Searching journal content for articles similar to Luca et al. 21 (7): 1087.

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  1. Research: Genotype imputation from low-coverage data for medical and population genetic analyses
    • Simone Andrea Biagini,
    • Sara Becelaere,
    • Mio Aerden,
    • Tatjana Jatsenko,
    • Laurens Hannes,
    • Philip Van Damme,
    • Jeroen Breckpot,
    • Koenraad Devriendt,
    • Bernard Thienpont,
    • Joris Robert Vermeesch,
    • Isabelle Cleynen,
    • and Toomas Kivisild
    Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
    ...). For evolutionary and population genetic studies, sequencing of large numbers of individuals at low depth provides a more comprehensive representation of variation in the population than sequencing of a small number of individuals at a higher depth (Fumagalli 2013). Importantly, imputation performed at sufficient...
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  2. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ..., followed by sequencing methods such as reduced representation bisulfite sequencing (RRBS) and whole- bisulfite sequencing (WGBS). These techniques capture only a fraction of the , with RRBS covering 20%–25% and WGBS capturing 50%–70% of all CpGs at sufficiently high coverage, thus limiting analysis...
  3. Review: Advancements in prospective single-cell lineage barcoding and their applications in research
    • Xiaoli Zhang,
    • Yirui Huang,
    • Yajing Yang,
    • Qi-En Wang,
    • and Lang Li
    Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
    ...not represent the true lineage differentiation path of a progenitor population without ground truth evidence support. In recent years, the incorporation of inheritable cell-specific DNA barcodes in lineage tracing, followed by barcode sequencing, has emerged as a powerful approach. This technique allows...
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  4. Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
    • Rita Tam,
    • Mareike Möller,
    • Runpeng Luo,
    • Zhenyan Luo,
    • Ashley Jones,
    • Sambasivam Periyannan,
    • John P. Rathjen,
    • and Benjamin Schwessinger
    Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
    ...kinetochore attachment sites pivotal for understanding karyotype diversity and evolution (Logsdon et al. 2024; Mastrorosa et al. 2024), as well as the notoriously repetitive ribosomal DNA (rDNA) arrays whose sequences have only been recently completed in humans (Nurk et al. 2022) and Arabidopsis (Fultz et al...
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  5. Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    • Romain Derelle,
    • Johanna von Wachsmann,
    • Tommi Mäklin,
    • Joel Hellewell,
    • Timothy Russell,
    • Ajit Lalvani,
    • Leonid Chindelevitch,
    • Nicholas J. Croucher,
    • Simon R. Harris,
    • and John A. Lees
    Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
    ...and Melinda Gates Foundation, Westminster, London SW1E 6AJ, United Kingdom ↵7 These authors contributed equally to this work. Corresponding author: jlees@ebi.ac.ukAbstractSequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses...
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  6. Perspective: The impact of long-read sequencing on human population-scale genomics
    • Tobias Rausch,
    • Tobias Marschall,
    • and Jan O. Korbel
    Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
    ...the relationships between centromere structure and genomic evolution, as well as the potential impact of centromere architecture on chromosomal instability.In the future, the integration of methylation data with genetic variation is likely to show value both in population-scale germline as well as somatic genetic...
  7. Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
    • Benjamin J. Auerbach,
    • Jian Hu,
    • Muredach P. Reilly,
    • and Mingyao Li
    Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
    ...and describe what we have learned so far from existing studies about human genetic variation. As single-cell technologies are becoming widely applicable in human disease studies, population-level studies have become a reality. We will describe how we should go about pursuing and designing these studies...
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  8. 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
    ...population size increased and reached its highest level (Wang et al. 2023). The decrease of body size of Orkney voles in the past centuries might thus be a long-term consequence of increased competition (Rowe-Rowe and Crafford 1992; Schmid et al. 2000).Human-influenced evolution of immunity?Our analyses...
  9. Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
    • Apurva Narechania,
    • Dean Bobo,
    • Kevin Deitz,
    • Rob DeSalle,
    • Paul J. Planet,
    • and Barun Mathema
    Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
    ...fixed by natural selection, and understanding geographic spread. KHILL is a coarse but informative measure of the amount of information diversity in aggregate. Clearly, even small differences mark important changes in an evolving pandemic population of viruses. More traditional evolutionary analyses...
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  10. Method: Modeling and predicting cancer clonal evolution with reinforcement learning
    • Stefan Ivanovic and
    • Mohammed El-Kebir
    Genome Res. July 2023 33: 1078-1088; Published in Advance June 21, 2023, doi:10.1101/gr.277672.123
    ...tasks regarding cancer evolution on increasingly available cohort-level data sets.Cancer results from an evolutionary process during which somatic mutations accumulate in a population of cells. This process results in a tumor composed of multiple subpopulations of cells, or clones, with varying sets...
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