Searching journal content for articles similar to He et al. 25 (12): 1903.

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  1. Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
    • Rashid Al-Abri and
    • Gamze Gürsoy
    Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
    ..., especially when their expansions are larger than the fragment sizes used in standard short-read sequencing. Here, we introduce ScatTR, a novel computational method that leverages a maximum likelihood framework to estimate the copy number of large TR expansions from short-read sequencing data. Scat...
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  2. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    .... Estimating the accuracy of these annotations can also guide users directly in deciding whether to accept a particular annotation. However, to the best of our knowledge, there are currently no specific reference selection tools or method-agnostic optimizers designed for single-cell omics analysis. Although...
  3. Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
    • Wenyu Zhang,
    • Anja Guenther,
    • Yuanxiao Gao,
    • Kristian Ullrich,
    • Bruno Huettel,
    • Aftab Ahmad,
    • Lei Duan,
    • Kaizong Wei,
    • and Diethard Tautz
    Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
    ...-length transcript enrichment protocol with 5′ CAP selection, we sequenced full-length RNA transcripts of 48 individuals from outbred populations and subspecies of Mus musculus, and from the closely related sister species Mus spretus and Mus spicilegus as outgroups. The data set represents the most extensive full...
  4. Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
    • Ali Osman Berk Şapcı and
    • Siavash Mirarab
    Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
    ...minimizers and finding taxon-specific k-mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset of k-mers present in an ultra-large data...
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  5. RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
    • Joshua L. Wetzel,
    • Kaiqian Zhang,
    • and Mona Singh
    Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
    ...(Supplemental Fig. S4). Thus, despite the fact that these previous approaches used combinatorial models that required hyperparameter tuning, as well as extensive preprocessing for alignment of PWMs and homeodomain position feature selection (Christensen et al. 2012), our automated probabilistic approach...
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  6. Research: Large palindromes on the primate X Chromosome are preserved by natural selection
    • Emily K. Jackson,
    • Daniel W. Bellott,
    • Ting-Jan Cho,
    • Helen Skaletsky,
    • Jennifer F. Hughes,
    • Tatyana Pyntikova,
    • and David C. Page
    Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
    ...used for quantifying gene expression or detecting mutations, automatically discard multimapping reads, rendering palindromes invisible in downstream analyses (Godfrey et al. 2020). The issue can be overcome by selection of tools like kallisto that probabilistically assign multimapping reads (Bray et al...
  7. Method: Detecting ancient positive selection in humans using extended lineage sorting
    • Stéphane Peyrégne,
    • Michael James Boyle,
    • Michael Dannemann,
    • and Kay Prüfer
    Genome Res. September 2017 27: 1563-1572; Published in Advance July 18, 2017, doi:10.1101/gr.219493.116
    ..., extending from the split between archaic and modern humans ca. 650,000 yr ago to the split of modern human populations from each other around 100,000 yr ago (Prüfer et al. 2014). While methods exist that can be used to scan the for the remnants of past or ongoing positive selection (Nielsen et al. 2007...
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  8. Method: A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets
    • Sunjin Moon and
    • Joshua M. Akey
    Genome Res. June 2016 26: 834-843; Published in Advance April 14, 2016, doi:10.1101/gr.203059.115
    ...and reference sites have different mutation rates (the test SFS was set to θ) for a different demographic model. The estimate of f in the population structure model is from population one. (C) Estimates of f as a function of strength of selection assuming the same demographic model as in B. (γ*) Baseline...
  9. Method: Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
    • Yu-Jui Ho,
    • Naishitha Anaparthy,
    • David Molik,
    • Grinu Mathew,
    • Toby Aicher,
    • Ami Patel,
    • James Hicks,
    • and Molly Gale Hammell
    Genome Res. September 2018 28: 1353-1363; Published in Advance July 30, 2018, doi:10.1101/gr.234062.117
    ...populations of cells prior to drug application.ResultsWorkflow for analyzing single-cell RNA-seq data with SAKEThe SAKE workflow is designed to robustly categorize gene expression profiles while avoiding unwanted noise. Following the generation of a table of estimated gene abundance counts across samples...
  10. 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
    ...compute the entropy estimates per population by bootstrapping 32 samples from the founders’ pool 50 times and average them. The choice of 32 is significant as it is half of the size of the smallest human superpopulation in the data set, and the choice of 50 corresponds approximately to the fraction...
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