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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
...-tissue connectivity degree of the corresponding gene.DiscussionIn the current study, we provided a multitissue atlas of regulatory variants in laying ducks, including 14,074, 6267, 4994 eGenes, sGenes, and apaGenes in the liver, ovary, shell gland of oviduct and spleen, respectively. Compared with previous e...
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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
...isoform expression levels and dynamic APA changes in each tissue and cell type. We identified a total of 40,748 PASs across 12,111 genes. Of these, 26.9% of genes had a single PAS, whereas 73.1% exhibited multiple PASs (Fig. 1B). Classification based on genomic annotation revealed that 63.1% of PASs were...
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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
...of scRNA-seq and scATAC-seq. Unlike the HuBMAP data, the fetal atlas provides cell-type annotations for cell clusters, allowing us to validate our embeddings at a more refined level. Results are presented in Figure 4, A and B (Supplemental Note 10). As the figure shows, GIANT is able to merge genes from...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...that the previously annotated “neural” cells were glia, in agreement with the authors of the Heart Cell Atlas (Kanemaru et al. 2023). Our analysis showed that male glia expressed XIST robustly (Fig. 1A–C). To study if this is specific to the heart, we then obtained human skeletal muscle scRNA-seq data for fibroblasts...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...Xiu Fan1,2,10, Qili Qian3,4,10, Wenran Li3,4, Tianzi Liu3,4, Changqing Zeng1,2,5, Peilin Jia1,2, Huandong Lin6, Xin Gao6, Li Jin4,7, Mingfeng Xia6, Sijia Wang3,8 and Fan Liu1,9 1China National Center for Bioinformation, Beijing 100101, China; 2Beijing Institute of Genomics, Chinese Academy...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...contributed equally to this work. Corresponding authors: ipm5219@psu.edu, izg5139@psu.eduAbstractDespite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying...
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Editorial: Revolutionizing genomics and medicine—one long molecule at a time
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. November 2024 34: ix-xi; doi:10.1101/gr.280179.124
....0/.References ↵Adams M, Vollmers C. 2024. Generation and analysis of a mouse multitissue annotation atlas. Genome Res (this issue) 34: 2108–2117. doi:10.1101/gr.279217.124 ↵Belchikov N, Hsu J, Li XJ, Jarroux J, Hu W, Joglekar A, Tilgner HU. 2024. Understanding isoform expression by pairing long-read sequencing...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...for why this question is important. First, from a basic biology standpoint, the answer would provide insights into whether the same variant, in the same epigenetic regulator, causes the same (or a highly similar) chromatin disruption in different cellular contexts. For example, is it the same genomic...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
..., in conjunction with miRNA–mRNA target prediction algorithms or pre-established miRNA–mRNA target databases, are frequently used to functionally annotate specific miRNAs of interest. These methods facilitate the inference of regulatory relationships between miRNAs and their target genes (Chang et al. 2020...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...al. 2019). We found that SCALE was able to distinguish different human age groups (linear regression, P-value < 0.001) (Supplemental Fig. S21). We then applied SCALE to a multitissue scRNA-seq atlas of rats undergoing aging and calorie restriction (CR), which is known to be one of the most effective...
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