Searching journal content for articles similar to Feng et al. 19 (7): 1214.

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  1. 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
    ...A; Supplemental Fig. S10). Luciferase reporter plasmids containing the full-length HBx-SINE or the truncated mutant sequences were constructed, and a dual-luciferase reporter assay was performed to verify the effect of HBx-SINE (Supplemental Table S5). The results revealed that HBx-SINE exerted...
  2. 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
    ...motif and coding sequences. METTL2A knockdown alters expression of S100A4 mRNA isoforms, which contains METTL2A-mediated m3C sites. Notably, many transcripts with METTL2A-mediated m3C sites are upregulated upon METTL2A knockdown. We reveal the transcriptome-wide presence of m3C sites in poly(A) RNA...
  3. Research: Loss of multilevel 3D genome organization during breast cancer progression
    • Roberto Rossini,
    • Saleh Oshaghi,
    • Maxim Nekrasov,
    • Aurélie Bellanger,
    • Renae Domaschenz,
    • Yasmin Dijkwel,
    • Mohamed Abdelhalim,
    • Rahul Agrawal,
    • Marit Ledsaak,
    • Philippe Collas,
    • Ragnhild Eskeland,
    • David Tremethick,
    • and Jonas Paulsen
    Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
    ...is accompanied by the formation of de novo enhancer contacts and activation of MYC, illustrating how structural genomic variants can alter the 3D during oncogenesis. In summary, our findings provide evidence for the loss of organization at multiple scales during breast cancer progression, revealing novel...
  4. 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
    ...and is expected to improve the interpretation of transcriptomic data in future genomic studies.RNA sequencing (RNA-seq) has become an essential tool for characterizing transcriptomes (Stark et al. 2019), enabling comprehensive profiling of gene expression, including tissue-specific patterns, disease...
  5. Method: CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
    • Kaiyuan Zhu,
    • Matthew G. Jones,
    • Jens Luebeck,
    • Xinxin Bu,
    • Hyerim Yi,
    • King L. Hung,
    • Ivy Tsz-Lo Wong,
    • Shu Zhang,
    • Paul S. Mischel,
    • Howard Y. Chang,
    • and Vineet Bafna
    Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
    ...-stage cancers. ecDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies...
    OPEN ACCESS ARTICLE
  6. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    .../bar030 ↵Kozomara A, Birgaoanu M, Griffiths-Jones S. 2019. miRBase: from microRNA sequences to function. Nucleic Acids Res 47: D155–D162. doi:10.1093/nar/gky1141 ↵Lai EC, Tomancak P, Williams RW, Rubin GM. 2003. Computational identification of Drosophila microRNA genes. Genome Biol 4: R42. doi:10.1186/gb...
  7. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
  8. Research: Stable genome structures in living fossil fishes
    • Cheng Wang,
    • Chase D. Brownstein,
    • Wenjun Chen,
    • Zufa Ding,
    • Dan Yu,
    • Yu Deng,
    • Chenguang Feng,
    • Thomas J. Near,
    • Shunping He,
    • and Liandong Yang
    Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
    ...the new s, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus, 83.35% of the s remain identical even though they diverged over 100 million years ago. Genome size variation among gars...
  9. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ..., the clearest one against GA-rich repeats in the human . However, our study reveals a systematic failure of both technologies to sequence and assemble specific exons of Drosophila melanogaster genes, indicating an overlooked limitation. Namely, multiple Y-linked exons are nearly or completely absent from raw...
  10. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    ...surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. Microb Genom 9: mgen000936. doi:10.1099/mgen.0.000936 ↵Fox EJ, Reid-Bayliss KS, Emond MJ, Loeb LA. 2014. Accuracy of next generation sequencing platforms. Next Gener Seq Appl 1: 1000106. doi:10.4172/jngsa.1000106 ↵Fu P, Zhou J...
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