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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
...those not residing 296 inside centromeres clustered in close proximity, with 62.7% found within 1 Mb of 297 centromeric regions (Wilcoxon test, p-value < 0.001, Supplemental Fig. S4D). This 298 pericentromeric enrichment pattern was further confirmed by re-alignment of 299 Chromosome 20 reads...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of a terminal distal deletion and an inverted duplication proximal to the Chromosome 8 centromere, termed invdupdel(8p) (Santucci et al. 2025). This rearrangement arises from aberrant pairing and recombination events during meiosis, which may be owing to the presence of the beta-defensin repeats and olfactory...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...–specific regulatory features that underlie chromatin accessibility.View larger version: In this window In a new window Figure 4. Interpreting sequence features underlying model predictions. (A–D) Proportion of identified transcription factor motifs in different cell lines: (A) GM12878, (B) K562, (C) IMR-90, and (D...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...SC-specific transcriptional, chromatin, and replication landscapes.scRNA-seq profiling of GSC-like and CySC-like cellsWe performed scRNA-seq on nanos- and tj-driven Upd-overexpressing tumor samples (upd tumors), with two replicates each. Across these four samples, we consistently identified distinct germline and somatic...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
..., is the primary determinant of 304 these degradation patterns. Additional examples of transcripts showing similar RNA 305 dynamics across the cell lines are shown in Supplemental Fig. S7A. However, we 306 identified exceptions in which transcripts exhibited cell type-specific RNA stability 307 trajectories (Fig...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...,877, and 5687, respectively. Training and independent test data sets were split as shown in Supplemental Table S1.Overview of the EnDeep4mC architectureThe EnDeep4mC framework employs a dual-phase architecture for species-model co-optimization: (1) a dynamic feature selection (DFS) module identifies optimal...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...with the up- and downregulation of genes and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity, and we leverage these features to reconstruct chromatin...
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Corrigendum: Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere
- Lee H. Wong,
- Kate H. Brettingham-Moore,
- Lyn Chan,
- Julie M. Quach,
- Melissa A. Anderson,
- Emma L. Northrop,
- Ross Hannan,
- Richard Saffery,
- Margaret L. Shaw,
- Evan Williams,
- and K.H. Andy Choo
Genome Res. June 2024 34: 979-980; doi:10.1101/gr.279693.124
...for the ribosomal genes 5S and 18S were decreased following ActD treatment, but the signals for the transcription of RNA polymerase II-driven genes (such as GAPDH, beta-actin, and alpha-tubulin) and those of α-satellite DNA (pTRA7 [chromosomes 13/14/21-specific], αXT [chromosomes 14/22-specific], and α...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...cohort. These selected SNPs, referred to as feature SNPs, effectively capture the breed diversity and serve as useful tools for breed differentiation and ancestry inference. The widely used selection methods in previous studies involve identifying the most distinguishing features based on typical...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...the advantage of the PacBio HiFi reads in assembly of highly repetitive s. To investigate the quality, we also quantified the satellite DNA distribution along each chromosome (Supplemental Fig. S1). The most dominant satellites are LmiSat02A-176 and LmiSat27A-57. In addition, we identified several centromere...

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