Searching journal content for articles similar to Mokrousov et al. 15 (10): 1357.

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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
    ...the method from Liu et al. (2018), originally designed for STITCH (Davies et al. 2016), to evaluate INFO scores with QUILT. The most notable comparison is between the GDI filtering approach and the GP-based filtering (max(GP) ≥ 0.99) (yellow vs. purple line in Fig. 2). It is evident that both filtering...
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  2. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ...that improves the original ScisTree. The input for running ScisTree2 is generated by processing single-cell DNA-seq or other types of single-cell sequencing data with genetic variants. Given single-cell sequencing data (reads), the first step is using a genotype caller (e.g., GATK [McKenna et al. 2010]) to call...
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  3. Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
    • Degui Zhi,
    • Xiaoqian Jiang,
    • and Arif Harmanci
    Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
    ...be used when imputation is being outsourced on an imputation server. Proxy panels are generated through a series of randomized protection mechanisms that anonymize the original sensitive panel's variants, coordinates, genetic maps, and genotypes. Compared with each other, the proxy panels and original...
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  4. Method: Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy
    • Moonseong Jeong,
    • Ali Pazokitoroudi,
    • Zhengtong Liu,
    • and Sriram Sankararaman
    Genome Res. September 2024 34: 1286-1293; Published in Advance July 22, 2024, doi:10.1101/gr.279207.124
    ...sizes β are drawn from an arbitrary distribution D with mean zero and variance of , and the environmental/noise effects ϵ are drawn from a distribution with variance . In the original work by Yang et al. (2010) and GCTA (Yang et al. 2011), the distribution D was chosen as a normal distribution. The SNP...
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  5. Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
    • Huiwen Che,
    • Peiyong Jiang,
    • L.Y. Lois Choy,
    • Suk Hang Cheng,
    • Wenlei Peng,
    • Rebecca W.Y. Chan,
    • Jing Liu,
    • Qing Zhou,
    • W.K. Jacky Lam,
    • Stephanie C.Y. Yu,
    • So Ling Lau,
    • Tak Y. Leung,
    • John Wong,
    • Vincent Wai-Sun Wong,
    • Grace L.H. Wong,
    • Stephen L. Chan,
    • K.C. Allen Chan,
    • and Y.M. Dennis Lo
    Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
    ...plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals...
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  6. Method: Predicting genotype-specific gene regulatory networks
    • Deborah Weighill,
    • Marouen Ben Guebila,
    • Kimberly Glass,
    • John Quackenbush,
    • and John Platig
    Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
    ...TFs for K562 in the ReMap 2018 database [Chèneby et al. 2018]), allowing us to use differential TF binding as a way of validating regulatory differences. These cell lines may have many regulatory differences that are due to difference in cell type of origin and not differences in genotype. However...
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  7. Resource: Discordant calls across genotype discovery approaches elucidate variants with systematic errors
    • Elizabeth G. Atkinson,
    • Mykyta Artomov,
    • Alexander A. Loboda,
    • Heidi L. Rehm,
    • Daniel G. MacArthur,
    • Konrad J. Karczewski,
    • Benjamin M. Neale,
    • and Mark J. Daly
    Genome Res. May 30, 2023 ; Published in Advance May 30, 2023, doi:10.1101/gr.277908.123
    ..., identification of DNA variants that are susceptible to technical bias when genotypes originate from multiple discovery strategies is vital in order to avoid falsepositive associations and analyses of the artificially inflated AFs. This is of particular concern in instances in which cases may originate from one...
  8. Research: A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization
    • Amit Blumberg,
    • Charles G. Danko,
    • Anshul Kundaje,
    • and Dan Mishmar
    Genome Res. August 2018 28: 1158-1168; Published in Advance July 12, 2018, doi:10.1101/gr.230409.117
    ...-score graph of a representative mt-DGF site, which overlaps a well-known regulatory element—the light strand origin of replication (OriL): (x-axis) mtDNA position; (y-axis) calculated F-score; (black curve) mean F-score values, surrounded by their calculated SD (gray area), based on all ENCODE samples. (E...
  9. Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
    • Jeanlin Jourdain,
    • Harmonie Barasc,
    • Thomas Faraut,
    • Anne Calgaro,
    • Nathalie Bonnet,
    • Camille Marcuzzo,
    • Amandine Suin,
    • Anne Barbat,
    • Chris Hozé,
    • Florian Besnard,
    • Sébastien Taussat,
    • Cécile Grohs,
    • Claire Kuchly,
    • Carole Iampietro,
    • Cécile Donnadieu,
    • Alain Pinton,
    • Didier Boichard,
    • and Aurélien Capitan
    Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
    ...available in cattle, we performed a series of complementary analyses to define the exact nature of these rearrangements, investigate their origins, and search for factors that may have favored their occurrence.We also evaluated the risks to the livestock industry and showed significant negative effects...
  10. Research: After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
    • Amine Namouchi,
    • Xavier Didelot,
    • Ulrike Schöck,
    • Brigitte Gicquel,
    • and Eduardo P.C. Rocha
    Genome Res. April 2012 22: 721-734; Published in Advance February 29, 2012, doi:10.1101/gr.129544.111
    ...After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection Amine Namouchi 1 , 7 , Xavier Didelot 2 , Ulrike Schöck 3 , Brigitte Gicquel 1 , 6 and Eduardo P...
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