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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
...with the Connectivity Map (CMap) database and the drug–target interactome (Fig. 1C). This approach facilitated the identification of candidate repurposable drugs for each major brain cell type across AD progression.Overview of snRNA-seq and snATAC-seq data across ADNC progressionAD progression staging based on ADNC...
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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
.... 4G).Enrichment of eQTLs and sQTLs in the 3′ UTRs of different cell typesTo explore the functional relationship between 3′ UTR length, gene expression, and splice site regulation across various tissues and cell types, we first retrieved eQTL and sQTL data from the PigGTEx database (Teng et al. 2024...
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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
...) have demonstrated rapid cell annotation capabilities without needing prior biological knowledge. These methods potentially enable the cell type identification that may be overlooked or difficult to ascertain through manual annotation and have been successfully extended to various scenarios...
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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
...-specific replication timing differences align with cell-type-specific chromatin features. For the first time, our results enable precise identification of specific chromosomal regions that differ in replication timing and chromatin landscapes between germline and somatic stem-cell populations in the in vivo context...
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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
..., Germany Corresponding authors: pnavarro@pasteur.fr, job.dekker@umassmed.eduAbstractMitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type– or species-specific. We...
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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
..., including cancers, when a well-matched benchmark data set is available.Although recent advances in single-cell/nucleus RNA sequencing (sc/snRNA-seq) offer valuable insights into cell types and states in healthy (Haniffa et al. 2021) and diseased tissues (Gohil et al. 2021; Zeng et al. 2023), highly...
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Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
- Iris Zhu and
- David Landsman
Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
...TFs bind. In this example, the two locations, denoted as enhancer A and enhancer B in the two cell types, have an optimal combination of a diversity of motifs located in proximity and, thus, best facilitate the collective recruitment of TFs expressed in each cell type. This results in cell type...
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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
...We have developed the inferring alternative polyadenylation from scRNA-seq (Infernape) pipeline to investigate PA usage from single-cell and spatial transcriptomic data generated from the 10x Genomics platforms. In conjunction with cell-type identification (Zheng et al. 2017; Butler et al. 2018...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...activation of quasi-prime-containing gene associations related to cancer, whereas simultaneously suppressing quasi-prime-containing genes are associated with cognitive, mental, and developmental disorders. We also show that human disease–causing variants, eQTLs, mQTLs, and sQTLs are 4.43-fold, 4.34-fold, 4...
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Method: Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data
- Jiebiao Wang,
- Kathryn Roeder,
- and Bernie Devlin
Genome Res. October 2021 31: 1807-1818; Published in Advance April 9, 2021, doi:10.1101/gr.268722.120
...for those cell types. Finally, we calculate CTS eQTLs for 11 brain regions by analyzing Genotype-Tissue Expression Project data, creating a new resource for biological insights.Gene expression quantified at the tissue level, bulk gene expression data, has been a useful resource for understanding...
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