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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...incidence (Egi et al. 2016). Conversely, in N. vitripennis, down-regulation of DNA methyltransferases enhanced diapause (Pegoraro et al. 2016). Additionally, the expression of multiple genes regulating histone methylation and acetylation changed with diapause (Reynolds et al. 2013, 2016). In Helicoverpa...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...and gene regulation.For Repli-seq analysis in PARTAGE, we took advantage of our optimized Repli-seq workflow, which reduced DNA loss and technical noise by minimizing transfer/handling steps, and increasing yields by 3× (Rivera-Mulia et al. 2022). We also applied the multifraction Repli-seq approach...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...Highly efficient and scarless editing via essential gene-coupled 1 homology-directed repair 2 Running title: Efficient scarless editing via essential gene HDR 3 4 Joo Hye Yeo1,2,3, Hyongbum Henry Kim2,3,4,5,6,7,8,9, Sang Ho Oh10, Jinu Lee1,* 5 6 1College of Pharmacy, Yonsei Institute...
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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...labels are transferred from well-annotated scRNA-seq data to less-annotated omics data, such as scATAC-seq. This approach leverages the gene expression profiles available in scRNA-seq to help annotate common cell types and even novel cell types for other omics data. However, the heterogeneous features...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
..., USA ↵10 Present address: Department of Biological Sciences and Ray and Stephanie Lane Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA Corresponding author: charles.gersbach@duke.eduAbstractA hallmark of heart disease is gene dysregulation and reactivation...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...). However, because MGEs are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short term and long term. By combining comparative...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole- doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regulation can be inferred from experimentally measured changes in chromatin accessibility at carefully selected gene loci. For this purpose, Förster resonance energy transfer combined with fluorescence in situ hybridization (FRET-FISH) was recently developed (Mota et al. 2022). This method takes advantage...
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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
...2016; Metzger et al. 2018; Galbraith et al. 2020; Gozashti et al. 2022, 2025; Hassan et al. 2024). There is also evidence supporting transfers of natterin-like toxin encoding genes involving marine animals (Gacesa et al. 2020), and the only known case of gene HT between vertebrates involves marine...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...Revisiting models of enhancer–promoter communication in gene regulation Gilad Barshad1,2 and Charles G. Danko1,2 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA; 2Department of Biomedical Sciences, College of Veterinary Medicine...

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