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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...prior to the WGD. Analysis of individual TE insertions, however, revealed enrichment of TE-CREs originating from WGD-associated TE activity, particularly for the DTT (Tc1-Mariner) DNA elements. Furthermore, coexpression analyses supported the presence of TE-driven gene regulatory network evolution...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...for SNVs, both deep convolutional network approaches (Clair3 and DeepVariant) show excellent recall with both ONT and PacBio above 20× sequence. Irrespective of the sequencing platform, sequence coverage at 8× or lower shows significant reduction in performance and is not advised for large-scale sequencing...
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Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
.... The lack of representation of gut-associated eukaryotic microbes likely undermines their utility in analyzing gut-derived metas. In addition, k-mer frequency merely represents metrics of simplified genomic contexts, whereas improved classification can be achieved using a convolutional neural network (CNN...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
..., and physiological genomics, illuminating processes such as environmental adaptation, species diversification, social behavior, or sex determination (Rittschof et al. 2014; Capel 2017; Salzburger 2018; Kim et al. 2019; Xie et al. 2019; Greenway et al. 2020). Around two hundred fish species have reference assemblies...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...research should aim to examine the environmental and social conditions that trigger this reproductive mode and the underlying proximate mechanisms mediating the hermaphroditic development. Ultimately, it would be interesting to screen the natural population for the presence of individuals that originate...
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Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
- Muhammad Yasir,
- A. Keith Turner,
- Sarah Bastkowski,
- David Baker,
- Andrew J. Page,
- Andrea Telatin,
- Minh-Duy Phan,
- Leigh Monahan,
- George M. Savva,
- Aaron Darling,
- Mark A. Webber,
- and Ian G. Charles
Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
...porin, ompF, were enriched in the presence of triclosan. Expression of acrAB and ompF are controlled by global stress response systems, marRA and soxRS; inserts within marR and soxR (both of which result in derepression of the cognate transcriptional activator genes, which then promote pump expression...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...on sample size as in traditional variational inference but depends on the network size (Shu et al. 2018). The VAE can be seen as an autoencoder with its latent space being regularized by a chosen prior distribution to make the inferred latent space more interpretable and to preserve global structure...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...of regulatory variants in farmed animals lags behind, although they have multiple advantages in developing GTEx-like resources, such as relatively easy pan-tissue collection across diverse biological and environmental contexts. Recently, the Farm Animal GTEx (FarmGTEx) project (Fang et al. 2025) has been...
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Resource: Global compositional and functional states of the human gut microbiome in health and disease
- Sunjae Lee,
- Theo Portlock,
- Emmanuelle Le Chatelier,
- Fernando Garcia-Guevara,
- Frederick Clasen,
- Florian Plaza Oñate,
- Nicolas Pons,
- Neelu Begum,
- Azadeh Harzandi,
- Ceri Proffitt,
- Dorines Rosario,
- Stefania Vaga,
- Junseok Park,
- Kalle von Feilitzen,
- Fredric Johansson,
- Cheng Zhang,
- Lindsey A. Edwards,
- Vincent Lombard,
- Franck Gauthier,
- Claire J. Steves,
- David Gomez-Cabrero,
- Bernard Henrissat,
- Doheon Lee,
- Lars Engstrand,
- Debbie L. Shawcross,
- Gordon Proctor,
- Mathieu Almeida,
- Jens Nielsen,
- Adil Mardinoglu,
- David L. Moyes,
- Stanislav Dusko Ehrlich,
- Mathias Uhlen,
- and Saeed Shoaie
Genome Res. June 2024 34: 967-978; Published in Advance July 22, 2024, doi:10.1101/gr.278637.123
...and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; 12Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; 13Department of Biotechnology and Biomedicine, Technical University of Denmark...
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