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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
...of the effect size. The fact that closely related lineages incur higher rates of HTT is consistent with studies of other types of horizontal transfer, such as gene transfers among viruses and prokaryotes, as well as cross-species transmission of viruses within ecosystems (Groussin et al. 2021; Sheinman et al...
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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
...into specific environmentally responsive networks. However, we have very little understanding about what environmental signals these networks are sensing.In this study, we characterize bacterial metabolic variation as well as variation in nematode gene networks that respond to these bacteria. Applying a systems...
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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
...are usually lost over short evolutionary timescales, but they can be retained through three primary mechanisms: conservation of wild-type function, in which duplicates alter gene dosage or provide redundancy; subfunctionalization, in which ancestral function is partitioned across copies...
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Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC
- Angela Gomez-Simmonds,
- Medini K. Annavajhala,
- Dwayne Seeram,
- Todd W. Hokunson,
- Heekuk Park,
- and Anne-Catrin Uhlemann
Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
...of carbapenem resistance genes (Conlan et al. 2014; Sheppard et al. 2016; David et al. 2020; Shropshire et al. 2022; Lerminiaux et al. 2023; Roberts et al. 2023). While these studies broadly advocate for expanding genomic surveillance to account for horizontal transfer, its potential impact remains unclear both...
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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...labels are transferred from well-annotated scRNA-seq data to less-annotated omics data, such as scATAC-seq. This approach leverages the gene expression profiles available in scRNA-seq to help annotate common cell types and even novel cell types for other omics data. However, the heterogeneous features...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...Systems Biology of Signal Transduction, German Cancer 15 Research Center (DKFZ), 69120 Heidelberg, Germany 16 8 These authors contributed equally. Either author can be listed first. 17 * Correspondence: falk.butter@fli.de (FB) 18 19 Abstract 20 A tightly regulated DNA damage response is critical...
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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
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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Resource: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
- Jane Hawkey,
- Ben Vezina,
- Jonathan M. Monk,
- Louise M. Judd,
- Taylor Harshegyi,
- Sebastián López-Fernández,
- Carla Rodrigues,
- Sylvain Brisse,
- Kathryn E. Holt,
- and Kelly L. Wyres
Genome Res. May 2022 32: 1004-1014; Published in Advance March 11, 2022, doi:10.1101/gr.276289.121
...in E. coli (Rousset et al. 2021), which showed that 7%–9% of roughly 3400 conserved genes were variably essential among 18 E. coli strains grown in three different conditions. Genomic comparisons of these E. coli implicated a key role for horizontal gene transfer in driving strain-specific essentiality...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
.... Such results suggest that the information of the gene regulatory network is at least partially coded in 3D genomic structures and transferred to RNA and protein levels along with the central dogma, in a way beyond correct coding and functioning of single genes, but also in the message-passage level in the form...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
..., as no individual dosage-sensitive gene within this region has been demonstrated to drive pathological development, and individuals with this disorder exhibit significant variability in the size and location of the chromosomal rearrangements (Lo Bianco et al. 2020; Okur et al. 2021; Vibert et al. 2022).A number...

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