Searching journal content for articles similar to Xu and Zhang 33 (10): 1806.

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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
    ...) for supervised link prediction in GRN inference, leveraging scRNA-seq data and existing regulatory information to predict latent TF–gene interactions. Similarly, Grace (Wang et al. 2024a) integrates structural causal models with graph neural networks to infer both GRNs and gene causality from scRNA-seq data...
  2. Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
    • Mengyuan Zhao,
    • Jiawei Li,
    • Xiaoyi Liu,
    • Ke Ma,
    • Jijun Tang,
    • and Fei Guo
    Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
    ...on transcriptomics expression profile but neglect genetic interactions that are not disturbed by the above factors.In contrast to scRNA-seq data sets, gene regulatory networks are independent of transcriptome sequencing technologies, which reflects the intrinsic regulatory mechanism in gene expression processes...
  3. Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
    • Charlie George Barker,
    • Eirini Petsalaki,
    • Girolamo Giudice,
    • Julia Sero,
    • Emmanuel Nsa Ekpenyong,
    • Chris Bakal,
    • and Evangelia Petsalaki
    Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
    ...explains some of the variation in the effect of kinase inhibitors tested in a manner that is feature specific to the ones that were used to construct the network model.Network propagation of activated TFs reveals differentially activated processes in the cell-shape regulatory networkAs TF activity remains...
    OPEN ACCESS ARTICLE
  4. 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
    ...-scale signaling network to generate synthetic data but did not incorporate large-scale biological network information. In future studies, we will develop novel multiscale models that integrate multiomics data across multiple layers to make better inferences of CCC and gene–gene regulation.In summary, st...
  5. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...leading to the clonal evolution of cancer cells (Qing et al. 2020; Chakravarty and Solit 2021). Somatic mutations in key genes and their regulatory sequences, especially oncogenes, tumor suppressors, and DNA repair genes, are frequently found in cancers and contribute to tumor progression and therapeutic...
    OPEN ACCESS ARTICLE
  6. Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
    • Yaqiang Cao,
    • Guoyu Chen,
    • Gang Wu,
    • Xiaoli Zhang,
    • Joseph McDermott,
    • Xingwei Chen,
    • Chi Xu,
    • Quanlong Jiang,
    • Zhaoxiong Chen,
    • Yingying Zeng,
    • Daosheng Ai,
    • Yi Huang,
    • and Jing-Dong J. Han
    Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
    ...activity of L2 elements. Our results reveal a previously unappreciated co-evolution and interaction between two TE families in shaping regulatory networks.Transposable elements (TEs) are widespread throughout the , covering more than 50% of the human (International Human Genome Sequencing Consortium 2001...
    OPEN ACCESS ARTICLE
  7. 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
    ...-precision gene expression analysis further revealed the roles of various genes in neural development and dysfunction across different brain regions. This approach effectively uses fine-grained, cell-level information extracted from the reconstructed cellular landscape and insights into the heterogeneity of cell...
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