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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
...and gene paralogs were grouped when they shared protein domains predicted to have equivalent functions because they belong to the same functional family in the CATH database (Sillitoe et al. 2015; Das et al. 2015b). These mutations can be mapped to a single 3D structural representative. Known functional...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...the ability of random proteins to confer beneficial phenotypes but allow direct tests of hypotheses about the transition to functionality during de novo gene birth. For example, the functional peptides identified by Knopp et al. (2019) were all membrane-associated, which coheres to the “transmembrane...
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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
...network approaches have been proposed to characterize gene interactions and dissect the regulatory relationships underlying tumorigenic pathways (Creixell et al. 2015). Gene coexpression networks are a mathematical model that assumes functionally related genes are coregulated as a cellular system and can...
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Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
- Shan Lu and
- Sunduz Keles
Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
...analysis of multiple differentiating human induced pluripotent stem cell (iPSC) lines yields biologically coherent gene groups that are associated with iPSC differentiation efficiency. Application with population-scale scRNAseq of oligodendrocytes from postmortem human tissues of Alzheimer’s disease...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...enriched in the protein cluster depicted in E.Another interesting group are orthologs that were only detected in the Caenorhabditis genus (568 orthology groups). These proteins are enriched with various knockout phenotypes and Gene Ontology terms reflecting functions in cell division (Supplemental Table S8...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...encompass genes displaying similar expression dynamics, suggesting that physical association is functionally relevant for the control of transcriptional activity (Dekker and Heard 2015). Higher-resolution studies have shown that TADs can be further subdivided into compartmental domains, which formation...
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Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
...metabolism and intracellular signaling when the estradiol and blank groups were considered, but not when the testosterone group was included (Fig. 2H).Overall, the gene coexpression network analysis offered clearer patterns of tissue specificity and functional specificity of each sex-biasing factor compared...
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Method: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
- Brendan F. Miller,
- Dhananjay Bambah-Mukku,
- Catherine Dulac,
- Xiaowei Zhuang,
- and Jean Fan
Genome Res. October 2021 31: 1843-1855; Published in Advance May 25, 2021, doi:10.1101/gr.271288.120
...with the pairwise distances between cells. SPARK identifies spatial gene expression heterogeneity that best fits the observed gene expression trends using multiple linear spatial models based on different Gaussian and periodic kernel functions that incorporate distances between cells. Thus, each method directly...
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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
...that the final correlation threshold λ effectively distinguishes biologically relevant correlated gene groups. Because geneCover provides functionality to monitor λ in the package, users can empirically determine suitable values based on their data set. Our proposed iterative approach also naturally supports...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...as a fundamental technique for characterizing the functional state of individual cells. Complementary to scRNAseq, single-cell DNA methylation (scDNAm) sequencing provides -wide maps of epigenetic modifications at single-cell resolution, offering insights into the regulatory mechanisms underlying gene expression...
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