Searching journal content for articles similar to Kaessmann 20 (10): 1313.

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  1. 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
    ...show that this convergent evolution in cell proportions globally impacts the transcriptome. First, variation in cell proportions correlates with coexpression modules: Modules upregulated in arid species correlate positively with cell populations whose proportions are enriched in these species...
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  2. 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
    ..., to predict mutations with likely functional impact and to capture putative rare driver events occurring later in lung tumor evolution. However, definitive proof that specific FIEs drive tumor progression and the underlying mechanisms require detailed experimental characterization.Other methods have used PPI...
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  3. 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
    ...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
  4. 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
    ...Evolution of -wide methylation profiling technologies Carolina Montano1,2 and Winston Timp1 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia...
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  5. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...). These results are consistent with previous reports that the HBV can be fragmented and integrated into the human in different orientations continuously at the same site (Zhuo et al. 2021). HBV integration is an early driver of tumor progression (Duan et al. 2018). We speculate that during clonal evolution, HBV...
  6. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ...genic elements (promoters, introns, exons) and regulatory features (CGIs, TFBS, enhancers) within the same DMR in order to elucidate their impact on gene expression and phenotypes.At present, few tools have been developed for annotating genomic intervals to genic and regulatory elements, including Gold...
  7. Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    ...origin of SSOGs (Fig. 1) to understand whether they originate mostly externally, as suggested before, and to search for evidence of de novo evolution.ResultsSSOGs are widespread in pans of human gut prokaryotesTo study prokaryotic SSOGs (Fig. 1), our first goal was to establish a conservatively defined...
  8. Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
    • Laura E. Tibbs-Cortes,
    • Tingting Guo,
    • Carson M. Andorf,
    • Xianran Li,
    • and Jianming Yu
    Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
    ...plasticity plays an important role in evolution of wild species, suggesting that it may also be an important origin of diversity for breeding in domestic species. In “plasticity first evolution,” changes in the environment give rise to a new phenotype via plasticity. Selection then acts on this new phenotype...
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  9. Perspective: The impact of long-read sequencing on human population-scale genomics
    • Tobias Rausch,
    • Tobias Marschall,
    • and Jan O. Korbel
    Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
    ...and disease diagnostics. DNA methylation signals directly obtained from long reads enhance the utility of single-molecule long-read sequencing technologies by enabling molecular phenotypes to be interpreted, and by allowing the identification of the parent of origin of de novo mutations. Despite this recent...
  10. Research: Evidence for compensatory evolution within pleiotropic regulatory elements
    • Zane Kliesmete,
    • Peter Orchard,
    • Victor Yan Kin Lee,
    • Johanna Geuder,
    • Simon M. Krauß,
    • Mari Ohnuki,
    • Jessica Jocher,
    • Beate Vieth,
    • Wolfgang Enard,
    • and Ines Hellmann
    Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
    ...Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, USA; 3Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark; 4Department of Hematology, Cell Therapy, Hemostaseology and Infectious...
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