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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
..., focusing on cell population levels and losing single-cell resolution. Scriabin (Wilk et al. 2024) analyzes LR interactions at the single-cell level but primarily relies on unimodal scRNA-seq data, limiting CCI inference ability owing to lack of spatial information. Because CCIs in tissue environments...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...-seq, positional barcodes were used to indicate the physical locations of captured transcripts within a tissue slice, with each location having a diameter of 100 µm and a center-to-center distance of 200 µm, resulting in a coarser-than-single-cell level of resolution (Ståhl et al. 2016). However, spatial...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...of transcriptome and chromatin accessibility at the single-cell level, thus allowing for an in-depth exploration of the cellular dynamics of tissue regeneration.Several studies have utilized single-cell/nucleus RNA sequencing (sc/snRNA-seq) to elucidate cell-type contributions, identify cell...
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Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...that direct cell state transitions at the single-cell level.ResultsOverview of the TFcomb frameworkWe developed TFcomb as a computational method for identifying reprogramming TF combinations directing cell state transitions from the source state to the target state (Fig. 1A). TFcomb takes both scRNA-seq data...
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Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...TBI at the single-cell level. We observed cell-specific gene expression changes following mTBI and unveiled diverse cell-to-cell interaction networks that influence a wide array of cellular processes. Moreover, we report novel neurogenesis lineage trajectories and related key transcription factors, which we...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
.... Undifferentiated embryonic cells are one of the “niches” adopted by TEs that facilitate their propagation (Haig 2016). Although the mobility of TEs is thought to be generally deleterious to the host, the accumulation of TEs in the represents a source of raw genetic material that may be co-opted during evolution...
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Research: Regulation of the ESC transcriptome by nuclear long noncoding RNAs
- Jan H. Bergmann,
- Jingjing Li,
- Mélanie A. Eckersley-Maslin,
- Frank Rigo,
- Susan M. Freier,
- and David L. Spector
Genome Res. September 2015 25: 1336-1346; Published in Advance June 5, 2015, doi:10.1101/gr.189027.114
...transcripts acting as miRNA “sponges” (Poliseno et al. 2010). To confirm nuclear localization and to investigate expression of lncRNAs at the single cell level, we selected 11 lncRNAs, including Firre, Tug1 (Young et al. 2005) and lncRNAs Platr2, -14, -15, -19 and -20 (see below) and performed single...
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Resource: A limited set of transcriptional programs define major cell types
- Alessandra Breschi,
- Manuel Muñoz-Aguirre,
- Valentin Wucher,
- Carrie A. Davis,
- Diego Garrido-Martín,
- Sarah Djebali,
- Jesse Gillis,
- Dmitri D. Pervouchine,
- Anna Vlasova,
- Alexander Dobin,
- Chris Zaleski,
- Jorg Drenkow,
- Cassidy Danyko,
- Alexandra Scavelli,
- Ferran Reverter,
- Michael P. Snyder,
- Thomas R. Gingeras,
- and Roderic Guigó
Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
...).Comparable multitissue RNA-seq data have become recently available at the single-cell level for 20 mouse organs and tissues through the Tabula Muris project (The Tabula Muris Consortium 2018). Principal component analysis (PCA) of the individual cells and hierarchical clustering of the primary cell types...
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Research: Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos
- Xinyi Wang,
- Denghui Liu,
- Dajian He,
- Shengbao Suo,
- Xian Xia,
- Xiechao He,
- Jing-Dong J. Han,
- and Ping Zheng
Genome Res. April 2017 27: 567-579; Published in Advance February 21, 2017, doi:10.1101/gr.198044.115
...Q, Han JD. 2015. Single-cell-level spatial gene expression in the embryonic neural differentiation niche. Genome Res 25: 570–581. Jackson SP, Bartek J. 2009. The DNA-damage response in human biology and disease. Nature 461: 1071–1078. Jaroudi S, SenGupta S. 2007...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...complexity. This integration allows for the connection of cells from the present to their historical lineage. Additionally, the refinement of clonal dynamics is achieved by leveraging transcriptome-derived differentiation trajectories and assessing gene expression changes over time (Kester and van...
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