Searching journal content for articles similar to Naseri et al. 33 (7): 1015.

Displaying results 1-10 of 29
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  1. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...inference by significantly increasing the number of samples used in network inference, leveraging large-scale publicly available and uniformly processed RNA-seq data from recount3 (Wilks et al. 2021) which includes human RNA-seq samples from GTEx (The GTEx Consortium 2020), TCGA (Tomczak et al. 2015...
    OPEN ACCESS ARTICLE
  2. Method: Fast and accurate out-of-core PCA framework for large scale biobank data
    • Zilong Li,
    • Jonas Meisner,
    • and Anders Albrechtsen
    Genome Res. September 2023 33: 1599-1608; Published in Advance August 24, 2023, doi:10.1101/gr.277525.122
    ...://creativecommons.org/licenses/by-nc/4.0/.References ↵Abraham G, Qiu Y, Inouye M. 2017. FlashPCA2: principal component analysis of biobank-scale genotype data sets. Bioinformatics 33: 2776–2778. doi:10.1093/bioinformatics/btx299 ↵Agrawal A, Chiu AM, Le M, Halperin E, Sankararaman S. 2020. Scalable probabilistic PCA for large-scale...
  3. Method: Ultrafast genome-wide inference of pairwise coalescence times
    • Regev Schweiger and
    • Richard Durbin
    Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
    ..., Gunnarsson ÁF, Cooper F, Palamara PF. 2023. Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nat Genet 55: 768–776. doi:10.1038/s41588-023-01379-x Ultrafast -wide inference of pairwise coalescence times Regev Schweiger and Richard Durbin Department...
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  4. 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
    ...Biobank.Understanding population structure is a cornerstone in population and evolutionary genetics as it provides insights into demographic events and evolutionary processes that have affected a population. The most common approaches for inferring population structure from genetic data are using...
  5. 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
    ...on alternative approaches, such as using ARGs to infer -wide genealogies that can be combined with GLLMs to improve power for rare variant association has recently been shown to scale to large biobank data sets (Nait Saada et al. 2020; Zhang et al. 2023; Gunnarsson et al. 2024; Christ et al. 2026). Although...
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  6. Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
    • Xiran Liu,
    • Lorin Crawford,
    • and Sohini Ramachandran
    Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
    ...at automatically inferring these patterns and highlighting them in gene-level summaries.Application to binary traitsTo test the generalizability of ML-MAGES, we applied it to the GWA results of two binary traits in the UK Biobank data: malignant neoplasm of breast (C50) and acquired absence of breast (Z90.1), both...
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  7. 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
    ...of granular population structure and inferring of informative latent factors. The learned latent spaces of VAEs are able to capture and represent differentiated Gaussian-like clusters of samples with similar genetic composition on a fine scale from single nucleotide polymorphisms (SNPs), enabling applications...
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  8. 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
    ...in matrices and vectors. These scaling factors are updated during the analysis to maintain precision based on the magnitude of data values. Our results demonstrate that this approach enables accurate probabilistic inference and sampling in our phasing algorithm. We detail the TX-Phase algorithm and techniques...
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  9. Method: Inferring ancestry with the hierarchical soft clustering approach tangleGen
    • Klara Elisabeth Burger,
    • Solveig Klepper,
    • Ulrike von Luxburg,
    • and Franz Baumdicker
    Genome Res. December 2024 34: 2244-2255; Published in Advance October 21, 2024, doi:10.1101/gr.279399.124
    ...the explainability of the method and allows to identify SNPs that differentiate between populations in the tangles tree. Concentrating on a smaller set of automatically inferred cluster-distinguishing SNPs can be beneficial for the analysis of large-scale data sets, such as biobanks. In addition, a cluster...
  10. 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
    ...such as The HapMap Consortium (International HapMap Consortium 2005; Locke et al. 2006), The 1000 Genomes Project (The 1000 Genomes Project Consortium 2015), and the population-scale projects such as UK Biobank, Genomics England, Trans-omics for Precision Medicine (TOPMed) (Kowalski et al. 2019), and All of Us...
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