Searching journal content for articles similar to Brandström and Ellegren 18 (6): 881.

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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: 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...
  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
    ...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...
  5. 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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  6. 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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  7. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...these questions, we first analyzed two independent data sets comprising PCR-free whole- sequencing (WGS) and -wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using Hip...
  8. Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    ...to as microsatellite instability (MSI), are a hallmark of certain cancer types (Vilar and Gruber 2010).A large number of disease-focused studies have implicated proteins involved in mismatch repair (MMR) in regulating STR stability. For example, Lynch syndrome, which results in a predisposition to colorectal and other...
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  9. Method: Minimizing reference bias with an imputed personalized reference
    • Kavya Vaddadi,
    • Mao-Jan Lin,
    • Sina Majidian,
    • Taher Mun,
    • and Ben Langmead
    Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
    ...Kavya Vaddadi1, Mao-Jan Lin1, Sina Majidian1, Taher Mun1, Ben Langmead1 1. Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA Abstract Pan indexes reduce reference bias in sequencing data analysis. However, bias can be reduced...
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  10. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...map spl-TRs in a -wide manner across tissues throughout the whole body by using the Genotype-Tissue expression (GTEx) v8 data set, a population-scale resource of whole- sequencing (WGS) and RNA sequencing (RNA-seq).ResultsGenome-wide identification of spl-TRs across 49 tissuesWe discovered cis spl...
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