Searching journal content for articles similar to Liu et al. 33 (7): 1124.

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  1. Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
    • Daijun Zhang,
    • Ren Qi,
    • Xun Lan,
    • and Bin Liu
    Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
    .... However, this method focuses solely on gene expression information within bins, leading to a partial understanding of the biological system as a whole. STitch3D (Wang et al. 2023) integrates data from multiple 2D tissue slices with paired single-cell RNA (scRNA) sequencing to characterize complex tissue...
  2. Method: Unified integration of spatial transcriptomics across platforms with LLOKI
    • Ellie Haber,
    • Ajinkya Deshpande,
    • Jian Ma,
    • and Spencer Krieger
    Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
    ...parameters and five different values for alpha (0.01, 0.05, 0.001, 0.005, 0.0001), using the best-performing parameter set for our comparison. We note that we run PASTE instead of PASTE2 (Liu et al. 2023b), because the advantage of PASTE2 is in partial alignment, and all of our analysis was on full...
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  3. Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
    • Hongyu Zheng,
    • Hirak Sarkar,
    • and Benjamin J. Raphael
    Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
    ...been partially addressed by recently developed spatial alignment based tools, SLAT (Xia et al. 2023) and SANTO (Li et al. 2024), which impute missing gene expression in one of the SRT data sets based on a learned spatial alignment. These tools do not handle platform-specific differences and overlook...
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  4. 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
    ...in reconstructing coherent 3D tissue structures from 2D slices (Fig. 6B), whereas PASTE achieved only partial alignment, and STAligner/SANTO failed to establish spatial correspondence. Quantitatively, stMSA outperformed all competing methods, achieving the highest Pearson correlation coefficient (PCC) and cell type...
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