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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...is that conventional motif enrichment analysis is hardly applicable to deconvoluting the degenerate motifs and examining the signal differences among genes. The deep learning modeling is well suited to address this question. Specifically, convolutional recurrent neural networks can quantitatively capture dynamic...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
..., interacting physiological systems. An increasing number of studies indicate that, beyond the traditionally emphasized hypothalamic–pituitary–gonadal (HPG) axis, metabolic and immune tissues are integral components of the regulatory network controlling laying performance. For instance, the liver sustains high...
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Research: Gene regulation and speciation in house mice
- Katya L. Mack,
- Polly Campbell,
- and Michael W. Nachman
Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
...Gene regulation and speciation in house mice Katya L. Mack 1 , Polly Campbell 2 and Michael W. Nachman 1 1Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA...
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Method: A new framework for exploratory network mediator analysis in omics data
- Qingpo Cai,
- Yinghao Fu,
- Cheng Lyu,
- Zihe Wang,
- Shun Rao,
- Jessica A. Alvarez,
- Yun Bai,
- Jian Kang,
- and Tianwei Yu
Genome Res. April 2024 34: 642-654; Published in Advance May 7, 2024, doi:10.1101/gr.278684.123
...mediators from the vast pool of candidate mediators, but also to identify groups of mediators that are connected to the existing signal transduction, protein interaction, or metabolic network. The selected mediators should collectively show a coherent functional implication (Fig. 1B). We name such small...
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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
..., also known as CYPA) signaling and further dominate plasma cells.View larger version: In this window In a new window Figure 7. Comprehensive analysis of the cell communication network for COVID-19. (A) The number of interactions of the cell communication networks. (B,C) Cell communication networks...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
..., Amherst, Massachusetts 01003, USA Corresponding authors: olivia.rissland@gmail.com, neelanjan.mukherjee@cuanschutz.eduAbstractThe poly(A) signal, together with auxiliary elements, directs cleavage of a pre-mRNA and thus determines the 3′ end of the mature transcript. In many species, including humans...
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Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
- Peng Xu and
- Bin Zhang
Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
...-enriched regions and open chromatin regions, respectively. The y-axis represents the number of cancer types with the module enrichment and open chromatins, ranging from a minimum of zero to a maximum of 30. (B) Boxplot showing the fold changes of ATAC-seq peak signals in cytobands with enriched or depleted network...
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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
...regulatory signal which is binary). As we illustrated, we thus needed to binarize target gene expression levels based on half maximal value, which allows quantitative determination of whether input and output are matching in time.Evaluating network inference accuracy using simulated single-cell data sets...

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