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  1. 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
    ...settings, even in the absence of paired omics data, which is a common issue owing to experimental constraints.To validate PRISM-GRN's ability to integrate unpaired omics data, we evaluated it on two benchmark data sets, GM12878 and A549, each containing independently obtained scATAC-seq data. Specifically...
  2. 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...
  3. Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
    • Kehan Lang,
    • Chenyang Jia,
    • Siyu Li,
    • Yi Guo,
    • Dingjun Hu,
    • and Shengquan Chen
    Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
    ...and consistency of scDNAm measurements. In practice, this results in high rates of missing or erroneous methylation calls, which pose a significant challenge for cross-modality translation methods.To assess the robustness of scBOND against noise-induced perturbations, we simulated common sources of error observed...
    OPEN ACCESS ARTICLE
  4. Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
    • Krzysztof H. Banecki,
    • Haoxi Chai,
    • Yijun Ruan,
    • and Dariusz Plewczynski
    Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
    ....280985.125. Freely available online through the Genome Research Open Access option. © 2026 Banecki et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4...
    OPEN ACCESS ARTICLE
  5. Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
    • Aliza B. Rubenstein,
    • Gregory R. Smith,
    • Zidong Zhang,
    • Xi Chen,
    • Toby L. Chambers,
    • Frederique Ruf-Zamojski,
    • Natalia Mendelev,
    • Wan Sze Cheng,
    • Michel Zamojski,
    • Mary Anne S. Amper,
    • Venugopalan D. Nair,
    • Andrew R. Marderstein,
    • Stephen B. Montgomery,
    • Olga G. Troyanskaya,
    • Elena Zaslavsky,
    • Todd Trappe,
    • Scott Trappe,
    • and Stuart C. Sealfon
    Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
    ...correlated patterns of activity within cell types across samples (see Methods) (Supplemental Fig. S5A). These analyses are used to identify common multiomic (gene and associated chromatin change) programs that are consistently either upregulated or downregulated in multiple muscle fiber types. Multiomic...
  6. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M. Riley,
    • Randa Elsayed,
    • Mark D. Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C. Nelson
    Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...), and regulates cell proliferation in the hindbrain in zebrafish (Coolen et al. 2012). As we discuss later, it is therefore highly likely that the significant enrichment for terms associated with the nervous system can be attributed to common neuro-pancreatic gene regulatory programs operating across...
  7. Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
    • Quanyou Cai,
    • Lihui Lin,
    • Xin Liu,
    • and Jiekai Chen
    Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
    .... To test if Polyomino can improve spatial gene expression, we used AllenISH tissue staining data as a standard reference (Fig. 3F; Supplemental Fig. S13A; (http://atlas.brain-map.org/atlas?atlas=1). We first examined the genes common to STARMAP and AllenISH; Polyomino successfully predicted the expression...
    OPEN ACCESS ARTICLE
  8. Method: Quantifying pathological progression from single-cell transcriptomic data with scPSS
    • Samin Rahman Khan,
    • M Saifur Rahman,
    • M. Sohel Rahman,
    • and Md Abul Hassan Samee
    Genome Res. February 2026 36: 375-386; Published in Advance January 14, 2026, doi:10.1101/gr.280411.125
    ...and pathway enrichment analyses between predicted pathological cells and control cells to confirm that the results are biologically meaningful. If not, then the user can repeat scPSS using a different cutoff for the P-value threshold. This iterative refinement approach is common in other single-cell analysis...
  9. Method: A unified analysis of atlas single-cell data
    • Hao Chen,
    • Nam D. Nguyen,
    • Matthew Ruffalo,
    • and Ziv Bar-Joseph
    Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
    ...and to enable large-scale joint analyses of atlas-level data, we developed a new method, gene-based data integration and analysis technique (GIANT), that focuses on genes rather than on cells. Genes provide a level of granularity, which, on the one hand, can serve as anchor points common to all modalities but...
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  10. Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
    • Shristi Pandey,
    • Anna J. Moyer,
    • and Summer B. Thyme
    Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
    ...telencephalic cell types is still missing.The aim of this study is to use single-cell RNA-seq across life stages to obtain a comprehensive picture of the transcriptionally distinct cell types of the zebrafish pallium and subpallium.ResultsIntegrated graph clustering identifies cell types in the zebrafish...
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  1. April 2026, 36 (4)
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