Searching journal content for articles similar to Lewenza et al. 15 (2): 321.

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  1. Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
    • Lianne B Cohen,
    • Tamara Hadzic,
    • Caitlin Sauer,
    • Julia R Gibbs,
    • and Zeba Wunderlich
    Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
    ...of how animals fight 32 infections. 33 Key words 34 Drosophila immunity/Immune-responsive enhancer/STARR-seq 35 36 Running Title 37 Genome-wide survey of fly immune enhancers 38 39 Introduction 40 When encountering pathogenic microbes, animals must regulate an effective immune response 41 to survive...
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  2. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ..., Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, et al. 2019. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570: 385–389. doi:10.1038/s41586-019-1272-6 ↵De Coster W, Weissensteiner MH, Sedlazeck FJ. 2021. Towards population-scale long-read sequencing. Nat Rev Genet 22: 572...
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  3. Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
    • Marian F. Laughery,
    • Bastian Stark,
    • Benjamin Morledge-Hampton,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
    ...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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  4. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...length as a function of the location of the midpoint of each fragment and colored the points based on their local density. The result is a near-nucleotide-resolution -wide view of chromatin occupancy for each deletion strain (Fig. 1D–F).View larger version: In this window In a new window Figure 1. Genome-wide...
  5. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...to annotate samples based on cell-type composition. By comparing aggregation strategies, we find that regressing confounders within studies and prioritizing larger studies optimizes network reconstruction. We apply these findings to infer three consensus networks (universal, cancer, noncancer) and 27 context...
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  6. Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    ...and gene expression regulatory elements of the 5′ gene, or encoding fusion proteins with altered molecular functions, all leading to alterations in the cellular circuitry that ultimately drive uncontrolled cellular proliferation.Identification of gene fusions has been an essential part of charting...
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  7. Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
    • Siyuan Chen,
    • Jiuming Wang,
    • Inkyung Jung,
    • Zhaowen Qiu,
    • Xin Gao,
    • and Yu Li
    Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
    ...classifier for -wide detection. The limitation of the supervised classification framework primarily manifests in its detection speed and relatively small reception fields. Genome-wide detection with a binary classifier can be computationally inefficient as the small window causes scanning to be resource...
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  8. Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
    • Yangyang Liu,
    • Bingqiang Liu,
    • and Juntao Liu
    Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
    ...lies in the difficulty in the prediction of precise TAD boundaries. We solve this problem by introducing a novel algorithm, called BINDER, which conducts a boundary consensus approach, and then precisely locate hierarchical TAD boundaries by developing a multifaceted boundary characterization strategy...
  9. Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
    • Pengfei Lv,
    • Xingzhuo Yang,
    • Xianguo Zhao,
    • Zhangwu Zhao,
    • and Juan Du
    Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
    ...of H3K9me3 and H3K27me3 in the nondiapause (C), prediapause (D), and diapause (E) stages. (F–H) Venn diagram shows the number of genes with H3K9me3 peaks, H3K27me3 peaks, or both at the nondiapause (F), prediapause (G), and diapause (H) stages. (I–K) Genome-wide correlation plots showing correlation...
  10. Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
    ...window Figure 2. Genome-wide diversity and differentiation for common voles, M. arvalis, from the Orkney archipelago (brown) versus continental individuals (green). Density distributions (top) and Manhattan plots (bottom) for π, Tajima's D, and FST in 50 kb windows along the . Different chromosomes...
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