Searching journal content for articles similar to Wangkumhang et al. 32 (8): 1553.

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  1. Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
    • Paige A. Byerly,
    • Alina von Thaden,
    • Evgeny Leushkin,
    • Leon Hilgers,
    • Shenglin Liu,
    • Sven Winter,
    • Tilman Schell,
    • Charlotte Gerheim,
    • Alexander Ben Hamadou,
    • Carola Greve,
    • Christian Betz,
    • Hanno J. Bolz,
    • Sven Büchner,
    • Johannes Lang,
    • Holger Meinig,
    • Evax Marie Famira-Parcsetich,
    • Sarah P. Stubbe,
    • Alice Mouton,
    • Sandro Bertolino,
    • Goedele Verbeylen,
    • Thomas Briner,
    • Lídia Freixas,
    • Lorenzo Vinciguerra,
    • Sarah A. Mueller,
    • Carsten Nowak,
    • and Michael Hiller
    Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
    ...on the lowest Akaike information criterion (AIC) value, although likelihood differences between models were not great (Table 3). The timing of the bottlenecks was largely consistent among the Alps, the Harz, and the Northeast, indicating a bottleneck event ∼∼3000 years ago. The Northwest model presented...
  2. Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
    • Jonas Meisner and
    • Anders Albrechtsen
    Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
    ...proportions or PCA. We show that HaploNet is capable of using haplotype information for inferring fine-scale population structure that outperforms ADMIXTURE with respect to signal-to-noise ratio. On real data sets, HaploNet infers similar population structure to ChromoPainter using PCA, while being much...
  3. Method: Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data
    • Anand Bhaskar,
    • Y.X. Rachel Wang,
    • and Yun S. Song
    Genome Res. February 2015 25: 268-279; Published in Advance January 6, 2015, doi:10.1101/gr.178756.114
    ...), to date historical population splits, migrations, admixture, and introgression events (Gravel et al. 2011; Li and Durbin 2011; Luki#1;c and Hey 2012; Sankararaman et al. 2012), to compute random match probabilities accurately in forensic applications (Balding and Nichols 1997; Graham et al. 2000...
  4. 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
    ...that arise from recent demographic events, patterns that are crucial for understanding rare variant effects. To address this challenge, we propose a novel method called spectral components (SPCs), which leverages identity-by-descent (IBD) graphs to capture and transform local, nonlinear fine-scale population...
    OPEN ACCESS ARTICLE
  5. Resource: A harmonized public resource of deeply sequenced diverse human genomes
    • Zan Koenig,
    • Mary T. Yohannes,
    • Lethukuthula L. Nkambule,
    • Xuefang Zhao,
    • Julia K. Goodrich,
    • Heesu Ally Kim,
    • Michael W. Wilson,
    • Grace Tiao,
    • Stephanie P. Hao,
    • Nareh Sahakian,
    • Katherine R. Chao,
    • Mark A. Walker,
    • Yunfei Lyu,
    • gnomAD Project Consortium,
    • Heidi L. Rehm,
    • Benjamin M. Neale,
    • Michael E. Talkowski,
    • Mark J. Daly,
    • Harrison Brand,
    • Konrad J. Karczewski,
    • Elizabeth G. Atkinson,
    • and Alicia R. Martin
    Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
    ...(purple), and variants that are only found in each comparison data set (blue). More information on exact numbers and comparisons by QC within and across data sets can be found in Supplemental Tables S11 and S12.Phased haplotypes improve phasing and imputation accuracy and flexibility compared...
  6. Method: Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos
    • Daniel Ariad,
    • Svetlana Madjunkova,
    • Mitko Madjunkov,
    • Siwei Chen,
    • Rina Abramov,
    • Clifford Librach,
    • and Rajiv C. McCoy
    Genome Res. January 2024 34: 70-84; Published in Advance December 1, 2023, doi:10.1101/gr.278168.123
    .... To ensure computational efficiency, we developed a scoring algorithm to prioritize reads based on their potential information content, as determined by measuring haplotype diversity within a reference panel at sites that they overlap. We emphasize that the priority score of a read only depends on variation...
  7. Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
    • Luis F. Paulin,
    • Jeremy Fan,
    • Kieran O'Neill,
    • Erin Pleasance,
    • Vanessa L. Porter,
    • Steven J.M. Jones,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
    ...interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors. While the detection of SVs has been markedly improved by the development of long-read sequencing, somatic variant identification...
  8. Review: Recent advances in methods to characterize archaic introgression in modern humans
    • David Peede,
    • Mayra M. Bañuelos,
    • Jazeps Medina Tretmanis,
    • Miriam Miyagi,
    • and Emilia Huerta-Sánchez
    Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
    ...of introgressed segment lengths is informative regarding the timing of gene flow events (Pugach et al. 2011; Sankararaman et al. 2012; Moorjani et al. 2016; Ni et al. 2016; Corbett-Detig and Nielsen 2017; Jacobs et al. 2019; Shchur et al. 2020; Iasi et al. 2021; Di Santo et al. 2023; Iasi et al. 2024).View larger...
    OPEN ACCESS ARTICLE
  9. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...an overly large window size, which might lose fine-grained structure) and encoding efficiency (not using an excessively small window size, which would require a large bottleneck to capture all local information). In our analysis, w = 2500 results in a good compromise between capturing local genomic...
    OPEN ACCESS ARTICLE
  10. Research: Stable genome structures in living fossil fishes
    • Cheng Wang,
    • Chase D. Brownstein,
    • Wenjun Chen,
    • Zufa Ding,
    • Dan Yu,
    • Yu Deng,
    • Chenguang Feng,
    • Thomas J. Near,
    • Shunping He,
    • and Liandong Yang
    Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
    ...gars into three clusters (K = 3) corresponding to the three included species. However, we also find evidence for admixture among species (Fig. 4B). Identity-by-descent (IBD) analysis revealed that some individuals of L. osseus and L. oculatus also share haplotype blocks (Supplemental Fig. S13B), and F3...
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