Searching journal content for articles similar to Pozzoli et al. 13 (5): 764.

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  1. Method: Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
    • Xinxin Wang,
    • Ryan Christ,
    • Erica Young,
    • Chul Joo Kang,
    • Indraniel Das,
    • Edward A. Belter, Jr.,
    • Markku Laakso,
    • Louis J.M. Aslett,
    • David Steinsaltz,
    • Nathan O. Stitziel,
    • and Ira M. Hall
    Genome Res. April 16, 2026 ; Published in Advance April 16, 2026, doi:10.1101/gr.280372.124
    ...the screening, we identified loci of interest as genomic regions with one or more variants with significant P-values by either LOCATER or SMT in any of the 101 traits. To compare LOCATER and SMT signals at these loci, we defined a common shared association interval bymerging the set of significantly associated...
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  2. Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
    • Isabela T. Pereira,
    • Izabela Mamede,
    • Paulo P. Amaral,
    • Gloria R. Franco,
    • and John L. Rinn
    Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
    ...and 861 GET genes in mice, we observed 113 genes in common. This suggests that intron retention and sedimentation patterns are conserved properties likely related to the formation of stable RNPs by specific RNA isoforms.View larger version: In this window In a new window Figure 3. Intron retention events...
  3. 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
    ...maximum or slightly offset. To quantify this property, we performed a systematic robustness test on all ConvNeXt-based models, measuring the variation in predicted ATAC-seq signal across common genomic regions when the input window is shifted (Toneyan et al. 2022) (Supplemental Fig. S4). For each ATAC...
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  4. 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
    ...with multiple breeds or varieties.DiscussionIn this study, we introduced HITSNP, a stable, effective, and automated tool for screening feature SNPs representing breed diversity from high-throughput data. Compared with four common filter methods, the feature SNPs selected by HITSNP algorithms provided a precise...
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  5. 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
    ..., and the complete training protocol, enabling exact replication of the model architectures and experimental results.Feature encoding schemesMore than 24 common feature encoding schemes are widely used in epigenetic site prediction. In the work of EpiTEAmDNA, Li et al. (2023) demonstrated that 10 feature encoding...
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  6. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    ...computational toolkit for genotyping the variable genes of the IG lambda and kappa, and the TR loci with short-read whole sequence data, using an integer linear programming formulation, as an update to the ImmunoTyper-SR suite, which focused on IGHV region only. We evaluate its genotyping performance using...
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  7. Research: Systematic identification and characterization of exon–intron circRNAs
    • Yinchun Zhong,
    • Yan Yang,
    • Xiaolin Wang,
    • Bingbing Ren,
    • Xueren Wang,
    • Ge Shan,
    • and Liang Chen
    Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
    ...RNAs (EIciRNAs) are a circRNA subclass with retained introns. Global features of EIciRNAs remain largely unexplored, mainly owing to the lack of bioinformatic tools. The regulation of intron retention (IR) in EIciRNAs and the associated functionality also require further investigation. We developed...
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  8. Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
    ...and detection of modified nucleotides. Also, the extent to which SVs act as methylation quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pan graph summarizing SVs in 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that are absent...
  9. Research: Transposon accumulation at xenobiotic gene family loci in aphids
    • Tobias Baril,
    • Adam Pym,
    • Chris Bass,
    • and Alex Hayward
    Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
    ...examining the contribution of TEs to resistance evolution suggest that there can be an additive effect of successive TE insertions at focal host loci over time. For example, in the well-known case of the CYP gene CYP6G1 and DDT resistance in Drosophila, successive TE insertions are linked with an increasing...
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  10. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
    ...-coding SHROOM3 variants and CFM-associated expression quantitative trait loci (eQTLs) of SHROOM3 expression. Further investigations implicate specific eQTL combinations, such as rs1001322 or rs344131, in combination with other significant CFM-associated eQTLs, which we term combined eQTL phenotype modifiers (Ce...
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