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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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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
...such as compaction and accessibility, whereas endogenous DNA allows for in cellulo analysis under physiological conditions. Similarly, proteins can be purified and studied in vitro, expressed exogenously from a plasmid, or endogenously produced within the cell from genomic DNA. Although plasmid-based expression...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...” as a microbial with sufficient genomic variation to be distinguished from other s within the same species. This definition aligns with previous studies (Vicedomini et al. 2021; Liao et al. 2023b), although we acknowledge that the term “strain” may be interpreted differently in traditional taxonomy and other...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...(Fingerhut et al. 2024). A complete assembly of the Drosophila Y is bound to shed light on some of these mysteries.The phenomenon of missing exons has obvious relevance for genomics and sequence technology; it most likely is not unique to Drosophila, and it is probably a matter of time before other cases...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...Rashid Al-Abri1,2 and Gamze Gürsoy1,2,3 1Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA; 2New York Genome Center, New York, New York 10013, USA; 3Department of Computer Science, Columbia University, New York, New York 10027, USA Corresponding author: gamze...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
....zambonelli@unibo.itAbstractThe genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive sequences...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...Research Institute, La Jolla, California 92037, USA; 3Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington 98101, USA; 4Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington 98105, USA; 5Department of Genome Science...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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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
...not elucidate its causes and underlying mechanisms (Carvalho et al. 2023).Recent large-scale studies using comparative genomics have revealed that HTT is pervasive in flowering plants (Baidouri et al. 2014), insects (Wallau et al. 2016; Peccoud et al. 2017; Reiss et al. 2019; de Melo and Wallau 2020...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...samples (Maynard et al. 2021), each consisting of four consecutive tissue slices, generated using the 10x Genomics Visium platform (Maynard et al. 2021). These sections are meticulously annotated with different cortical layers (layers I through VI) and white matter (WM) regions. These annotations serve...

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