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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
...provides the evidence counts for each gene. (B) Predicted repurposable drug candidates by network proximity and GSEA clustered by ATC first-level class. Left panel shows enriched drug candidates identified by network proximity method, in which gradient colors reflect absolute Z-scores. Right panel shows...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...exhibit 532 heterogeneous distribution patterns, with some, such as finTRIMs, in gene groups dispersed 533 across the while others, including MHC class I genes, form a few or a unique cluster 534 on a specific location (Van der Aa et al., 2009; Lukacs et al., 2010). These findings 535 underscore...
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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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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
....27 × 10−22) consisting almost entirely of LINE sequence. The LINE sequence was inserted 8.3 kb downstream from MYH7 and increased mRNA abundance (β = 1.37). The expression of LOC112443864 (ENSBTAG00000053433) encoding MHC class I polypeptide-related sequence B-like was associated with an 11.6-kb insertion...
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Method: Modeling gene interactions in polygenic prediction via geometric deep learning
- Han Li,
- Jianyang Zeng,
- Michael P. Snyder,
- and Sai Zhang
Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
...Table S4). GSEA of PRS-Net-identified genes highlighted numerous immune-related pathways and the major histocompatibility complex (MHC) protein complex (Supplemental Fig. S7), agreeing well with the literature (Traugott 1987; Lee et al. 1990; Multiple Sclerosis Genetics Group et al. 1998; Dyment et al...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...mechanisms driving the variation in regulatory state across the GC cell lines. To understand how the activity of TFs in Mes-like and Epi-like cell lines correlated with known genetic variation in GC, we examined TF gene expression in TCGA-STAD patients. CDH1, a recurrently mutated GC driver gene...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between g...
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Research: Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
- Can Cenik,
- Elif Sarinay Cenik,
- Gun W. Byeon,
- Fabian Grubert,
- Sophie I. Candille,
- Damek Spacek,
- Bilal Alsallakh,
- Hagen Tilgner,
- Carlos L. Araya,
- Hua Tang,
- Emiliano Ricci,
- and Michael P. Snyder
Genome Res. November 2015 25: 1610-1621; Published in Advance August 21, 2015, doi:10.1101/gr.193342.115
...modulate ribosome occupancy—many of these differences lie close to start codons and upstreamORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. [Supplemental material...
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Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
- Leslie O. Goodwin,
- Erik Splinter,
- Tiffany L. Davis,
- Rachel Urban,
- Hao He,
- Robert E. Braun,
- Elissa J. Chesler,
- Vivek Kumar,
- Max van Min,
- Juliet Ndukum,
- Vivek M. Philip,
- Laura G. Reinholdt,
- Karen Svenson,
- Jacqueline K. White,
- Michael Sasner,
- Cathleen Lutz,
- and Stephen A. Murray
Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
...disrupt the coding sequence of endogenous genes in half of the lines, frequently involving large deletions and/or structural variations at the insertion site. Furthermore, we identify a number of unexpected sequences in some of the transgenes, including undocumented cassettes and contaminating DNA...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...hand, when we investigated GO enrichment of genes in or surrounding lineage-specific EBRs (±50 kbp consistent with our enhancer analysis), we found that genes linked to inflammatory response (including SAA1, SAA3, and SAA4) and MHC class II protein complex were enriched in cetartiodactyl EBRs (FDR < 0...

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