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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
...mutation cluster or hotspot (35% of cases; significance level of 5%). The majority of cases in which mutations were not clustered occurred in tumor-suppressor genes (TP53, PTEN, and VHL) (Supplemental Note 1; Supplemental Fig. 14), which acquire loss-of-function variants across a larger proportion of sites...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...), and we looked for repeated amino acid evolution in coding sequences of kidney-expressed genes. Second, we evaluated the influence of species relatedness and of the age of the transitions on these signals (Fig. 1B). For this, we applied a variety of methods (Fig. 1C).View larger version: In this window...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...genomics. Early works in molecular biology on gene expression were limited, because purified RNA is unstable and difficult to work with. However, the discovery (and use in the laboratory) of reverse transcriptase, permitting the controlled synthesis of RNAs into cDNAs (Maniatis et al. 1976...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...of the paerucumarin biosynthesis gene cluster showed the strongest and most consistent effect (Supplemental Fig. S4). Closer examination of the presence of these genes in our data set revealed that these orthologs are exclusively present in some strains of the genus Serratia. Because the paerucumarin gene cluster has...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...in the evolution of these genes, we identified all chimeras derived from HLAU genes in head and larval transcriptomes. We found a total of 28 (head) and 24 (larvae) HLAU genes producing chimeric transcripts. Although D. buzzatii had 11-fold fewer chimeras than did species from the mojavensis cluster, we observed...
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Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Anna K. Pöntinen,
- Sergio Arredondo-Alonso,
- Stephen D. Bentley,
- and Jukka Corander
Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
.../absence of genes in prokaryotic s is a complex and error-prone process. Annotation and clustering errors, as well as sampling bias and differences in the underlying population structure of strains and species, can all complicate the analysis of pan dynamics. To address these problems, we developed Panstripe...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-C heatmap based on the strong inter-chromosomal contact peaks (“bowtie” shapes) caused by Rabl centromere clustering (Fig. 1B; Varoquaux et al. 2015; Muller et al. 2019). These interaction sites were enriched for TEs and overlapped with gene-sparse regions spanning hundreds of kilobases (Figs. 1A, 2A...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...of the fifth carbon atom of cytosine, typically in mammals in a CG dinucleotide context. This dinucleotide is depleted largely across the and found predominantly in clusters known as “CpG islands” (Bird 1986). Cytosine methylation is catalyzed by methyltransferases (e.g., DNMT1, DNMT3A) that transfer a methyl...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...to the evolution of gene regulatory networks in mammals (Imbeault et al. 2017; Senft and Macfarlan 2021), we first evaluated the amino acid sequence similarity of mouse and human KZFP proteins across mammalian species using the BioMart web tool. Notably, a subset of mouse KZFPs was present only in mice...

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