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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...in the preimplantation embryo, allowing the formation of totipotent cells. The paternal undergoes rapid demethylation before the first DNA replication, owing, at least in part, to the action of the TET3 methylcytosine dioxygenase (Shen et al. 2014). In contrast, the maternal undergoes passive demethylation during...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...of origin). Some widely adopted techniques include ADMIXTURE (Pritchard et al. 2000; Alexander et al. 2009), a clustering technique based on probabilistic non-negative matrix factorization, and its more recent neural counterpart—Neural ADMIXTURE (Dominguez Mantes et al. 2023); Locator (Battey et al. 2020...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...and biochemical studies revealed that condensins play a more complex role during the rapid cell cycle of mouse embryonic stem cells (mESCs) (Fazzio and Panning 2010). It has been shown in Xenopus leavis that mitotic chromosomes from sperm nuclei are folded as long and thin structures but become increasingly...
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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
...of heritability explained by QTLs (blue; n = 7); and (III) traits with low heritability and a low or negligible proportion of heritability explained by QTLs (yellow; n = 9). Wei et al. 2 Genome Research www..org QTLs using a bivariate genetic relationship matrix (GRM) model. We hypothesized that the presence...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...this growing volume of bacterial data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...examples like histone genes (Maxson et al. 1983), rDNA arrays (Hall et al. 2022), and immunoglobulin genes (Watson and Breden 2012). Tandem repeats are prone to rapid copy number changes mediated through mechanisms such as unequal crossing over, replication slippage, gene conversion, and intrachromatid...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...in the centromeric regions of Dt1BS (left), Dt6BS (middle), and Dt7AS (right), compared to their corresponding regions in CS wheat. Neocentromeres and their syntenic positions in CS are highlighted in gray. IGV snapshot showing DNA methylation levels (CG, CHG, and CHH contexts), gene annotations, and genomic...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...and the translocation of one of its members, Cni-neib-1, to the center of Chr IV (Xie et al. 2024), we initially anticipated that the genomic region encompassing Cni-neib-1 would also exhibit rapid evolution. Unexpectedly, the ∼40 kb region surrounding Cni-neib-1 is invariant (>99% sequence identity) across both the c...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...in an accessible chromatin state, 456 allowing for rapid transcriptional activation upon stimulation (Bahrami and Diablos, 2016). 457 Alternatively, these genes may be regulated post-transcriptionally following poly I:C 458 stimulation, a mechanism often observed in innate immune responses, which could involve 459...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
.... The eigenvectors corresponding to the smallest eigenvalues of this matrix comprise the set of SPCs.Evaluating performance to detect fine-scale population structure on a simulated data setTo evaluate the performance of SPCs for capturing fine-scale population structure in genomic data sets, we first simulated...
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