Searching journal content for articles similar to Xu et al. 31 (7): 1150.

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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...biological functions (Le and Maizel 1997; Cheng et al. 2001). The VAE-GMM k-mer clustering model, by combining deep neural networks with probabilistic clustering and dimensionality reduction techniques, offers a promising framework for decoding high-dimensional RNA sequence structures and uncovering latent...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...://great.stanford.edu/) was used to map DETEs to nearby genes (5 kb upstream of to 1 kb downstream from the TSS, with distal extension up to 1000 kb). Enriched GO terms were extracted from GREAT output.Visualization of TE-chimeric transcriptsbigWig files were generated from BAM files using deepTools v3.5.6 (Ramírez et al. 2014...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
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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
..., Sichuan 8 University, Chengdu, Sichuan, 610041, China 9 3. Deep Underground Space Medical Center, West China Hospital, Sichuan University, 10 Chengdu, Chengdu, Sichuan, 610041, China 11 12 # These authors contributed equally 13 * Corresponding author 14 E-mail: danxie@scu.edu.cn (DX), liujifeng777@wchscu...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...trained a deep neural network, which pinpointed the causal variant for strong effect variants with >90% accuracy. Taken together, this study provides a functional assessment of the sequence requirements for the occupancy of four essential regulators and identifies new dependency relationships...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...organization. Effector-like SSPs showed no significant enrichment within TE hotspots (sample size = 8701; X2 = 1.6749, P = 0.25).Chromoviridae-related Gypsy elements dominate the repeat landscape in the Chinese white truffle Because of the significant contribution of Gypsy elements to the high TE content...
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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
..., oviduct shell gland, and spleen, along with matched whole- sequencing data from 307 egg-laying ducks. We map cis-regulatory variants associated with gene expression (eQTL), alternative splicing (sQTL), and 3′ alternative polyadenylation (apaQTL), yielding 14,074, 6267, and 4994 genes with at least one...
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Research: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai,
- Peipei Bian,
- Dexiang Hu,
- Funong Luo,
- Yongzhen Huang,
- Shaohua Jiao,
- Xihong Wang,
- Mian Gong,
- Ran Li,
- Yudong Cai,
- Jiayue Wen,
- Qimeng Yang,
- Weidong Deng,
- Hojjat Asadollahpour Nanaei,
- Yu Wang,
- Fei Wang,
- Zijing Zhang,
- Benjamin D. Rosen,
- Rasmus Heller,
- and Yu Jiang
Genome Res. August 2023 33: 1284-1298; Published in Advance September 15, 2023, doi:10.1101/gr.277481.122
...A Chinese indicine pan reveals a wealth of novel structural variants introgressed from other Bos species Xuelei Dai1,8, Peipei Bian1,8, Dexiang Hu1,8, Funong Luo1,8, Yongzhen Huang1,8, Shaohua Jiao1, Xihong Wang1, Mian Gong1, Ran Li1, Yudong Cai1, Jiayue Wen1, Qimeng Yang1, Weidong Deng2, Hojjat...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...for false discovery rate (FDR). BAM files were converted to bedGraph format using deepTools (version 3.5.2) (Ramírez et al. 2016). The genomic coordinates of the exons for each transcript were extracted from the BED12 files, which were generated by converting the GTF file with AGAT (version 1.1.0) (Dainat...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...SVs are difficult to identify using short-read sequencing (Sakamoto et al. 2020). Although previous studies have revealed distinct mechanisms in the generation of germline and somatic SVs in liver cancer by analyzing complete breakpoint sequences derived from long reads, the -wide landscape of somatic...
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