Searching journal content for articles similar to Garrigues et al. 25 (1): 76.

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  1. 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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  2. 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...
  3. 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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  4. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...G methylation signals associated with the long-read sequence data used to generate these ape assemblies (Yoo et al. 2025), we investigated methylation at the euchromatin–heterochromatin boundary defined here as the last proximal subterminal pCht satellite unit. Within 200 kbp of this transition, we observe...
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  5. 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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  6. 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...
  7. Method: Ultrafast genome-wide inference of pairwise coalescence times
    • Regev Schweiger and
    • Richard Durbin
    Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
    ..., Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528: 499–503. doi:10.1038/nature16152 ↵McVean GAT, Cardin NJ. 2005. Approximating the coalescent with recombination...
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  8. Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • Yongbin Li,
    • Xiao Liu,
    • Peter Sarkies,
    • and Zhongying Zhao
    Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
    ...elegans, a well-established model organism, mostly reproduces through selfing as a hermaphrodite, albeit with a rare chance of outcrossing with males in the wild (Brenner 1974). It has a significantly smaller than its most closely related outcrossing species (The C. elegans Sequencing Consortium 1998; Li...
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  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 oscillations in G + C density and sequence conservation
    • Zarmik Moqtaderi,
    • Susan Brown,
    • and Welcome Bender
    Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
    ...://creativecommons.org/licenses/by-nc/4.0/.References ↵Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. 2013. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339: 1074–1077. doi:10.1126/science.1232542 ↵Assaf ZJ, Tilk S, Park J, Siegal ML, Petrov DA. 2017. Deep sequencing of natural...
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