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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...), dehydration experiments to study the plasticity of gene expression (Kim and Shin 2016; Bittner et al. 2021; Blumstein and MacManes 2023), genomic analyses (Cheng et al. 2023; Peng et al. 2023), and population genomic analyses (Tigano et al. 2020; Rocha et al. 2023).Most of the studies of transitions to arid...
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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...for understanding gene regulation. Although DNA-binding specificities for thousands of transcription factors (TFs) have been determined, the specific amino acid–base interactions comprising their structural interfaces are largely unknown. This lack of resolution hampers attempts to leverage these data in order...
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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
...an important class of driver events in many cancer types (Zack et al. 2013; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020; Watkins et al. 2020). Tumors with WGD have more diverse patterns of aneuploidy because of the resilience provided by extra functional gene copies (Klockner...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...target genes -wideTFs exert their regulatory functions through direct interactions with DNA sites across the . Because TF-TF competition is a critical determinant of TF-DNA binding, we asked whether its influence is also reflected at the level of gene expression regulation. In the Cbf1-Pho4 model system...
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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
...-proficient cells. By 35 leveraging essential-gene co-editing, ESS-HDR enables precise and scarless 36 modification with enhanced efficiency. CRISPR–Cas9 induces double-strand breaks at 37 both the target locus and an essential gene, accompanied by two donor templates: one 38 introducing the desired edit...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...–specific, and changes during development in coordination with gene expression. Moreover, RT alterations are linked to abnormal gene expression, instability, and structural variation in multiple diseases, including cancer. However, mechanistic links between RT, large-scale 3D architecture, and transcriptional regulation...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...); blue represents targets are both DEGs and TFs’ targets; and yellow denotes genes located within AD-associated GWAS loci. When multiple criteria apply, the most specific class is displayed (blue → yellow → green). An annular ring around each target indicates the six comparisons of ADNC stage(s) at which...
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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
...subclasses within two GABAergic (GABA) classes, eleven subclasses within three glutamatergic (Glut) classes, as well as one specific subclass of dopaminergic (Dopa) class. We validated our annotations by examining the expression of representative marker genes (Supplemental Fig. S3). The number of cells per...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...and orientation (Banerji et al. 1981; Benoist and Chambon 1981; Gruss et al. 1981). Today we know of numerous examples in which enhancers regulate gene expression from long genomic distances (∼10–100 kb) and are occasionally found >1 Mb away from the target promoter (Lettice et al. 2003; Spitz et al. 2003...

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