Searching journal content for articles similar to Zhao et al. 32 (9): 1627.

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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
...). In particular, single-cell multi-omics technologies like SHARE-seq (Ma et al. 2020) can simultaneously profile transcriptomic and epigenomic data within individual cells, enabling the interrogation of cellular heterogeneity and molecular hierarchy (Cao et al. 2024). Consequently, numerous methods have emerged...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...Interdisciplinary Studies, Nankai University, Tianjin 300071, China ↵4 These authors contributed equally to this work. Corresponding author: chenshengquan@nankai.edu.cnAbstractSingle-cell multiomic sequencing technologies have offered unprecedented insights into cellular heterogeneity by jointly profiling gene...
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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...or cell maturation. Our approach integrates scHi-C contact data with single-cell trajectory information and is based on applying simultaneous modeling of a number of cells ordered along the progression of a given cellular process. The approach is able to successfully recreate known nuclear structures...
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Method: Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data
- Shuze Wang,
- Mary P. Lee,
- Scott Jones,
- Jie Liu,
- and Joerg Waldhaus
Genome Res. October 2021 31: 1885-1899; Published in Advance April 9, 2021, doi:10.1101/gr.271080.120
..., this study provides a strategy to spatially reconstruct the formation of a lineage-specific regulatory landscape using a single-cell multi-omics approach.The mammalian was estimated to encode approximately 30,000 protein-coding genes (Shabalina and Spiridonov 2004), and numerous unique combinations...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...(Fig. 5B).View larger version: In this window In a new window Figure 5. Regulatory importance of MHBs in human embryonic development. (A) Number of MHBs identified from bulk bisulfite sequencing of early human embryos. (B) Validation of MHBs using single-cell bisulfite sequencing data. An enrichment...
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Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
- Jianing Yao,
- Jinglun Yu,
- Brian Caffo,
- Stephanie C. Page,
- Keri Martinowich,
- and Stephanie C. Hicks
Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
...in Healthcare, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: shicks19@jhu.eduAbstractRecent advances in spatially resolved single-omic and multi-omics technologies have led to the emergence of computational tools to detect and predict spatial domains. Additionally, histological...
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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
...they are specifically involved in complex diseases is largely unknown. Here, we investigate the cellular heterogeneity of RTEs using 12 single-cell transcriptome profiles covering three neurodegenerative diseases, Alzheimer's disease (AD), Parkinson's disease, and multiple sclerosis. We identify cell type marker RTEs...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...to this work. Corresponding authors: fluca@wayne.edu, rpique@wayne.eduAbstractSynthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional...
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Method: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee,
- Qingqing Guo,
- Mijeong Kim,
- Joonhyuk Choi,
- Alia Segura,
- Alper Genceroglu,
- Lucy LeBlanc,
- Nereida Ramirez,
- Yu Jin Jang,
- Yeejin Jang,
- Bum-Kyu Lee,
- Edward M. Marcotte,
- and Jonghwan Kim
Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
...fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem...
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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code...
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