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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
...differential gene expression for six major cell types intensified at severe ADNC. Integrating peak-to-gene linkages and motif enrichment analyses, we reconstruct transcription factor (TF)–target gene networks across six major brain cell types. By integrating -wide association study (GWAS) loci with cell type...
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Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
- Hongyu Zheng,
- Hirak Sarkar,
- and Benjamin J. Raphael
Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
...of the observations with latent dimension equal to the number of cell types. By constraining the number of latent factors (rows of Q or columns of P) reflecting underlying cell types, SIID jointly estimates P and Q, enabling imputation of the absent Xenium genes and deconvolution of the Visium spots.View larger...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...in influencing functional pathways critical for specific brain functions (Supplemental Fig. S1D).View larger version: In this window In a new window Figure 2. Landscape of global 3′ UTR usage across 261 cell types. (A) The circular plot summarizing APA trends across 1231 genes. The outer heat map track...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...issues with the annotation of rod cells in the reference data, in which some bipolar neurons also expressed the gene rho, which is the marker of the rod cell (Supplemental Fig. S4B,C; Hoang et al. 2020). Rod cells happen to be the most prevalent cell type in the Macosko data set (Fig. 3E). This indicates...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...NNLS framework to address the consistently observed technological discrepancy at the gene level. The distinct advantage of DeMixSC lies in its superior deconvolution accuracy and broad generalizability. As demonstrated in the benchmarking study, DeMixSC achieves more accurate estimates of cell type proportions...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...in mitotic mESCs. A second important question raised by our findings is to what extent mitotic binding by CTCF could be functional. Recent work has shown that, whereas mitotic CTCF binding correlates with rapidly reactivated genes after mitosis (Owens et al. 2019; Zhang et al. 2019; Pelham-Webb et al. 2021...
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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
...highlights STMSC's potential to enhance our understanding of complex tissue structures. In the mouse brain coronal data set, STMSC accurately identified and distinguished fine spatial structures, showcasing advantages in spatial region segmentation accuracy and gene expression pattern analysis. High-precision...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...undetectable at baseline. To explore this possibility, we examined the overlap of eGenes with GWAS loci assembled from 402 brain-relevant traits in each cell type (Methods; Supplemental Table S7). Across cell types, we identified 571 eGenes implicated in GWAS of brain-related traits. Furthermore, eGenes...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-expressing), and an unidentified wb-expressing somatic lineage (Fig. 1C; Supplemental Fig. S1H; Supplemental Table S1; Kuhn et al. 1991; Kelly et al. 2002). For this study, we focus on the GSC-like and CySC-like clusters.The GSC-like and CySC-like clusters followed expected gene expression patterns for known cell-type- and stage...
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Method: Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
- Bowei Kang,
- Yalan Yang,
- Kaining Hu,
- Xiangbin Ruan,
- Yi-Lin Liu,
- Pinky Lee,
- Jasper Lee,
- Jingshu Wang,
- and Xiaochang Zhang
Genome Res. October 2023 33: 1774-1787; Published in Advance October 31, 2023, doi:10.1101/gr.277864.123
...a prominent role. In the adult mouse brain, we uncover cell type–specific PAs and visualize such events using spatial transcriptomic data. Over two dozen neurodevelopmental disorder–associated genes such as Csnk2a1 and Mecp2 show differential PAs during brain development. This study presents Infernape...
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