Searching journal content for articles similar to Yang et al. 31 (3): 349.

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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...) were performed. Finally, data analysis and visualization were performed to generate CNV, RT, and gene expression profiles (9).PARTAGE sample preparation preserves DNA and RNA integrityTo test PARTAGE, we exploited the HepG2 human cell line, a reference cell line used at the ENCODE (The ENCODE Project...
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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
...–specific cis-regulatory DNA elements (CREs), we pinpoint 141 ADNC-associated genes. Using gene set enrichment analysis (GSEA) and network proximity analysis, we further identify nine candidate repurposable drugs that were associated with these ADNC-related genes. In summary, this cell type–specific multiomic...
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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
...analysis by incorporating the regulatory annotation of open chromatin regions, as assessed through ATAC-seq, across 63 tissues available in the Encyclopedia of DNA Elements (ENCODE) (The ENCODE Project Consortium et al. 2020). The ENCODE data exhibited wide variation in sample sizes across tissues, leading...
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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
...). Statistical modeling showed no significant compositional changes with age after correcting for multiple tests.View larger version: In this window In a new window Figure 2. Profiling of age-associated gene expression variations across substantia nigra cell subclasses. (A) UMAP representation of all nuclei...
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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...transcriptomic and epigenomic data across 26 human tissues from the EN-TEx (ENCODE-GTEx) project. We uniformly annotate promoters with chromatin features (histone modifications, chromatin accessibility, and DNA methylation), sequence motifs, and evolutionary conservation, generating an online catalog. Leveraging...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...feature analysis modules to explore RTE dynamics in a user-defined condition. To our knowledge, scARE represents the first systematic investigation of RTE dynamics at the single-cell level within the context of neurodegenerative diseases.Transposable elements (TEs) are DNA elements that are capable...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...-co1 (C) and Mt-cyb (E).DiscussionWe report a class of previously undocumented chimeric mtRNAs, which increase in multiple conditions associated with mitochondrial pathology and predict mtDNA deletion frequency and altered transcription of genes essential for mitochondrial function. The new class...
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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
...independent of copy number changes; these processes increase the tumor mutation burden and thus the likelihood of novel driver mutations. Mutations arise through impairments in DNA-damage repair pathways (Wu et al. 2020), endogenous processes including APOBEC mutagenesis, and exogenous factors such as smoking...
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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
.... Order determined by a coin flip. Corresponding author: braphael@princeton.eduAbstractSpatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active...
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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...semantic entailment, generating multiple approximate models of 89 GO, and aggregating predictions across these models to exploit GO’s axiomatic 90 structure. Recent state-of-the-art methods have increasingly incorporated InterPro 91 domains (Paysan-Lafosse et al. 2023) as explicit features. These domains...
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