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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...found no evidence for an increased point mutation rate in animals born via in vitro fertilization (IVF) (Caperton et al. 2007), a retrospective comparative analysis in humans uncovered a significantly higher de novo point mutation rate in IVF-born children (Wang et al. 2021). However, the underlying...
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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
...in postduplication FIE-gene and FIE-functional family diversity, relative to background mutations, compared with preduplication.These observed increases in diversity indicate the selection for gene duplication events, which can broaden the range of possible functional adaptations available to the tumor. Somatic copy...
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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
...emerged transcription of a pre-existing ORF. (B) De novo gene emergence from a frameshifted gene sequence. (Created with BioRender; https://www.biorender.com/.)Merging comparative genomic and transcriptomic data allow detection of both the lineage-specific transcripts and the mutations responsible...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...for common disease vary continuously among individuals in a population. Studies in 36 numerous species have shown that quantitative traits have a complex genetic basis, in which 37 they are shaped by DNA variants at dozens to thousands of genes (Mackay and Anholt 2024). 38 Each causal variant typically has...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...for this deviation from the prediction of the theory may lie in the adaptability offered by a higher mutation rate, as we were able to show that the of the widely studied Hydra magnipapillata strain 105 has undergone a process of strong positive selection since the strain's cultivation 50 years ago. This most likely...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...). Despite aging being the greatest risk factor for developing PD, the mechanisms by which aging promotes PD are not fully understood. High-resolution studies of cellular and molecular changes during aging could yield essential insights into the disease's pathophysiology.Recent advances in single...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...Full-resolution HLA and KIR gene annotations for human assemblies Ying Zhou1, Li Song2 and Heng Li1,3 1Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; 2Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire 03755, USA; 3...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...acid sequences when necessary, and, most importantly, integrate other sequencing data types with single-nucleotide resolution, in which specific nucleotide positions convey sequence read information. Together, ggRibo enables parallel comparisons of multiomic data sets, facilitating the study of gene...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...and adaptive sampling with a bioinformatic pipeline to produce haplotype-resolved, annotated IGH assemblies. Notably, our strategy overcomes prior limitations in phasing resolution, enabling single-contig haplotype assemblies that span the entire IGH locus. We apply this method to four individuals and validate...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...in modeling gene expression changes resulting from sequence variants. Yet, few methods operate at the resolution necessary to capture subtle effects of single-nucleotide changes. Furthermore, it remains unclear which architectural components, such as residual connections, normalization strategies...
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