Searching journal content for articles similar to Wang et al. 21 (5): 748.

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  1. Methods: Calling cards for DNA-binding proteins
    • Haoyi Wang,
    • Mark Johnston,
    • and Robi David Mitra
    Genome Res. August 2007 17: 1202-1209; Published in Advance July 10, 2007, doi:10.1101/gr.6510207
    ...proteins Calling cards for DNA-binding proteins Haoyi Wang , Mark Johnston , and Robi David Mitra 1 Department of Genetics, Washington University, School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA Abstract Identifying genomic targets of transcription factors is fundamental...
  2. Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
    • Yiming Kang,
    • Nikhil R. Patel,
    • Christian Shively,
    • Pamela Samantha Recio,
    • Xuhua Chen,
    • Bernd J. Wranik,
    • Griffin Kim,
    • R. Scott McIsaac,
    • Robi Mitra,
    • and Michael R. Brent
    Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
    ...cards. One such technology is DamID, in which a DNA-methyltransferase is tethered to a DNA-binding protein and changes in DNA methylation relative to a control are assayed to determine binding location (van Steensel and Henikoff 2000; Hass et al. 2015; Tosti et al. 2018). Another is CUT&RUN, in which...
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  3. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ..., and the released DNA can be sequenced to identify all DNA sequences bound to the protein of interest using high-throughput platforms (Park 2009). Standard controls include comparing this immunoprecipitation to DNA binding by nonimmunized IgG raised in the same species as the protein targeting antibody, using q...
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  4. Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
    ...h sequencing plus ∼12 h GPU basecalling on a high-end card (total ∼60 h). In contrast, the PacBio Revio platform enables multiplexing of up to five libraries per SMRT Cell, with each library comprising six samples, effectively allowing 30-plex sequencing. It generates ∼15–20 Gb HiFi data per sample...
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