Searching journal content for articles similar to Gorkin et al. 22 (11): 2290.

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  1. Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
    • Dongwon Lee,
    • Ashish Kapoor,
    • Alexias Safi,
    • Lingyun Song,
    • Marc K. Halushka,
    • Gregory E. Crawford,
    • and Aravinda Chakravarti
    Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
    ..., ChIP-seq data are superior, but the general lack of TF-specific antibodies is a major roadblock to this approach. We solve these major impediments instead by using a generalizable sequence-based machine learning approach (Lee et al. 2011, 2015; Ghandi et al. 2014). This method learns the short...
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  2. Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
    • Marjan Farahbod,
    • Aboud Diab,
    • Paul Sud,
    • Meenakshi S. Kagda,
    • Ian Whaling,
    • Mehdi Foroozandeh,
    • Ishan Goel,
    • Habib Daneshpajouh,
    • Benjamin Hitz,
    • J. Michael Cherry,
    • and Maxwell W. Libbrecht
    Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
    ...-based measurements of genomic activity, including ChIP-seq measurement of transcription factor binding and histone modifications and DNaseseq and ATAC-seq measurement of chromatin accessibility (Luo et al. 2020; Moore et al. 2020; Snyder et al. 2020). The fourth and final phase of ENCODE has greatly expanded the set...
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  3. Research: High-throughput functional testing of ENCODE segmentation predictions
    • Jamie C. Kwasnieski,
    • Christopher Fiore,
    • Hemangi G. Chaudhari,
    • and Barak A. Cohen
    Genome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014, doi:10.1101/gr.173518.114
    ...reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res 22: 2290–2301. Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017–1018. Gupta S, Stamatoyannopolous JA, Bailey TL, Noble WS. 2007. Quantifying similarity...
  4. Research: Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition
    • Dan E. Webster,
    • Brook Barajas,
    • Rose T. Bussat,
    • Karen J. Yan,
    • Poornima H. Neela,
    • Ross J. Flockhart,
    • Joanna Kovalski,
    • Ashley Zehnder,
    • and Paul A. Khavari
    Genome Res. May 2014 24: 751-760; Published in Advance January 17, 2014, doi:10.1101/gr.166231.113
    ...D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. 2012. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res 22: 2290–2301. Grisanzio C, Freedman ML. 2010. Chromosome 8q24...
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