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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. 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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  4. 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
    ...their genomic evolution is likely affected by adaptive processes.Genome-wide relaxation of purifying selectionThe overall increased dN/dS ratios in Orkney voles compared with continental voles suggest a lower effectiveness of selection in the population that experienced long-term isolation (Fig. 1...
  5. 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
    ...the correlation between H3K27me3 and gene expression, in a study by Hu et al. (2020), conducted on the African turquoise killifish (Nothobranchius furzeri), it was reported that H3K27me3 does not show a correlation with gene expression (see Supplemental Fig. S7H in Hu et al. 2020). Additionally, analysis of data...
  6. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...abundances of accessible ssDNA and accessible DNA). (C) KAS-seq, ATAC-seq, and KAS-ATAC mitochondrial profiles in human GM12878 cells. (D) Fragment length distribution in biotin-ATAC-seq and KAS-ATAC libraries (GM12878 cells). (E) Genome-wide TSS metaprofiles for biotin-ATAC-seq and KAS-ATAC libraries (GM...
  7. 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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  8. Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
    • Kavitha Uthanumallian,
    • Andrea Del Cortona,
    • Susana M. Coelho,
    • Olivier De Clerck,
    • Sebastian Duchene,
    • and Heroen Verbruggen
    Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
    ...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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  9. 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
    ...in parallel across 7150 jobs. (At 0.85 sec per pair, this is slower than the value given above, essentially because of masking and pre- and postprocessing.)We illustrate the results by showing an example of inference at a single position (Fig. 4). We show a heatmap of the posterior mean TMRCA between each...
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  10. Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
    • Clotilde Garrido,
    • Cintia Gómez-Muñoz,
    • Etienne Kornobis,
    • Nicolas Agier,
    • Oana Ilioaia,
    • Gilles Fischer,
    • and Zhou Xu
    Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
    ...) Global TL distributions of the natural North American diploid strain YPS128 and the experimentally generated isogenic tetraploid. (B) Global TL distributions of the natural West African diploid strain DBVPG6044 and the experimentally generated isogenic tetraploid. (C) Boxplots of extremity-specific TL...
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