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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
..., Stanford University School of Engineering, Stanford, California 94305, USA Corresponding author: geleta@berkeley.eduAbstractModern biobanks are providing numerous high-resolution genomic sequences of diverse populations. In order to account for diverse and admixed populations, new algorithmic tools...
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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
...a signalling cascade leading to the 65 phosphorylation of the Janus kinases Tyk2 and JAK1, as well as the “signal transducers and 66 activators of transcription” STAT1 and STAT2 (Platanias, 2005). These phosphorylated 67 STAT1 and STAT2 molecules then bind with a third subunit, interferon regulatory factor 9...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...concatenations) will be filled with random nucleotides. Third, we concatenated multiple copies of the repeat unit to generate a longer sequence, with the frequency of units being three, five, 10, and 20. Fourth, we introduced random errors at rates of 10% and 20%. Fifth, at the end, we inserted random strings...
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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
...with interpretability because of its black-box nature. Here, we evaluate 12 ML models alongside GBLUP and BayesR to identify key factors influencing genomic prediction performance across traits with different genetic architectures in multiple agricultural species, including pigs, chickens, horses, and maize, and we use...
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Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
..., which is consistent with recent experimental results for the aging effect such as neuron function loss in the mouse brain (Stanley et al. 2012; Oh et al. 2022). The third-ranked cell type is NSC, which was reported by the original spatial aging clock paper as an informative cell type. Moreover, we also...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...approach, allows for the investigation of the binding of multiple TFs. The DNA sequences obtained from these methodologies provide crucial biological insights into TF activities, such as their DNA-binding specificities. Furthermore, DNA sequencing is also utilized to study the effect of gene editing...
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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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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
..., if their sum of IBD sharing surpassed a minimum threshold of 6 cM. Third, we generated an adjacency matrix representation of this graph. Lastly, we calculated the spectral components of this matrix as SPCs. To conduct comparative analysis, we further calculated alternative PCs of this graph, along with the PCs...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...Chromosomes, suggesting that multiple chromosome splits or joins have happened in the S. lineatus lineage or that chromosome joins have occurred after the split with S. lineatus in the common ancestor of the other species (Table 1). We found that the third X Chromosome (Chr X3) in S. lineatus appears...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...of the challenges facing the current methods, including DeltaSplice, in learning tissue– or cell type–specific splicing, despite extensive efforts in recent studies (Cheng et al. 2021; Zeng and Li 2022; Celaj et al. 2023). Third, although we demonstrated the benefits of longer input sequences and larger networks...
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