Searching journal content for articles similar to Glöckner et al. 8 (10): 1060.

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  1. Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
    • Matthew M. Hong,
    • David Froelicher,
    • Ricky Magner,
    • Victoria Popic,
    • Bonnie Berger,
    • and Hyunghoon Cho
    Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
    ...relatives, and local removal results in 18% of remaining samples still having a relative in the joint data set. We plot the fraction of significant loci (P-value < 0.05) on even numbered chromosomes that are designed to be noncausal in the simulation (A), and the inflation factor λGC in B. The filled boxes...
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  2. Method: High-fidelity, large-scale targeted profiling of microsatellites
    • Caitlin A. Loh,
    • Danielle A. Shields,
    • Adam Schwing,
    • and Gilad D. Evrony
    Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
    ...in stutter by capillary electrophoresis and amplicon sequencing, even when the reaction was multiplexed for three loci. However, low-temperature amplification has not yet been applied to large-scale microsatellite genomic libraries.Here, we further developed the above low-temperature PCR method for large-scale...
  3. Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
    • Reuben M. Buckley and
    • Elaine A. Ostrander
    Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
    ...with individual-level phenotype data are included in such studies, additional loci contributing to more nuanced parts of a phenotype will be found.View larger version: In this window In a new window Figure 1. Genomic analyses help resolve the genetics of shared human–canine traits. (A) Approximately 50...
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  4. 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
    ...analyses in cancer genomics.The ability of ScisTree2 to analyze a large number of cells may be useful in large-scale cancer genomics analyses. One such analysis is identifying rare cancer subclones, which can drive disease recurrence and therapy resistance. For example, relapse of acute myeloid leukemia...
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  5. Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
    • Sophia N. Lee,
    • Erin C. Banda,
    • Lu Qiao,
    • Sarah L. Thompson,
    • Karan Singh,
    • Ryan A. Hagenson,
    • Teresa Davoli,
    • Stefan F. Pinter,
    • and Jason M. Sheltzer
    Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
    ...). qPCR of CLN8, UNC5D, and four other genes encoded within the rearranged region on 8p confirmed the changes in expression expected based on the copy number of these loci (Fig. 4D).Interestingly, we observed that a majority of differentially expressed genes were located outside of Chromosome 8p (Fig...
  6. Review: The superpowers of imprinting control regions
    • Bertille Montibus,
    • Franck Court,
    • and Philippe Arnaud
    Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
    ...development of strategies to infer parent-of-origin effects in humans using large-scale biobanks may lead to the discovery of novel imprinted loci (Hofmeister et al. 2025). However, technically and conceptually, it is difficult to identify all the genes subject to imprinting. Beyond the canonical image...
  7. 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
    ...computational toolkit for genotyping the variable genes of the IG lambda and kappa, and the TR loci with short-read whole sequence data, using an integer linear programming formulation, as an update to the ImmunoTyper-SR suite, which focused on IGHV region only. We evaluate its genotyping performance using...
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  8. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...gene family, which is similarly located on the right arm of Chr IV (Fig. 6B). In accordance with our previous findings in JU1421, all Cni-neib-1 loci are centrally positioned on Chr IV, except in ZF1220, which lacks a Cni-neib-1 gene locus (Fig. 6B; Xie et al. 2024). The remaining fbxn genes form...
  9. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...; pentagons represent human genomic regions with HBV integration (colors indicate distinct chromosomes). The arrows mark the 3′-end. (D) Proportion of integration loci classified into the five categories depicted in panel C.Based on the mapping results of the chimeric reads, several patterns of HBV...
  10. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...loci in the major QTL region impede the model’s ability to integrate features and 168 develop effective branching structures, ultimately diminishing its predictive power. 169 We used sequencing data to locally enhance the density of genetic features 170 (Supplemental Fig. S4) and developed two new sets...
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