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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
..., compression, classification, and simulation of genomic data with several worldwide whole data sets from both humans and canids, and evaluate the performance of the proposed applications with and without ancestry conditioning. The unsupervised setting of autoencoders allows for the detection and learning...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...increased, opening exciting new avenues for studying human evolution. Here, we review recent methodological advances in the study of archaic introgression. We begin by providing an overview of the genealogical and genomic signatures left behind by introgression events before reviewing recent methods...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...algorithm tuning. Subsequently, the SHAP method was introduced to 93 assess the effects of genomic variants and generate effect distribution maps of SNPs at the 94 individual, site, and population levels. This study developed a comprehensive set of AI 95 prediction toolkits that integrate feature selection...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...D3 mappings fall within the lowest 3% of the permutations (red line), suggesting a nonrandom association between TBC1D3 and breakpoints in synteny. (D) Synteny plot showing orthologous alignments between human TBC1D3 and mouse lemur flanking genomic sequence.To test if the association with TBC1D3...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.The imperfection of DNA replication serves as a source of variations for evolution and biodiversity (Nei 2013). Such genetic variations underpin...
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Method: spRefine denoises and imputes spatial transcriptomics 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 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...selected124 based on the imputed HEST-1k data Jaume et al (2024) to better predict survival or125 disease states of patients from The Cancer Genome Atlas (TCGA) database Wein-126 stein et al (2013). Our results show the strong capacity of spRefine in transferring127 the learned knowledge to biomedical data...
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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
...stimulation. We identified a set of 197 ISGs with regulatory elements showing increased 23 chromatin accessibility and H3K27ac signal in concert with increased gene expression in 24 response to poly I:C. Fifty-four of these genes were conserved ISGs in rainbow trout, 25 zebrafish, and human. Our analysis...
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Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
- An Wang,
- Stephanie Hicks,
- Donald Geman,
- and Laurent Younes
Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
...Methods for details of data set processing and marker panels generation from other label-free methods): The DLPFC data set (Maynard et al. 2021) offers spatial mapping of gene expression across the six layers of the human dorsolateral prefrontal cortex using the 10x Genomics Visium platform. With manual...
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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
...). These findings suggest that C. nigoni populations may experience substantially higher selection pressure from pathogens in their native environments compared with C. briggsae populations.Genes encoding Cullin-E3 ubiquitin-ligase-adaptors are major contributors to both gene family and genomic sequence divergence...
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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
...Ruhollah Shemirani1, Gillian M. Belbin1,9, Sinead Cullina1,2, Christa Caggiano1, Christopher R. Gignoux3,4, Noah Zaitlen5,6,7 and Eimear E. Kenny1,2,8 1Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 2Department of Genetics and Genomic Sciences...
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