Searching journal content for articles similar to Zhou et al. 35 (11): 2461.

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  1. Review: The structure, function, and evolution of plant centromeres
    • Matthew Naish and
    • Ian R. Henderson
    Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
    ...with Z. mays or Lepidium oleraceum CENH3 transgenes (Maheshwari et al. 2017). Despite the CENH3 proteins being divergent and adapted to unrelated centromere sequences, both variants remarkably localized to the A. thaliana CEN178 satellite arrays (Maheshwari et al. 2017). This implies that centromere...
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  2. Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
    ...in C. albicans. Together, these findings highlight that SVs and TEs are common across diverse clinical isolates of C. albicans and that the centromeres of this organism are important sites of rearrangement.Genomes are under constant evolutionary pressure from environmental stressors. Populations...
  3. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...). Although informative, they are not quantitative, incapable of determining direct enhancer activity, and cannot uncouple epigenomic from genomic mechanisms. On the other hand, reporter assays overcome some of these limitations by measuring enhancer activity on nonchromatinized DNA templates, isolating...
  4. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...and Shen 2024). SSA dynamically adjusts search directions via global–local integration, avoiding grid search’s exhaustive computations to drastically reduce complexity and time, especially in high-dimensional spaces, and adapts to better capture global optima. In contrast, grid search may miss optimal...
  5. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...of segments that could be classified as European and West African ancestry (Ali-Khan and Daar 2010). To characterize these different genomic segments, one can use local ancestry inference (LAI) methods like RFMix (Maples et al. 2013). These can rely on neural networks as well, for instance LAI-Net (Montserrat...
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  6. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...epigenomic 121 changes in chromatin state following this stimulation and shed light on regulatory elements 122 and TFBSs influencing antiviral transcriptional responses in a complex teleost . 123 Genomic sequencing data and sample metadata 124 Thirty-eight datasets were generated, comprising ATAC-seq (12...
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  7. Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
    • Xiaoyu Zhuo,
    • Silas Hsu,
    • Deepak Purushotham,
    • Prashant Kumar Kuntala,
    • Jessica K. Harrison,
    • Alan Y. Du,
    • Samuel Chen,
    • Daofeng Li,
    • and Ting Wang
    Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
    ...and adaptation of genomic features can be drawn. Comparative genomics thus has become an important tool to decipher genomic code (Alföldi and Lindblad-Toh 2013). Comparative epigenomics, which compares the epigenomic features of orthologous regions of multiple species, is also gaining popularity (Xiao et al...
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  8. Method: Fast sequence alignment for centromeres with RaMA
    • Pinglu Zhang,
    • Yanming Wei,
    • Qinzhong Tian,
    • Quan Zou,
    • and Yansu Wang
    Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
    ...). Centromeres are critical for stability, fertility, and healthy development as they ensure the proper distribution of genetic material during cell division; thus, given their detailed assembly, deep analysis is essential to understand their roles in genomic integrity and their associations with cancer...
  9. Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
    • David C.H. Metzger,
    • Imogen Porter,
    • Brendan Mobley,
    • Benjamin A. Sandkam,
    • Lydia J.M. Fong,
    • Andrew P. Anderson,
    • and Judith E. Mank
    Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
    ...expansion on the P. picta X Chromosome, which is absent in closely related species that lack dosage compensation. Taken together, our results present compelling support that a disruptive wave of repetitive element insertions carrying YY1 motifs resulted in the remodeling of the X Chromosome epigenomic...
  10. Perspective: The genetics and epigenetics of satellite centromeres
    • Paul B. Talbert and
    • Steven Henikoff
    Genome Res. April 2022 32: 608-615; Published in Advance March 31, 2022, doi:10.1101/gr.275351.121
    ...the structures of satellite arrays and sparked rethinking of how they evolve, and new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification. Centromeres are the genomic loci where the proteinaceous...
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