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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
...applied distinct approaches both to the identification of drivers (i.e., by predicting FIEs) and to their analysis with respect to gene duplication.FunVar was designed to detect mutations with impacts on functional sites, predict rare drivers, and provide insights into the structural and functional...
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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. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
..., ontology analysis confirmed that these variant genes are associated with processes regulating the cell cycle progression (Fig. 5E; Supplemental Fig. S7). Notably, the number of cell cycle regulated genes is substantially smaller than previous reports based on synchronized cells. Exemplary PARTAGE tracks...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...×E) interactions—that is, response eQTLs—might create situations where VG calculated on baseline data will not fully capture genetic variability under a different cell state. However, major G×E effects affect a relatively small number of genes (Manuck and McCaffery 2014; Kim-Hellmuth et al. 2017; Wang et al. 2019...
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Resource: PWAS Hub for exploring gene-based associations of common complex diseases
- Guy Kelman,
- Roei Zucker,
- Nadav Brandes,
- and Michal Linial
Genome Res. October 2024 34: 1674-1686; Published in Advance October 15, 2024, doi:10.1101/gr.278916.123
...a similar case-control design, while restricting the variants to the coding region (coined coding GWAS, cGWAS). A total of 639,323 imputed variants (out of the 97,013,422 imputed variants) were included for analysis across the 18,053 protein-coding genes. Note that the set of variants used by PWAS and c...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...The grasshopper reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution Xinghua Li1,2, Judith E. Mank3 and Liping Ban1 1Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University...
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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
..., highlighting the extensive gene interactions within organisms. Therefore, we propose scHGR, an automated annotation tool designed to leverage gene regulatory relationships in constructing gene-mediated cell communication graphs for single-cell transcriptome data. This strategy helps reduce noise from diverse...
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Method: Predicting genotype-specific gene regulatory networks
- Deborah Weighill,
- Marouen Ben Guebila,
- Kimberly Glass,
- John Quackenbush,
- and John Platig
Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
...(hg38) for future analyses. By design, EGRET can be applied to data of any reference provided that the positions of variants, eQTLs, gene promoters, and motifs are all mapped to the same reference . However, we note that, whereas there are some differences between hg19 and hg38, the key elements...
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Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
- Peng Xu and
- Bin Zhang
Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
...by comparing normalized gene expressions between tumor and normal tissues in 17 cancer types. We performed differential expression analysis using the moderated t-test implemented in the limma package (Ritchie et al. 2015). Patient age, gender, and race were treated as covariates in the design matrix. We...
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Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
...−3, hypergeometric test), suggesting there is a core set of eQTLs identified across study designs and cell states. However, genes containing context-dependent eQTLs did not overlap with GTEx LCL eGenes (P = 0.465), suggesting that our cellular perturbations revealed previously uncharacterized genetic effects on gene...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...functional properties of PSGs.ResultsGenTree is an integrated database for new genes in the human As a new-gene–focused database, GenTree is designed to enable users to evaluate when and how a gene arises and what type of function it may have (Fig. 1).View larger version: In this window In a new window...
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