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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...: Genes in the genomic regions corresponding to those in Figure 2; APG, MHC-II, extended class II, and framework genes are indicated as colored blocks; MHC-I genes are shown individually; the width of the rectangles indicates gene lengths; filled rectangles below MHC-I genes show the maximum relative...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...partitioned dnSNVs by flanking nucleotide context and assigned spectra to known mutation signatures (Alexandrov et al. 2020). The resulting trinucleotide mutation count matrix is sparse, with seven of 96 mutation classes with no observable dnSNVs in either cohort and with 28 mutation classes featuring dn...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...). The samples from the Sea of Japan side have lower α-values than those from the Pacific Ocean side. When the sample from Okinawa (a subtropical island) was excluded and the other samples were divided into two classes according to the central watershed of Japan, the Pacific-side samples had significantly higher...
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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
...exhibit 532 heterogeneous distribution patterns, with some, such as finTRIMs, in gene groups dispersed 533 across the while others, including MHC class I genes, form a few or a unique cluster 534 on a specific location (Van der Aa et al., 2009; Lukacs et al., 2010). These findings 535 underscore...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...characterize these complex regions to gain insight into the impact of genomic diversity on health and disease. Here we resolve the organization of complete major histocompatibility complex (MHC) class II regions in rhesus macaques by using a long-read sequencing strategy (Oxford Nanopore Technologies...
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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
...(Roberts 2011). The term ancestry refers to a class of genetic similarity that can be associated with a shared origin (Xie et al. 2001; Fujimura and Rajagopalan 2011). The framework for classifying or regressing genetic ancestry uses the sequence for its features (Nelson et al. 2018). Indeed, an individual...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...when corresponding single-cell data are not available. To verify the applicability of our devised signature in bulk tumors, we used RNA-seq from The Cancer Genome Atlas (TCGA) data sets and scored both our cancer-cell EMT and hallmark EMT signatures.Scores of the ANS-derived signature showed higher...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...contributor to isoform diversityTo analyze the characteristics of the gene loci that contribute significantly to the overall isoform diversity, we classified all the detected gene loci into three roughly similar-sized classes based on their splicing isoform numbers (Fig. 5A): (i) few-isoform genes (FG...
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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
...as an example.We evaluated the top 20 features via average SHAP values (Fig. 4A, presented in descending order) and found a correlation D E Figure 2. Prediction accuracy comparison using real and simulated data. (A–C) Real data categorized into three classes, employing GBLUP (dark blue dashed line) and Bayes...
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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
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...

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