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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...ADAR targets do not pose an immunogenic risk, and the search for the few critical targets is ongoing(Levanon et al. 2024; Li et al. 2022). cis-NAT editing targets, which are long and perfect dsRNAs, are prime candidates for critical ADAR targets. Identifying these may help to better understand ADAR...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...search approach to find optimal trees. ScisTree2 also calls single-cell genotypes based on the inferred cell lineage tree. Experiments on simulated and real biological data show that ScisTree2 achieves better overall accuracy while being significantly more efficient than existing methods. To the best...
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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
...; Supplemental Fig. S3B). Nevertheless, we observed subtle differences in the distribution of various molQTL. For instance, apaQTL and sQTL are more frequently enriched around the TES and gene body, respectively (Fig. 3C), which is consistent with the previous results reported by chicken GTEx pilot analysis...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...al. 2015). Genome-wide increases in DNA methylation levels, particularly at CHH sites, were detected in cultured samples during somatic embryogenesis in soybean (Ji et al. 2019). In sweet orange, the global CHH methylation levels were significantly decreased at the callus induction stage...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...Assembly of a pan for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history Yang Zhou1,6, Lv Yang1,6, Xiaotao Han1, Jiazheng Han1, Yan Hu1, Fan Li1, Han Xia1, Lingwei Peng1, Clarissa Boschiero2, Benjamin D...
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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
...and differentiation (Ji et al. 2009; Shepard et al. 2011; Wei et al. 2020), organ development (Liu et al. 2024), and complex traits and diseases (Hong et al. 2020; Li et al. 2021). A previous study constructed a multitissue human 3′ UTR APA quantitative trait loci (3′aQTLs) map, revealing that genetic variants within...
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Method: Protein domain embeddings for fast and accurate similarity search
- Benjamin Giovanni Iovino,
- Haixu Tang,
- and Yuzhen Ye
Genome Res. September 2024 34: 1434-1444; Published in Advance September 5, 2024, doi:10.1101/gr.279127.124
...embeddings. Such protein-level embeddings have been applied to enable fast searches of similar proteins; however, limitations have been found; for example, PROST is good at detecting global homologs but not local homologs, and knnProtT5 excels for proteins with single domains but not multidomain proteins...
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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
...pseudobulk analyses of cortical hem cells (Fig. 4A). Concordantly, our topic-based approach revealed a modest correlation between ABCA1 QTL estimates and topic 6 (Pearson's correlation 0.26), which is defined primarily by radial glia.View larger version: In this window In a new window Figure 4. Organoid eQTLs...
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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
...vary in the ratio of Eu to St animals even when grown under the same environmental conditions, indicating a strong effect of genetic background on mouth-form development (Ragsdale et al. 2013). A recent study employed recombinant inbred lines and QTL mapping with two strains from clade B (Dardiry et al...
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