Searching journal content for articles similar to Hu et al. 35 (6): 1415.

Displaying results 1-10 of 6020
For checked items
  1. 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
    ...diverse ST platforms.LLOKI enhances cross-technology spatial gene program detectionTo assess LLOKI's utility for downstream analysis, we integrated data from four ST platforms—MERFISH, MERSCOPE, CosMx, and Xenium—and evaluated whether LLOKI embeddings improve cross-technology analyses using Spice...
    OPEN ACCESS ARTICLE
  2. Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
    • Hang Zhang,
    • Yi Zhang,
    • Kai Ming Ting,
    • Jie Zhang,
    • and Qiuran Zhao
    Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
    ...cluster and to discover clusters of dissimilar characteristics. The identified transcriptomically similar clusters assist in further characterizing tissue organization and uncovering potential biomarkers or therapeutic targets.Existing methods for spatial domain detection have primarily focused on data...
    OPEN ACCESS ARTICLE
  3. Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
    • Lin Li,
    • Xianbin Su,
    • and Ze-Guang Han
    Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
    .... Recent advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies have empowered the comprehensive characterization of gene programs at both single-cell and spatial resolutions. Here, we present DeCEP, a computational framework designed to characterize context...
  4. Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
    • An Wang,
    • Stephanie Hicks,
    • Donald Geman,
    • and Laurent Younes
    Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
    ...(see Supplemental Fig. S6 for matching quality comparisons on all 10x Genomics reference clusters). This result highlights geneCover's ability to enhance the resolution of spatial transcriptomics discovery, particularly in identifying highly refined spatial organizations, using a compact and minimally...
  5. 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
    .... Order determined by a coin flip. Corresponding author: braphael@princeton.eduAbstractSpatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active...
    OPEN ACCESS ARTICLE
  6. Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
    • Jianing Yao,
    • Jinglun Yu,
    • Brian Caffo,
    • Stephanie C. Page,
    • Keri Martinowich,
    • and Stephanie C. Hicks
    Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
    ...demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark data sets and technological platforms.Spatially resolved multi-omics technologies enable the profiling of multiple omic measurements, such as the transcriptome and proteome, in individual tissue sections, leading...
    OPEN ACCESS ARTICLE
  7. Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
    • Vishvak Raghavan,
    • Yumin Zheng,
    • Yue Li,
    • and Jun Ding
    Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
    ...agent states for each cell: gene expression from scRNA-seq, cell type/cluster information, and LR database. Spatial coordinates (from spatial transcriptomics data) are optional. (B) The receptor receiving rate is the probability that an interaction is received by a receptor, calculated by non...
    OPEN ACCESS ARTICLE
  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
    ...technologies. Furthermore, stMSA effectively deciphers complex developmental trajectories by integrating spatial proteomics and transcriptomics data and excels in cross-slice matching and alignment for 3D tissue reconstruction.Spatial omics (SO) technologies have greatly enhanced our understanding of molecular...
  9. Method: Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data
    • Lulu Yan,
    • Jinyu Cheng,
    • Qing Nie,
    • and Xiaoqiang Sun
    Genome Res. June 2025 35: 1400-1414; Published in Advance April 22, 2025, doi:10.1101/gr.279857.124
    ...Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data Lulu Yan1,4, Jinyu Cheng2,4, Qing Nie3 and Xiaoqiang Sun1 1School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China; 2Zhongshan School of Medicine, Sun Yat-sen University...
  10. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...of circularized consensus sequencing with PacBio (Table 1; Al'Khafaji et al. 2024).View this table: In this window In a new window Table 1. Comparison of clustering methods for single-cell long-read sequencingSpatial sequencingA key drawback of creating a single-cell or -nucleus suspension is the resulting loss...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research