Searching journal content for articles similar to Kang et al. 30 (3): 459.

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  1. Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
    • Alexander Morin,
    • Eric Ching-Pan Chu,
    • Aman Sharma,
    • Alex Adrian-Hamazaki,
    • and Paul Pavlidis
    Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
    ...that their evidence rarely converges.Despite these complexities, ChIP-seq and perturbation experiments remain important strategies for biological discovery that continue to proliferate (Luo et al. 2020). These data sets (or their intersection) are also often used as the “gold standard” for evaluating computational...
  2. Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
    • Alexander Xi Fu,
    • Kathy Nga-Chu Lui,
    • Clara Sze-Man Tang,
    • Ray Kit Ng,
    • Frank Pui-Ling Lai,
    • Sin-Ting Lau,
    • Zhixin Li,
    • Maria-Mercè Garcia-Barcelo,
    • Pak-Chung Sham,
    • Paul Kwong-Hang Tam,
    • Elly Sau-Wai Ngan,
    • and Kevin Y. Yip
    Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
    ...can be further studied by other downstream analyses, such as gene set enrichment and single-cell expression analyses. (I) TFs with recurrently perturbed match scores in different regulatory elements are collected to infer a network that highlights the phenotype-associated perturbations.Using simulated...
  3. Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
    • Siwei Chen,
    • Yuan Liu,
    • Yingying Zhang,
    • Shayne D. Wierbowski,
    • Steven M. Lipkin,
    • Xiaomu Wei,
    • and Haiyuan Yu
    Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
    ...of TP53-reactivating small molecules have been discovered (for review, see Bykov et al. 2018); many of them were shown to rescue TP53's binding to DNA, whereas the same interface has a dual function in mediating TP53's binding to BCL2L1 (Mihara et al. 2003; Petros et al. 2004). Besides, it was found...
  4. Perspective: What does our genome encode?
    • John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
    ...a significant challenge. And just howmuch functional validation using traditional approaches will ultimately be required is unclear—a topic I consider further below. The genus ‘gene’ The dual concept of the gene both as the agent of heredity and as a physical, information-laden entity embodied in a specific DNA...
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