Searching journal content for articles similar to Flannick et al. 16 (9): 1169.

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  1. 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
    ..., particularly for unsupervised cellular state annotation based on maximum signature score values. However, this application requires robust and comparable score distributions across diverse signatures and experimental conditions. Our systematic evaluation of established scoring methodologies—Seurat, SCANPY...
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  2. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ..., the leading pan aligners. Although currently best suited for aligning to localized pans owing to computational constraints, Moni-align offers a robust foundation for future optimizations that could further broaden its applicability.Pan references enable read aligners to account for intra-species variations...
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  3. 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
    ...scores for both orientations (Fig. 6D), with 2D visualizations further validating coherent integration (Supplemental Fig. S18B). Together, these results demonstrate stMSA's robustness in aligning multiple SO slices, enabling accurate 3D tissue reconstruction.DiscussionThe rapid advancement of sequencing...
  4. Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
    • Zhitao Huang,
    • Ruiqing Zheng,
    • Pengzhen Jia,
    • Xuhua Yan,
    • Jinmiao Chen,
    • and Min Li
    Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
    ...ATAC-seq features, which keeps the difference between omics. However, its interomics alignment is unreliable because of lacking reasonable and robust assumption for alignment, which can even lead to over-alignment. The second type of methods transforms scATAC-seq data into Gene Activity Scores (GAS) based on prior...
  5. Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
    • Yidi Deng,
    • Jiadong Mao,
    • Jarny Choi,
    • and Kim-Anh Le Cao
    Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
    ...(KNN) principal component (PC) regression on gene expression data to efficiently 80 construct robust, cell-specific coexpression networks. Intuitively, the coexpression between two 81 genes in a given cell is quantified by how strongly one gene embedded within the PCs (i.e., predictor 82 genes...
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  6. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...'s accuracy underscores the advantages of full-text indexes, which offer a more precise solution compared with k-mer indexes designed for a specific k value.Compressed indexes are increasingly used for read alignment (Garrison et al. 2018; Armstrong et al. 2020; Sirén et al. 2021) and classification (Ahmed et...
  7. Method: Robust chromatin state annotation
    • Mehdi Foroozandeh Shahraki,
    • Marjan Farahbod,
    • and Maxwell W. Libbrecht
    Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
    ...of states, such that the models learn multiple similar states that are not confidently distinguishable from one another. This suggests that reducing the number of states may give more robust annotations. It is common for practitioners to merge similar states as a postprocessing step of SAGA annotations...
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  8. Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
    • Wenhao Zhang,
    • Lan Cao,
    • Xiaoxuan Gu,
    • Yongyu Long,
    • and Ying Wang
    Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
    ...PRISM-GRN to effectively handle unpaired omics data, providing a more comprehensive understanding of GRNs. This capability, combined with its robustness and accuracy in reconstructing cell type–specific regulatory networks, posits PRISM-GRN as a powerful tool for advancing the study of gene regulation...
  9. Method: Fast sequence alignment for centromeres with RaMA
    • Pinglu Zhang,
    • Yanming Wei,
    • Qinzhong Tian,
    • Quan Zou,
    • and Yansu Wang
    Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
    ..., reliable regions of RaMA based on the rare match and the UniAligner alignment results. (D) Distribution of the multiplicity of HOR indels in RaMA alignment results, reliable regions of RaMA based on the rare match, and the UniAligner alignment results.For long indels, given that the canonical HOR on the X...
  10. Method: Partial alignment of multislice spatially resolved transcriptomics data
    • Xinhao Liu,
    • Ron Zeira,
    • and Benjamin J. Raphael
    Genome Res. July 2023 33: 1124-1132; Published in Advance August 8, 2023, doi:10.1101/gr.277670.123
    ...multiple slices can help recover this information and improve downstream expression analyses, but multislice alignment and integration remains a challenging task. Existing methods for integrating SRT data either do not use spatial information or assume that the morphology of the tissue is largely preserved...
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