Searching journal content for articles similar to Chen et al. 35 (5): 1219.

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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
...and target genes (Gao et al. 2023).Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at the individual cell level, revealing cellular heterogeneity with single-cell resolution and significantly enhancing the understanding of cell type–specific gene regulation (Chen and Liu 2022; Kartha...
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Method: Unified integration of spatial transcriptomics across platforms with LLOKI
- Ellie Haber,
- Ajinkya Deshpande,
- Jian Ma,
- and Spencer Krieger
Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
...alignment across data sets. Optimal transport-guided feature propagation adjusts data sparsity to match scRNA-seq references through graph-based imputation, enabling single-cell foundation models such as scGPT to generate unified features. Batch alignment then refines scGPT-transformed embeddings...
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Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
- Vishvak Raghavan,
- Yumin Zheng,
- Yue Li,
- and Jun Ding
Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
...Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics Vishvak Raghavan1,2,3, Yumin Zheng2, Yue Li1,3 and Jun Ding1,2,3 1School of Computer Science, McGill University, Montreal, Quebec H3A 2A7, Canada; 2Meakins...
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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
...degeneration, impaired postnatal neurogenesis, and synaptic dysfunction, also play crucial roles in disease progression (Ballard et al. 2011; Long and Holtzman 2019; Murdock and Tsai 2023). This intricate pathology poses significant challenges for developing effective therapies. Recent advances in single-cell...
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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
...algorithms for predicting cell disease stage using a combination of RTE and gene expression features suggests dynamic regulation of RTEs in AD. Furthermore, we construct a single-cell atlas of retrotransposable elements in neurodegenerative disease (scARE) using these data sets and features. scARE has six...
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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
...Science and Engineering, Central South University, Changsha 410083, China Corresponding authors: guofei@csu.edu.cn, jj.tang@siat.ac.cnAbstractCell identity annotation for single-cell transcriptome data is a crucial process for constructing cell atlases, unraveling pathogenesis, and inspiring therapeutic...
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Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
- Yingxin Lin,
- Tung-Yu Wu,
- Xi Chen,
- Sheng Wan,
- Brian Chao,
- Jingxue Xin,
- Jean Y.H. Yang,
- Wing H. Wong,
- and Y.X. Rachel Wang
Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
.... Corresponding authors: rachel.wang@sydney.edu.au, whwong@stanford.eduAbstractSingle-cell technologies offer unprecedented opportunities to dissect gene regulatory mechanisms in context-specific ways. Although there are computational methods for extracting gene regulatory relationships from scRNA-seq and sc...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...percentage of cells, requiring single-cell analysis. However, single-cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes. To circumvent these issues, we use multiplexed error-robust fluorescent in situ hybridization (MERFISH) spatial transcriptomics that allows...
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Research: Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
- John T. Chamberlin,
- Younghee Lee,
- Gabor T. Marth,
- and Aaron R. Quinlan
Genome Res. February 2024 34: 179-188; Published in Advance February 14, 2024, doi:10.1101/gr.278253.123
..., with and without intronic reads, from both studies with STARsolo (Methods) (Kaminow et al. 2021). Finally, we analyzed preprocessed data from a single-cell atlas of human fetal development to understand the range of pre-mRNA recovery across tissues and its contribution to gene length bias. Because the nomenclature...
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Method: Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation
- Yang Zhou,
- Qiongyu Sheng,
- Jing Qi,
- Jiao Hua,
- Bo Yang,
- Lei Wan,
- and Shuilin Jin
Genome Res. May 2023 33: 750-762; Published in Advance June 12, 2023, doi:10.1101/gr.277522.122
...single-cell integration (scInt), an integration method based on accurate, robust cell–cell similarity construction and unified contrastive biological variation learning from multiple scRNA-seq data sets. scInt provides a flexible and effective approach to transfer knowledge from the already integrated...

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