Searching journal content for articles similar to Reifsnyder et al. 10 (10): 1568.

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  1. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ..., and gene-by-gene-by 354 environment interactions of the MKT1 and SAL1 causal alleles 355 To explore the extent of epistasis between MKT1-30G and SAL1-nfs (i.e., GxG) and the 356 environmental dependence of the effects of these alleles (i.e., GxE), we grew our strains 357 carrying all combinations...
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  2. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...of the mammalian . We use whole- sequencing to identify de novo mutations in cohorts of age-matched ART-derived and naturally conceived mice. Our reliance on mice of a single inbred strain background allows us to rigorously control for potential genetic influences and environmental exposures on mutation rates...
  3. Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
    • Natnatee Dokmai,
    • Kaiyuan Zhu,
    • S. Cenk Sahinalp,
    • and Hyunghoon Cho
    Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
    ...-Phase's program binary within the secure enclave, ensuring it has not been tampered with. Next, the user establishes a secure channel with the enclave to protect sensitive inputs and outputs from leakage or tampering. The user then uploads one or more input genotype samples directly to the enclave via this secure...
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  4. 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
    ...(Bayindir et al. 2015; Vermeesch et al. 2016). Approximately 80% of NIPS performed in Belgium rely on low-pass -wide sequencing, making this technology a cornerstone of prenatal care in the country. More than 200,000 LPS s have been generated so far for NIPS in Belgium alone.Imputation of maternal genotypes...
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  5. 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
    ...of proxy panel usage in genotype imputation tasks is implementing an easy-to-use infrastructure. Although we do not anticipate that established servers may be reluctant to adopt proxy panel–based imputation protocols, we believe that localized projects and regional local collaborations can use the proxy...
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  6. Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
    • Divya Selvaraju,
    • Filip Wierzbicki,
    • and Robert Kofler
    Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
    ...of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defense, we introduced the P-element, one of the most widely studied...
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  7. Research: Selective maternal seeding and environment shape the human gut microbiome
    • Katri Korpela,
    • Paul Costea,
    • Luis Pedro Coelho,
    • Stefanie Kandels-Lewis,
    • Gonneke Willemsen,
    • Dorret I. Boomsma,
    • Nicola Segata,
    • and Peer Bork
    Genome Res. April 2018 28: 561-568; Published in Advance March 1, 2018, doi:10.1101/gr.233940.117
    .../nonmaternal strains were summarized in each circle as median per individual. Even if the similarity to the mother increased in later time points, the original distinction of maternal/nonmaternal was kept for each child-mother pair through all further time points.After establishing colonization with maternal strains...
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  8. 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
    ...as message passing to integrate this prior network with gene expression and TF protein–protein interaction data to produce a refined, genotype-specific regulatory network. We used EGRET to infer gene regulatory networks for two blood-derived cell lines and identified genotype-associated, cell line...
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  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
    ...syndrome 1) (Beaussant Cohen et al. 2012) 22 No gene—breakpoint putatively located in centromere t(3;8) 3 Six genes Deleted No deleterious phenotype reported in heterozygous mutant mice 8 FOCAD Disrupted No deleterious phenotype reported in heterozygous mutant mice MLLT3 Putative deregulation H: Growth...
  10. Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
    • Eugenio López-Cortegano,
    • Jobran Chebib,
    • Anika Jonas,
    • Anastasia Vock,
    • Sven Künzel,
    • Peter D. Keightley,
    • and Diethard Tautz
    Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
    ...Janvier Labs (https://janvier-labs.com), and mated within the facilities of the Max Planck Institute for Evolutionary Biology. From the founders, mice were bred by full-sib mating to establish MA lines for each strain. The C3H, BL6, and FVB MA lines were bred for 15, 8, and 10 generations, respectively...
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