Searching journal content for articles similar to Wiens et al. 34 (8): 1196.

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  1. 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
    ...single-cell data (Baysoy et al. 2023). Single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) are two commonly used technologies to study cellular heterogeneity and regulatory mechanisms (Gayoso et al. 2021; Hao et al. 2021). However, the extreme high dimension and sparsity...
  2. 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
    ...sets with paired scRNA-seq and scATAC-seq data, demonstrating its superior performance over seven baseline methods in GRN reconstruction, especially its higher precision under the inherently imbalanced scenario in which the true regulatory interaction is sparse. Furthermore, benchmarking on directed...
  3. Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
    • Chuanyuan Wang and
    • Zhi-Ping Liu
    Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
    ...space modeling, DigNet is robust to the presence of noise in scRNA-seq data and the sparsity of GRNs. Benchmark evaluation results against more than a dozen state-of-the-art network inference methods demonstrate that DigNet achieves superior performance across various single-cell GRN reconstruction...
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  4. Method: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
    • Yi Qiao,
    • Xiaomeng Huang,
    • Philip J. Moos,
    • Jonathan M. Ahmann,
    • Anthony D. Pomicter,
    • Michael W. Deininger,
    • John C. Byrd,
    • Jennifer A. Woyach,
    • Deborah M. Stephens,
    • and Gabor T. Marth
    Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
    ...of cells are already known. We acquired bulk DNA sequencing and single-cell RNA sequencing (10x Genomics Chromium 5′ capture protocol) data from three chronic lymphocytic leukemia patients (Supplemental Fig. 4A). The bulk DNA sequencing data are from isolated B cells and B cells (as germline control...
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  5. 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
    ...the developmental and immune microenvironment for tissue organization. We utilized a seqFISH data set (Lohoff et al. 2022) alongside scRNA-seq (Pijuan-Sala et al. 2019) data obtained from the 10x Chromium platform to investigate intercellular communication events in a mouse E8.5 embryo (Fig. 4A,B). The seqFISH data...
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  6. Review: Advancements in prospective single-cell lineage barcoding and their applications in research
    • Xiaoli Zhang,
    • Yirui Huang,
    • Yajing Yang,
    • Qi-En Wang,
    • and Lang Li
    Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
    ...barcode diversity (Bramlett et al. 2020). Bramlett et al. (2020) suggested that a library of 40,000–50,000 barcodes typically allows tracking of ∼1000 cells with a >95% probability, i.e., >95% of the barcodes represent single cells. Barcode libraries that are compatible with scRNA-seq, such as LARRY...
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  7. Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
    • Arthur Dondi,
    • Nico Borgsmüller,
    • Pedro F. Ferreira,
    • Brian J. Haas,
    • Francis Jacob,
    • Viola Heinzelmann-Schwarz,
    • Tumor Profiler Consortium,
    • and Niko Beerenwinkel
    Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
    ..., to examine these interlinked features jointly (Foord et al. 2023) by capturing genetic and transcriptomic variants at the single-cell level (Mansoori et al. 2017; Dagogo-Jack and Shaw 2018; Marine et al. 2020).Droplet-based scRNA-seq (e.g., 10x Genomics Chromium) can detect same-cell genetic...
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  8. 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
    ...for Imaging Science, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: awang87@jhu.eduAbstractThe selection of marker gene panels is critical for capturing the cellular and spatial heterogeneity in the expanding atlases of single-cell RNA sequencing (scRNA-seq) and spatial...
  9. Method: Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
    • Sindri Emmanúel Antonsson and
    • Páll Melsted
    Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
    ...Sindri Emmanúel Antonsson and Páll Melsted Faculty of Industrial Engineering, Mechanical Engineering, and Computer Science, University of Iceland, 102 Reykjavík, Iceland Corresponding author: pmelsted@hi.isAbstractAs the number of experiments that employ single-cell RNA sequencing (scRNA-seq) grows...
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  10. Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...amount in tumor divided by that in normal with ploidy adjusted and we 567 used their estimates for the TCGA dataset. 568 Single-cell data analysis 569 A publicly available single-cell RNA-seq (scRNA-seq) dataset was downloaded for cutaneous 570 squamous cell carcinoma (cSCC) samples along...
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