Searching journal content for articles similar to MacNeil and Walhout 21 (5): 645.

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  1. 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
    ...Chuanyuan Wang and Zhi-Ping Liu Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China Corresponding author: zpliu@sdu.edu.cnAbstractA gene regulatory network (GRN) intricately encodes the interconnectedness of identities...
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  2. Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
    • Benjamin D. Umans and
    • Yoav Gilad
    Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
    ...between genetic variants and environmental stressors is key to understanding the mechanisms underlying neurological diseases. In this study, we use human brain organoids to explore how varying oxygen levels expose context-dependent gene regulatory effects. By subjecting a genetically diverse panel of 21...
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  3. 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. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...D architecture and transcriptomes have been developed (Cao et al. 2018; Chen et al. 2019; Liu et al. 2023). However, to date, there is no robust method for the joint mapping of RT and gene expression. In addition, distinct challenges remain to align 3D features to gene regulation due to data...
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  4. 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. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...disorders, it will be necessary to decipher gene regulatory networks (GRNs) underpinning normal development. Zebrafish is an excellent model organism for dissecting gene regulatory control of cell fate and behavior (Figiel et al. 2021). Large clutch sizes, ex utero development, and the availability of well...
  5. Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
    • Yueying He,
    • Yue Xue,
    • Jingyao Wang,
    • Yupeng Huang,
    • Lu Liu,
    • Yanyi Huang,
    • and Yi Qin Gao
    Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
    ...a reliable and quantitative understanding of the alterations of genomic structures under different cellular conditions. The genomic structure yielded by CTG serves as an architectural blueprint of the dynamic gene regulatory network, based on which cell-specific correspondence between gene–gene...
  6. 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...
  7. Method: Modeling gene interactions in polygenic prediction via geometric deep learning
    • Han Li,
    • Jianyang Zeng,
    • Michael P. Snyder,
    • and Sai Zhang
    Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
    ...of a well-defined PPI network on the robustness and effectiveness of PRS-Net.Subsequently, we evaluated the performance of PRS-Net with different GGI networks. Specifically, we employed gene representations generated by Gene2vec (Du et al. 2019). This machine learning approach leverages gene coexpression...
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  8. Method: Dissecting and improving gene regulatory network inference using single-cell transcriptome data
    • Lingfeng Xue,
    • Yan Wu,
    • and Yihan Lin
    Genome Res. September 2023 33: 1609-1621; Published in Advance August 14, 2023, doi:10.1101/gr.277488.122
    ..., 100871; 3Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871 Corresponding author: yihan.lin@pku.edu.cnAbstractSingle-cell transcriptome data has been widely used to reconstruct gene regulatory networks (GRNs) controlling...
  9. Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
    • Shan Lu and
    • Sunduz Keles
    Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
    ...the phenotypes of interest (Lareau et al., 2015). Instead of focusing on high centrality genes within a single coexpression network, detecting genes with differential centrality between phenotypic groups can elucidate regulatory alterations. Savino et al. (2020) offer insights into the potential regulatory...
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  10. Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
    • Anguo Liu,
    • Nini Wang,
    • Guoxiang Xie,
    • Yang Li,
    • Xixi Yan,
    • Xinmei Li,
    • Zhenliang Zhu,
    • Zhuohui Li,
    • Jing Yang,
    • Fanxin Meng,
    • Mingle Dou,
    • Weihuang Chen,
    • Nange Ma,
    • Yu Jiang,
    • Yuanpeng Gao,
    • and Yu Wang
    Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
    ...cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between g...
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