need to be considered. The state...
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  2. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...modifications assayed by ChIP-seq in C57BL/6J mouse ESCs under the Mouse ENCODE Project (Stamatoyannopoulos et al. 2012) and early mouse embryos (Liu et al. 2016). dnSNV coordinates were first lifted over to mm10 reference coordinates to ensure compatibility with ChIP-seq peak positions reported in ENCODE data...
  3. Method: Correcting signal biases and detecting regulatory elements in STARR-seq data
    • Young-Sook Kim,
    • Graham D. Johnson,
    • Jungkyun Seo,
    • Alejandro Barrera,
    • Thomas N. Cowart,
    • William H. Majoros,
    • Alejandro Ochoa,
    • Andrew S. Allen,
    • and Timothy E. Reddy
    Genome Res. May 2021 31: 877-889; Published in Advance March 15, 2021, doi:10.1101/gr.269209.120
    ...in the mappability of short read sequences to the reference human , for example, owing to repetitive sequences (Derrien et al. 2012).View larger version: In this window In a new window Figure 1. Technical biases affect STARR-seq signal. (A) STARR-seq input libraries have higher signal variance than ChIP-seq input...
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  4. Method: Sequential regulatory activity prediction across chromosomes with convolutional neural networks
    • David R. Kelley,
    • Yakir A. Reshef,
    • Maxwell Bileschi,
    • David Belanger,
    • Cory Y. McLean,
    • and Jasper Snoek
    Genome Res. May 2018 28: 739-750; Published in Advance March 27, 2018, doi:10.1101/gr.227819.117
    .../tissues profiled by ChIP-seq, and 595 unique cells/tissues profiled by CAGE. We processed these data with a pipeline that includes additional computation to make use of multimapping reads and to normalize for GC bias (Methods). Though additional data modalities may require slight modification, this base pipeline...
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  5. Research: Enhancer RNA profiling predicts transcription factor activity
    • Joseph G. Azofeifa,
    • Mary A. Allen,
    • Josephina R. Hendrix,
    • Timothy Read,
    • Jonathan D. Rubin,
    • and Robin D. Dowell
    Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
    ...to include 139 TF ChIP-seq experiments and observed a wide spectrum of association between TF binding sites and eRNA presence, suggesting that eRNA presence alone is not sufficient to fully explain TF binding (Fig. 1A). These data are consistent with the observation that only a fraction of TF binding sites...
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