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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
...s (Van de Peer et al. 2009; Kondrashov 2012; Wang et al. 2012). Although increased ploidy following WGD incurs fitness costs to an organism, it can confer advantages during times of environmental change and stress, including increased adaptability and robustness of gene regulatory networks (Ebadi et...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...53715, USA Corresponding author: sroy@biostat.wisc.eduAbstractThree-dimensional (3D) organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation data sets, such as Hi-C, have become...
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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
...a data set of 247 animal species (Supplemental Dataset S1), on which we built a dated phylogenetic tree (Supplemental Methods; Supplemental Dataset S2). We ran BUSCO v.5.4 (Manni et al. 2021) on the 247 s to assess their completeness and to extract core genes for downstream analyses, using the most...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...properties of topologically associating domains (TADs) are overall maintained, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD–TAD interactions...
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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
...–specific level, revealing a subset of genes that increasingly express with age and are enriched in PD-related pathways, notably in oligodendrocytes at late aging stages. Integration with five public PD single-cell RNA-seq data sets highlights 85 genes consistently differentially expressed with aging and PD. Key...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...in an elasmobranch fish for the first time. Their orthologies were confirmed with molecular phylogenetic trees, which also indicated elevated molecular evolutionary rates with long branches for elasmobranch Hox C genes (Fig. 6B). Our RNA-seq data showed the transcription of these Hox C genes (except for Hoxc12...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...of gene expression levels in mammalian organs. Nature 478: 343–348. doi:10.1038/nature10532 ↵Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, et al. 2002. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic...
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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...Balancing Gene Ontology annotation specificity in protein function prediction 1 based on the protein sequence large graph 2 Jiangyi Shao1,2, Shutao Chen1, Ziwen Wang 1, Zixu Chen1,2, Bin Liu1,2* 3 1 School of Computer Science and Technology, Beijing Institute of Technology, 4 Beijing 100081, China...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...Highly efficient and scarless editing via essential gene-coupled 1 homology-directed repair 2 Running title: Efficient scarless editing via essential gene HDR 3 4 Joo Hye Yeo1,2,3, Hyongbum Henry Kim2,3,4,5,6,7,8,9, Sang Ho Oh10, Jinu Lee1,* 5 6 1College of Pharmacy, Yonsei Institute...
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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
...profiles of P. pacificus nematodes in response to diverse microbiota and used them to test the hypothesis that the adaptation to novel microbiota might be facilitated by the evolution of novel genes (Athanasouli et al. 2023). This revealed evidence that novel genes might be preferentially integrated...

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