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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...k-mer cross-species profiling reveals taxon-specific TE expansions accompanied 1 by KZFP co-option and functional impacts in ruminants 2 3 Pengju Zhao1,2*, Jiayi He1,2, Chen Peng1,2, Yuelang Zhang1,2, Chong Wang1,2, 4 Dongyou Yu1,2, Lingzhao Fang3*, Zhengguang Wang1,2* 5 6 1Hainan Institute...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
..., Houston, Texas 77030, USA; 6Department of Computer Science and Engineering, University of Michigan, Ann Arbor, Michigan 48103, USA ↵7 These authors contributed equally to this work. Corresponding authors: Xiaotian.Zhang@uth.tmc.edu, drjieliu@umich.eduAbstractChromatin stripes are architectural chromatin...
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Method: Automated interpretable artificial intelligence genomic prediction with AlGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...on phenotypic variation, uncovering interactions between loci and samples within a population, as well as the roles of individuals and loci in population-level decision making. For a given SNP j, its encoded genotype (0/1/2) for each individual is substituted into the SHAP formulation to estimate how the model...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...currently driving issues in a universal manner. In addition, from a methodological perspective, existing strain-level profiling methods rely solely on plain linear reference s. This common limitation prevents them from effectively capturing and representing genetic variations among strains within a species...
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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
...tasks, including identifying active regulatory elements and interpreting disease-associated genetic variation. However, despite the widespread applications of SAGA methods, no principled approach exists to evaluate the statistical significance of chromatin state assignments. Here, we propose the first...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...opportunities to uncover novel genomic and epigenomic mechanisms implicated in disease. Sequencing reads generated by LRS not only detect single nucleotide variations (SNVs) and structural variations (SVs) but also probe previously uncharacterized repetitive regions and regions with atypical GC content...
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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
...tracks. Although these methods are highly accurate, this coarse formulation (i.e., predicting chromatin accessibility profiles at 128bp or lower resolution) is still insufficient to study local changes in chromatin accessibility caused by point mutations. Moreover, it hinders their applicability...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...model exhibited slight enrichment (FDR=0.04), suggesting a more specific association between aging-related transcriptional changes and PD pathology. A C D EB F G Figure 2. Profiling of age-associated gene expression variations across substantia nigra cell subclasses. (A) UMAP representation of all...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...of Ash1 and Set2 to H3K36me3To investigate the roles of Ash1 and Set2 in H3K36me3 and transcriptional regulation, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to profile H3K36me3 distribution in PH-1, Δset2, and Δash1 strains. In PH-1, we identified 8390 significant H3K36me3 peaks...
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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
...samples, with breakpoint variations confined within 10 bp. Short-read sequencing in the samples failed to detect this DEL, primarily due to the tandem-repeated Alu sequences present within the corresponding region of the reference (Supplemental Fig. S10A,B).To assess the functional impact...
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