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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...and INSs, further validating the unique strength of LRS 572 technology in resolving multi-scale genomic rearrangements. A key issue to explore further is 573 how to define the boundary between CNVs identified through sequencing depth and 574 DEL/INS/DUP detected by long reads. Furthermore, we investigated...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...for SNP data and demonstrated how it can be integrated into existing SNP data set compression pipelines. We have also benchmarked VAE-based global ancestry classification against PCA-based classification...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...identifies epigenomic changes associated to the induction of core ISGs 193 To uncover the regulatory mechanisms underlying the transcriptome response induced by 194 poly I:C, we integrated data from RNA-seq, ATAC-seq, and ChIP-seq for the active histone 195 mark H3K27ac and repressive histone mark H3K27me3...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...in control and SETD3 KO HCT116 colorectal cancer cells using two independent gRNAs (Fig. 1A). ACTB genomic distribution was significantly reduced across the whole in the SETD3 KO cells (Fig. 1B–D). Integrative Genomics Viewer (IGV) tracks of different genomic regions in SETD3 control and SETD3 KO cells...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...prediction; however, it often struggles with interpretability because of its black-box nature. Here, we evaluate 12 ML models alongside GBLUP and BayesR to identify key factors influencing genomic prediction performance across traits with different genetic architectures in multiple agricultural species...
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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
..., our findings may also offer insights into the genetic basis of reproductive disorders in other vertebrates, including humans.By integrating coexpression modules, we identified that the liver emerged as a central regulatory hub, with its modules showing extensive cross-tissue correlations. In humans...
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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
.... briggsae strains and nine C. nigoni strains, including both reference strains. Through comparative pan-genomic analyses of both nematode species, we aim to identify the critical structural and genetic variations that drive intra- and interspecific evolution, ultimately leading to speciation...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
...of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-5674, USA Corresponding author: song.xiaoyu@duke-nus.edu.sgAbstractRecent advances in spatially resolved transcriptomics (SRT) have provided valuable avenues for identifying cell...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...for safeguarding genomic stability. Due to their intricate and fragile nature, centromeres are susceptible to chromosomal rearrangements. However, the mechanisms preserving their functional integrity and supporting nuclear homeostasis following breakages remain enigmatic. In this study, we use wheat ditelosomic...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...Ruhollah Shemirani1, Gillian M. Belbin1,9, Sinead Cullina1,2, Christa Caggiano1, Christopher R. Gignoux3,4, Noah Zaitlen5,6,7 and Eimear E. Kenny1,2,8 1Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 2Department of Genetics and Genomic Sciences...
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