Searching journal content for articles similar to Parts et al. 21 (7): 1131.

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  1. 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
    ...of population-scale and disease studies. This capacity of long-read sequencing to detect genetic variants in regions inaccessible by short-read sequencing is positioning long-read technologies as a pivotal tool for human genetics, revealing connections between previously unexplored genetic variations and human...
  2. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...indicating various categories. Post-ALPINE application, batch effects from sequencing technologies are removed, resulting in aligned clusters of similar cell types across species, although adipocytes remain distinct due to biological differences. (B) Condition embeddings reveal associations between cell...
  3. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...al. 2020; Zaidi and Mathieson 2020).Large-scale sequencing studies have revealed patterns of recently arisen rare variants and have shown that they tend to be geographically localized (Gravel et al. 2011; Fu et al. 2013). This fine-scale population structure impacting rare variants has been detected...
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  4. Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
    ...elements, and tandem repeats. More generally, the DNA sequences omitted from current reference s are likely a source of substantial epigenetic activity. Expanding the nonreference results to a larger number of human s and epis can expose population variation with potential new insights on trait variation...
  5. Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
    • Daniel Schmitz,
    • Adam Ameur,
    • and Åsa Johansson
    Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
    ...(Lichtenstein et al. 2002). The remaining 58 individuals were selected from the Northern Swedish Population Health Study (NSPHS) (Igl et al. 2010). NSPHS individuals were selected based on their genetic PCs as well. Library preparation and WGS were responsibility of Sweden's National Genomics Infrastructure...
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  6. 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
    ...at the scale of tens of thousands to millions of individuals. With decreasing costs of sequencing, low-pass (at coverage <1×) whole- sequencing followed by imputation has become a cost-effective alternative for trait mapping and estimation of polygenic scores (PGSs) (Martin et al. 2021; Wasik et al. 2021...
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  7. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...into the large numbers of patient s sequenced with short-reads, albeit with reduced performance in repetitive sequences. Nevertheless, the genotyping process not only enhances the sensitivity and specificity of variant calling but also serves as a critical step in population genetics, quantitative trait locus...
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  8. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
  9. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    ...rigorous statistical approaches, we applied best practices including covariate adjustment for sex, age, and population stratification via principal component analysis. Our initial analysis revealed several alleles with nominally significant associations with COVID-19 clinical outcomes. Specifically, we...
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  10. Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
    • Can Luo,
    • Zimeng Jamie Zhou,
    • Yichen Henry Liu,
    • and Xin Maizie Zhou
    Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
    ...abundant form of genetic variation in humans and can be efficiently detected using short-read sequencing technologies. Therefore, -wide association studies (GWASs) have primarily focused on SNVs to investigate the genetic basis of phenotypic traits. In contrast, structural variants (SVs)—larger genomic...
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