Searching journal content for articles similar to Salehi-Ashtiani et al. 19 (12): 2334.

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  1. 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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  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
    ...per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling—“stutter” artifacts—with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed...
  3. 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
    ...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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  4. Resource: CGC1, a new reference genome for Caenorhabditis elegans
    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Dae-Eun Jeong,
    • Chie Owa,
    • Haruka Kobayashi,
    • Yoshihiko Suzuki,
    • Manami Kanamori,
    • Yu Toyoshima,
    • Yuichi Iino,
    • Ann E. Rougvie,
    • Lamia Wahba,
    • Andrew Z. Fire,
    • Erich M. Schwarz,
    • and Shinichi Morishita
    Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
    .... 2015). The combination of powerful computational tools for predicting gene functions, efficient methods for large-scale DNA synthesis, and effective protocols for targeted mutagenesis (e.g., CRISPR) has made it practical to analyze a , devise a model for how that could be functionally modified (e...
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  5. Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    ...prediction. We build on these data, implementing further filtering steps to remove families with homology with other species, to identify putative SSOGs in the gut microbiome and to study them systematically. By looking for patterns in large-scale comparisons, we attempt to disentangle the evolutionary...
  6. 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
    ..., morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read s for capturing structural variants. In addition, we consider how large-scale collections of whole- sequence data...
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  7. Method: Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
    • Van Hoan Do,
    • Francisca Rojas Ringeling,
    • and Stefan Canzar
    Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
    .... 2018), RCA (v2.0) (Li et al. 2017), TSCAN (v1.24.0) (Ji and Ji 2016), RaceID3 (v0.2.1) (Herman et al. 2018), CIDR (v0.1.5) (Lin et al. 2017), and RtsneKmeans (Duò et al. 2018) as well as to a geometric sketching–based clustering approach (Hie et al. 2019b). SC3 and Seurat consistently showed superior...
  8. Method: PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments
    • Peng Liu,
    • Alexandra A. Soukup,
    • Emery H. Bresnick,
    • Colin N. Dewey,
    • and Sündüz Keleş
    Genome Res. November 2020 30: 1655-1666; Published in Advance September 21, 2020, doi:10.1101/gr.252445.119
    ...as such task largely depends on the completeness of the transcript annotation and a definition of “transcriptional noise,” a consensus for which is lacking in the literature. All of the 30 input RNA-seq data sets and target transcript annotations are available at GitHub (https://github.com/pliu55/PRAM...
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  9. Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
    • Jun Kim,
    • Haoyu Wang,
    • and Sevinç Ercan
    Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
    ...communication between cis-regulatory elements. Many organisms, including S. cerevisiae, C. elegans, and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features...
  10. 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
    ...a window-based optimization scheme that enables accelerated convergence while improving the accuracy. Additionally, PCAone incorporates out-of-core and multithreaded implementations for the existing Implicitly Restarted Arnoldi Method (IRAM) and RSVD. Through comprehensive evaluations using multiple large-scale...
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