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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
...Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease Yunxiao Ren1,2, Ming Hu3,4, Yang E. Li5, Andrew A. Pieper6,7,8,9,10,11, Jeffrey Cummings12 and Feixiong Cheng1,2,4,13 1Cleveland Clinic Genome Center, Cleveland Clinic Research...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...or silencing of the wild-type allele and has been investigated by examining the enrichment of mutant allele in RNA relative to DNA. Here we show that this mutation-based approach can be confounded by gene expression differences in tumor and normal cells that coexist in most bulk tumor samples. We model mutant...
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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
...and mutations using data sets from tumor sequencing projects, such as The Cancer Genome Atlas (TCGA) (Hutter and Zenklusen 2018; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). These tools employ a variety of approaches, including analysis of mutations using gene sequences, protein...
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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
...promoter testing) or upstream of a known promoter linked to a reporter gene (for enhancer testing), encoding an easily assayed protein such as GFP, LacZ, or luciferase. Reporter assays involve DNA transcription within cells to evaluate their regulatory activity (Romanov et al. 2021), if the regulatory...
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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
....To further explore the different gene–gene relationships profiled in the HuBMAP (adult human) and human fetal atlases, for each tissue that is common between the two atlases, we identified unique gene modules in the gene-embedding components of each atlas (Supplemental Note 11). Notably, we observed...
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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...RNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA. ♱Corresponding authors: izg5139@psu.edu, nadav.ahituv@ucsf.edu Abstract Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...Generation and analysis of a mouse multitissue annotation atlas Matthew Adams1 and Christopher Vollmers2 1Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA; 2Department of Biomolecular Engineering, University...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...cancers (Hu and Lu 2015; Gu et al. 2018; Yu and Chen 2019; Song et al. 2022). Additionally, the protein-coding genes FAM83A, ITGA3, ITGB4, L1CAM, MUC16, and SAA1 have been reported to promote cancer progression (Chen et al. 2018; Cheriyamundath and Ben-Ze'ev 2020; Lei et al. 2020; Li et al. 2020; Tian et...
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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. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...at late aging stages, while genes involved in 35 myelination are downregulated at early aging stages in oligodendrocyte. Our multiomic atlas 36 underscores the substantial regulatory network changes during aging that may predispose to 37 PD, providing valuable insights for furthering understanding of PD...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...inference. Curated databases, such as TRUST (Han et al. 2018), ChEA3 (Keenan et al. 2019), and ChIP-Atlas (Oki et al. 2018), offer experimentally validated TF–gene interactions that serve as a solid foundation for supervised approaches. GeneLink (Chen and Liu 2022) introduces a graph attention network (GAT...

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