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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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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...-Iseppi et al. 2021). In our study, we developed a workflow designed to streamline the analysis aspect of high-throughput long-read RNA sequencing data, enabling the identification of transcript isoforms at the single-cell level. Our workflow modified the 10x Genomics scRNA-seq protocol (Gupta et al. 2018...
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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
...-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we use scBayes, which integrates bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for subclone-defining mutations. Although the most common...
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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
..., facilitating the development of future targeted therapeutics.In this study, we aim to address the knowledge gap by performing single-cell RNA sequencing to profile m6A RNA methylation patterns in individual cells of the hippocampus. A myriad of different m6A sequencing detection methods exist, such as m6A RNA...
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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
..., resting control participants were sampled and analyzed at the same two times of day as the exercised participants (Fig. 1A; Supplemental Table S1). Nuclei isolated from the 12 skeletal muscle samples underwent single-nuclei (sn) multiome library construction and sequencing to generate same-nucleus RNA...
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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
.... This makes them insensitive in complex environments where the detailed dynamics of cell interactions matter. We introduce CellAgentChat, an agent-based model (ABM) designed to decipher CCIs from single-cell RNA sequencing and spatial transcriptomics data. This approach models biological systems...
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Method: Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach
- Fabien Wehbe,
- Levi Adams,
- Jordan Babadoudou,
- Samantha Yuen,
- Yoon-Seong Kim,
- and Yoshiaki Tanaka
Genome Res. January 2025 35: 135-146; Published in Advance December 2, 2024, doi:10.1101/gr.278812.123
...is applicable across multiple independent single-cell RNA sequencing (scRNA-seq) data sets. Using the pretrained model of the PD scRNA-seq data set (midbrains of young and aged healthy donors and PD patients) (as used in Fig. 1; Adams et al. 2024), we inferred disease progression levels of individual cells...
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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: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
- Yi Qiao,
- Xiaomeng Huang,
- Philip J. Moos,
- Jonathan M. Ahmann,
- Anthony D. Pomicter,
- Michael W. Deininger,
- John C. Byrd,
- Jennifer A. Woyach,
- Deborah M. Stephens,
- and Gabor T. Marth
Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
...cells from scRNA-seq experiments (both full-transcript and end-capture protocols) is the primary goal of our method, we showed that it is generally applicable to a wide range of single-cell sequencing technologies that are capable of assessing the presence of somatic mutations. We provided proof...
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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
...of misidentifying the correct cell groups. These inaccuracies introduce biases into the depiction of the complexity of biological processes, impeding an accurate understanding of the molecular mechanisms involved (Kester and van Oudenaarden 2018).The recent breakthrough in single-cell RNA sequencing (scRNA-seq) has...
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