Searching journal content for articles similar to Groff et al. 29 (10): 1705.

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  1. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
  2. Method: Ultrafast functional profiling of RNA-seq data for nonmodel organisms
    • Peng Liu,
    • Jessica Ewald,
    • Jose Hector Galvez,
    • Jessica Head,
    • Doug Crump,
    • Guillaume Bourque,
    • Niladri Basu,
    • and Jianguo Xia
    Genome Res. April 2021 31: 713-720; Published in Advance March 17, 2021, doi:10.1101/gr.269894.120
    ...evaluated using both simulated and real RNA-seq data sets from mouse (Mus musculus), chicken (Gallus gallus), zebrafish (Danio rerio), and roundworm (Caenorhabditis elegans) (Supplemental Table S3). For these benchmark tests, the Seq2Fun MEM mode aligns the translated reads to a database containing only...
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  3. Method: Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
    • Wanqing Shao and
    • Ting Wang
    Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120
    ...present an analytical framework tailored to TE expression quantification in scRNA-seq data sets. We systematically evaluated scRNA-seq reads that mapped to TEs and showed that quantifying TE expression in single cells using transcripts assembled from bulk RNA-seq effectively reduces noise. Applying our...
  4. Method: SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection
    • Shibiao Wan,
    • Junil Kim,
    • and Kyoung Jae Won
    Genome Res. February 2020 30: 205-213; Published in Advance January 28, 2020, doi:10.1101/gr.254557.119
    ...-and-conquer, random projection (RP), weighted-based metaclustering, and similarity-based metaclustering. (B,C) Running time (B) and clustering performance (C) based on ARI (Hubert and Arabie 1985) of SHARP in 20 single-cell RNA-seq data sets with numbers of single cells ranging from 124 to 10 million (where data sets...
  5. Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
    • Felicia Peng,
    • C. Erik Nordgren,
    • and John Isaac Murray
    Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
    ..., the stage of the embryo from which it came from was estimated by correlating its transcriptome with a whole-embryo bulk RNA seq time series (Hashimshony et al. 2015; Packer et al. 2019). The cells here cover a similar range of stages as those in the existing C. elegans embryo single-cell atlas (from...
  6. Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
    • Xin Huang,
    • Xiaohan Tang,
    • Xuemei Bai,
    • Honglei Li,
    • Huan Tao,
    • Junting Wang,
    • Yaru Li,
    • Yu Sun,
    • Yang Zheng,
    • Xiang Xu,
    • Longteng Wang,
    • Yang Ding,
    • Meisong Lu,
    • Pingkun Zhou,
    • Xiaochen Bo,
    • Hao Li,
    • and Hebing Chen
    Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
    ...stages in different resolutions. When using these tools, alternatives are available for the species (human or mouse), signal type (“RNA-seq,” “ATAC-seq,” or “ChIP-seq”), or developmental stage (“oocyte,” “sperm,” “zygote,” “early two-cell,” “two-cell,” “late two-cell,” “four-cell,” “eight-cell,” “morula...
    OPEN ACCESS ARTICLE
  7. 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
    ...–expression associations, neglect of biological relevance in evaluation, and poor performance in limited paired training data. To fill these gaps, we introduce scBOND, a bidirectional cross-modal translation framework tailored for scRNA-seq and scDNAm profiles. scBOND leverages a mixture-of-experts block to capture...
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  8. Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
    • Lakshana Sruthi Sadu Murari,
    • Quinn Dickinson,
    • Silvia Meyer-Nava,
    • and Juan Carlos Rivera-Mulia
    Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...obtained from the standard method.We also evaluated the robustness of the RNA-seq data generated in PARTAGE and found high reproducibility across replicates. Moreover, although PARTAGE RNA-seq was performed on low-input samples (20 K nuclei), it faithfully recapitulated the transcriptome obtained...
    OPEN ACCESS ARTICLE
  9. Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...information based on the RNA-seq data from The Cancer Genome Atlas (TCGA) (Weinstein et al. 2013). Here, we utilized the imputed profiles to select marker genes across the samples from the HEST-1k data set with different disease states and included the overlapped genes between the marker genes and genes from...
    OPEN ACCESS ARTICLE
  10. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    ...as a promising resource for standardizing cell type annotations across studies. Although the current early-access release is limited to bulk RNA-seq data, the developers have announced that single-cell modalities are in active development. Once available, these synthetic single-cell data sets could provide...
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