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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
...) Collection and preprocessing of snRNA-seq and snATAC-seq data sets in physical space. (B) Multiple analysis to identify an AD-associated gene list including differential gene expression analysis; identification of cCRE; cell type–specific, AD-associated risk variants; and peak-to-gene linkages. (C) Two...
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Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
- Brian S. Roberts,
- Ashlyn G. Anderson,
- E. Christopher Partridge,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
...Corresponding authors: gcooper@hudsonalpha.org, rmyers@hudsonalpha.orgAbstractDifferential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
.... Finally, our cancer consensus network solely included cancerous samples. We restricted our context-specific networks to noncancerous samples grouped by tissue context. We did not examine differential coregulation resulting from noncancer disease and regressed these effects from gene expression. Thus...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...transposition. Following post-GEM cleanup, libraries were preamplified by PCR, after which the sample was split into three parts: one part generated the snRNA-seq library, one part generated the snATAC-seq library, and the rest was kept at −20°C. SnATAC and snRNA libraries were indexed for multiplexing...
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Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
- Shan Lu and
- Sunduz Keles
Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
...paper with single-nucleus consensus WGCNA (scWGCNA) using both single-cell and bulk RNA-seq data. To directly compare donor-specific coexpression networks with the scWGCNA results, we started with the same set of 1,252 genes that scWGCNA utilized leveraging both the snRNA-seq and bulk RNA-seq data. When...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...nucleus RNA-seq [snRNA-seq]) data from 20 healthy child and adult human hearts, which were collected from a variety of sources (Supplemental Table S1; Sim et al. 2021; Mehdiabadi et al. 2022; Kanemaru et al. 2023). We unexpectedly observed XIST expression in male hearts. To study this in more detail, we...
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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
...MIND is to provide the posterior mean of the CTS expression () for each sample i, gene j, and K cell types.View larger version: In this window In a new window Figure 1. Overview of bMIND algorithm and CTS differential expression analysis (CTS DE). With prior information from scRNA/snRNA-seq data for case and control...
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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
...a comprehensive APA atlas for 261 cell types across 19 porcine tissues based on single-nucleus RNA sequencing (snRNA-seq) data. This analysis reveals tissue- and cell type–specific patterns of APA. We find that many genes display a clear correlation between the average length of 3′ untranslated regions (3′ UTRs...
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Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
...and other distal regulatory elements, such as enhancers. Furthermore, snRNA may not fully capture a cell's transcriptional profile, as it primarily detects mRNA levels. Thus, to understand a comprehensive picture of transcriptional regulation that dictates microglia identity, we compared global chromatin...
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Research: Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code
- Marina Murillo,
- Marina Salvadores,
- Aina Vaquer Picó,
- Lina Tsapanou,
- Adrian Gabriel Torres,
- Fran Supek,
- and Lluis Ribas de Pouplana
Genome Res. April 15, 2026 gr.281022.125; Published in Advance April 15, 2026, doi:10.1101/gr.281022.125
...load is also detectable in other Pol III-transcribed genes such as ribosomal RNA (rRNA), small 110 nuclear RNA (snRNA) and unclassified RNAs (miscRNA), as was reported in the human germline 111 mutations (Seplyarskiy et al. 2023). Mutational densities at 5S rRNAs, snRNAs, and miscRNAs genes 112...
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