Searching journal content for articles similar to Pellow et al. 33 (7): 1154.

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  1. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ...minimize parameter sensitivity and further improve efficiency. Through extensive experiments, we13 demonstrate that WSD outperforms current state-of-the-art (SOTA) methods, achieving an average speedup of ∼2.33×14 and reducing memory usage by two orders of magnitude when analyzing human TRs.15 Introduction...
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  2. Method: Efficient mapping of accurate long reads in minimizer space with mapquik
    • Bariş Ekim,
    • Kristoffer Sahlin,
    • Paul Medvedev,
    • Bonnie Berger,
    • and Rayan Chikhi
    Genome Res. July 2023 33: 1188-1197; Published in Advance June 30, 2023, doi:10.1101/gr.277679.123
    .... 2022; Owen et al. 2022).We recently introduced the concept of minimizer-space computation (Ekim et al. 2021), in which only a small fraction of the sequenced bases is retained as a latent representation of the sequencing data, enabling orders of magnitude improvements in efficiency without loss...
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  3. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ..._LH and Jasmine_OR settings) (Noureen et al. 2022), and UCell (Andreatta and Carmona 2021). Like Seurat and SCANPY, Seurat_AG and Seurat_LVG first compute the average expression of the genes, sort them in increasing order, and divide them into 25 equally sized expression bins. Although Seurat_AG selects all genes...
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  4. Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
    • Fan Feng,
    • Sean Moran,
    • Anders S. Hansen,
    • Xiaotian Zhang,
    • and Jie Liu
    Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
    ...is performed with the efficient dynamic programming approach (Fig. 1C, bottom).In the end, the significance (P-value) of the stripe is determined through the calculation(4) Minimizing computational costDuring Quagga's statistical tests, the slowest step is calculating the Poisson P-values. Because...
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  5. 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
    ...technique that allows direct computation on encrypted data. We combine this approach with our efficient distributed computation techniques to minimize the overhead of cryptographic operations. Overall, our study provides the first practical demonstration of secure relative identification across large...
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  6. 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
    ....The key technical contribution of the new ScisTree2 approach is an SPR local search algorithm that runs in O(Kn2m) time, which is one order of magnitude faster than a naive alternative. Moreover, the SPR local search is made more efficient by a branch and bound heuristic, which enables ScisTree2 to infer...
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  7. Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    • Dmitry Antipov,
    • Mikko Rautiainen,
    • Sergey Nurk,
    • Brian P. Walenz,
    • Steven J. Solar,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
    ...% of total runtime for the HG002 human assembly (Rautiainen et al. 2023). Verkko2 introduces a more efficient overlapper to reduce runtime. The previous method was originally designed for Sanger (Sanger et al. 1977) data and thus was limited to small k-mers, did not use minimizers, and extended single k...
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  8. Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
    • Han Shu,
    • Jing Chen,
    • Chang Xu,
    • Jialu Hu,
    • Yongtian Wang,
    • Jiajie Peng,
    • Qinghua Jiang,
    • Xuequn Shang,
    • and Tao Wang
    Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
    ...observed in the 10x Visium data set. This trend continued in the Stereo-seq data set, confirming successful integration across donors. Additionally, we evaluated computational efficiency. stMSA processed up to 20 slices with <12 GB of GPU memory, whereas Stitch3D, SPACEL, and SEDR struggled to handle...
  9. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...increasing. This poses a major computational challenge to the profilers in terms of memory usage, index construction, and query time.Several approaches for the efficient indexing and querying of large collections of reference sequence sets have been developed over the past few years to overcome these issues...
  10. Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
    • Irmgard U. Haussmann,
    • Thomas C. Dix,
    • David W.J. McQuarrie,
    • Veronica Dezi,
    • Abdullah I. Hans,
    • Roland Arnold,
    • and Matthias Soller
    Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
    ...the performance of a Drosophila sgRNA data set (Ren et al. 2014) according to the sgRNA design parameters described above. Our design tool PlatinumCRISPr selected 12 from 39 sgRNAs and those showed a cleavage efficiency of 58% or more (Fig. 4A). We then analyzed a number of sgRNA prediction tools for this data...
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