Article
Plant Sciences
Fangming Zhu, Mingyan Li, Manwen Yan, Fei Qiao, Xuefei Jiang
Summary: DNA methylation plays a crucial role in plants' response to osmotic stress, with genes related to plant hormone synthesis, signal transduction, osmoregulatory substance, and antioxidant enzymes rapidly responding. Additionally, demethylation of key enzyme genes can alleviate the inhibition of cell growth caused by osmotic stress.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Chen Li, Maria C. Virgilio, Kathleen L. Collins, Joshua D. Welch
Summary: This paper introduces a model called MultiVelo, which extends the RNA velocity framework using differential equations to incorporate epigenomic data. The model improves the accuracy of cell fate prediction by estimating the temporal relationship between chromatin accessibility and gene expression. The study reveals different classes of genes and cell states, and identifies time lags between transcription factor expression and binding site accessibility, as well as disease-associated SNP accessibility and linked gene expression.
NATURE BIOTECHNOLOGY
(2023)
Review
Chemistry, Physical
Yingwen Chen, Jia Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong Yang
Summary: Cells are fundamental building blocks of biological systems, and studying single cells can provide insights into cell diversity and disease processes. Single-cell RNA sequencing technologies allow cellular heterogeneity to be dissected at unprecedented resolution.
Article
Biochemistry & Molecular Biology
Menghua Lyu, Xuyang Shi, Yang Liu, Hongyan Zhao, Yue Yuan, Run Xie, Ying Gu, Yuliang Dong, Meiniang Wang
Summary: In this study, we investigated the immunological dynamics of H5N1 HA-specific immune response in alpaca PBMCs at the single-cell level. We found that the immune response demonstrated multiple cellular immunities, which is important for understanding the anti-viral immune system and facilitating the development of more potent vaccines and antibodies in camelid animals.
Review
Biochemical Research Methods
Dohun Yi, Jin-Wu Nam, Hyobin Jeong
Summary: Structural variants (SVs) are diverse genomic rearrangements that accumulate in the genome during cell development and aging, potentially impacting cancer development. Detecting somatic SVs is challenging but crucial for understanding their functional implications. This review summarizes recent advances in whole-genome sequencing (WGS)-based approaches for somatic SV detection, including computational algorithms for bulk WGS data and cutting-edge single-cell techniques. The advantages and limitations of bulk and single-cell approaches are discussed, along with their potential for linking somatic SVs to functional readouts.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Immunology
Benjamin D. Solomon, Hong Zheng, Laura W. Dillon, Jason D. Goldman, Christopher S. Hourigan, James R. Heath, Purvesh Khatri
Summary: The human leukocyte antigen (HLA) locus is important for adaptive immune function and clinical applications. This study evaluates computational tools for predicting HLA genotypes using single-cell data and compares them to gold-standard genotyping.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Peng Zhao, Zenglin Xu, Junjie Chen, Yazhou Ren, Irwin King
Summary: Single cell RNA sequencing allows researchers to explore tissue heterogeneity and find novel cellular subtypes. Existing clustering methods for scRNA-seq data are sensitive to noise and outliers. This study introduces self-paced clustering methods that can reduce the influence of noisy data and achieve better performance on both simulation data and real scRNA-seq data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Hongcang Gu, Ayush T. Raman, Xiaoxue Wang, Federico Gaiti, Ronan Chaligne, Arman W. Mohammad, Aleksandra Arczewska, Zachary D. Smith, Dan A. Landau, Martin J. Aryee, Alexander Meissner, Andreas Gnirke
Summary: The integration of DNA methylation and transcriptional state within single cells is of broad interest for studying cellular heterogeneity and rare cell populations. The Smart-RRBS protocol combines Smart-seq2 and RRBS to generate paired epigenetic promoter and RNA-expression measurements for approximately 24% of protein-coding genes in typical single cells, and can also be applied to tissue samples comprising hundreds of cells. The protocol, excluding flow sorting of cells and sequencing, takes around 3 days to process up to 192 samples manually and requires basic molecular biology expertise and laboratory equipment.
Article
Chemistry, Physical
Xi Zeng, Shaowei Jiang, Zhixing Zhong, Xiaoping Yang, Qiuyue Chen, Jin Li, Zhi Zhu, Jia Song, Chaoyong Yang
Summary: DIRECT is a digital microfluidics-based method that allows for simultaneous analysis of DNA methylation and gene expression in a single library construction, providing a cost-effective and simplified approach for single-cell analysis.
Article
Chemistry, Multidisciplinary
Xing Xu, Li Lin, Jian Yang, Weizhou Qian, Rui Su, Xiaoxu Guo, Linfeng Cai, Zirun Zhao, Jia Song, Chaoyong Yang
Summary: This article introduces a nanoliter-scale single-cell multi-omics sample preparation platform called DMF-DR-seq, based on digital microfluidics. DMF-DR-seq demonstrates improved performance compared to current technology, with lower amplification bias, higher genome-wide coverage in DNA sequencing, and better gene detection ability in RNA sequencing. DMF-DR-seq was used to identify genome variation-induced abnormal transcriptome expression, revealing potential essential genes involved in the pathologic progress. The unique flexibility, sensitivity, and accuracy of DMF-DR-seq suggest its potential utility in deeper multi-omics analysis for inheritance mechanism study in single-cell biology.
Article
Chemistry, Physical
Jingyu Qi, Haibin Zhu, Yijian Li, Xiangyu Guan, Ying He, Guanhua Ren, Qiang Guo, Longqi Liu, Ying Gu, Xuan Dong, Ya Liu
Summary: Cell-cell interaction is an important way for transmitting information and activating the effects of functional cells. Researchers propose a droplet-based microfluidic platform for cell-cell interaction sequencing and screening, which allows for efficient analysis and interpretation of single-cell transcriptomes in cell interactions. This work fills a gap in the current experimental platform for cell-cell interaction research and has significant practical implications in biomedicine.
Article
Microbiology
Cody A. Despins, Scott D. Brown, Avery Robinson, Andrew J. Mungall, Emma Allen-Vercoe, Robert A. Holt
Summary: The study found that F. nucleatum-induced host cell transcriptional modulation involves strong upregulation of genes related to immune migration and inflammatory processes, in addition to identifying genes strongly upregulated in a cell line-specific manner. Furthermore, extensive host cell epigenomic changes specific to host cell type were observed upon F. nucleatum exposure.
Article
Biochemistry & Molecular Biology
Xirong Zhang, Yini Li, Xiaopan Chen, Bihui Jin, Chongyi Shu, Wanmao Ni, Yinshen Jiang, Jing Zhang, Lijia Ma, Jing Shu
Summary: Infertility is a global social and medical problem, and thin endometrium (TE) poses a great challenge to infertility treatment. This study used single-cell RNA sequencing to construct a transcriptomic atlas and identified cellular and molecular heterogeneity in TE. Differential expressed genes (DEGs) were found to affect cell-type ratio and impair endometrial receptivity in TE.
Article
Immunology
Minyuan Cao, Yun Deng, Yiqi Deng, Jing Wu, Chongyi Yang, Zijun Wang, Qianqian Hou, Huancheng Fu, Zhixiang Ren, Xuyang Xia, Yue Li, Wei Wang, Heng Xu, Xin Liao, Yang Shu
Summary: This study explores the heterogeneity and evolution of neuroectodermal cells within immature ovarian teratomas (PDT) at the single cell level through single-cell RNA sequencing and bioinformatic analysis. The study also reveals the role of immune cells in the tumor microenvironment and highlights the potential usage of CDTs as a model for PDT research.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Pengfei Liang, Lei Zheng, Chunshen Long, Wuritu Yang, Lei Yang, Yongchun Zuo
Summary: The development of HelPredictor, a machine learning platform that integrates feature selection methods and classifiers, has shown high accuracy in predicting human embryo lineage based on single-cell sequencing data. It can efficiently classify different embryonic lineages and explore transitions of embryonic heterogeneity.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Jinchen Li, Shanshan Hu, Kun Zhang, Leisheng Shi, Yi Zhang, Tingting Zhao, Lin Wang, Xin He, Kun Xia, Chunyu Liu, Zhongsheng Sun
MOLECULAR PSYCHIATRY
(2019)
Article
Oncology
Yue-Lei Chen, Yihe Zhang, Junwen Wang, Na Chen, Weiying Fang, Jianing Zhong, Yi Liu, Rui Qin, Xinxin Yu, Zhongsheng Sun, Fei Gao
MOLECULAR ONCOLOGY
(2019)
Review
Endocrinology & Metabolism
Yan Wang, Haodo Wu, Zhong Sheng Sun
FRONTIERS IN NEUROENDOCRINOLOGY
(2019)
Article
Neurosciences
Jianghong Zhang, Meiying Xue, Yue Mei, Zhigang Li, Zeng Ceng, Yuanyuan Li, Yi Zhang, Na Li, Huajing Teng, Zhong Sheng Sun, Yan Wang
PSYCHOPHARMACOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Zhuang Miao, Yan Wang, Zhongsheng Sun
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Huajing Teng, Wenqing Wei, Qinglan Li, Meiying Xue, Xiaohui Shi, Xianfeng Li, Fengbiao Mao, Zhongsheng Sun
NUCLEIC ACIDS RESEARCH
(2020)
Article
Psychiatry
Yi Zhang, Na Li, Chao Li, Ze Zhang, Huajing Teng, Yan Wang, Tingting Zhao, Leisheng Shi, Kun Zhang, Kun Xia, Jinchen Li, Zhongsheng Sun
TRANSLATIONAL PSYCHIATRY
(2020)
Article
Biochemical Research Methods
Xiaohui Shi, Huajing Teng, Leisheng Shi, Wenjian Bi, Wenqing Wei, Fengbiao Mao, Zhongsheng Sun
Summary: This study evaluates and compares the performance of different algorithms based on network, function, and frequency in identifying mutation driver genes. The results show that the frequency-based driverMAPS and network-based HotNet2 methods perform the best. Network-based algorithms using protein-protein interaction networks outperform function- and frequency-based methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Xiaohui Shi, Huajing Teng, Zhongsheng Sun
Summary: This article provides an updated overview of the conformation, current sequencing technologies, and computational identification methods for non-canonical nucleic acid structures, as well as their roles in related biological processes and diseases.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Xia Ran, Jinyuan Xiao, Fang Cheng, Tao Wang, Huajing Teng, Zhongsheng Sun
Summary: This study profiles tissue-specific codon optimality in human tissues and investigates the impact of synonymous mutations on codon optimality in human cancers. The findings suggest that optimal codon gain can promote tumor cell proliferation and serve as a prognostic biomarker in certain cancer types.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Oncology
Xia Ran, Jinyuan Xiao, Yi Zhang, Huajing Teng, Fang Cheng, Huiqian Chen, Kaifan Zhang, Zhongsheng Sun
THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY
(2020)
Article
Medicine, Research & Experimental
Huajing Teng, Meiying Xue, Jialong Liang, Xingxing Wang, Lu Wang, Wenqing Wei, Chao Li, Ze Zhang, Qinglan Li, Xia Ran, Xiaohui Shi, Wanshi Cai, Weihu Wang, Hengjun Gao, Zhongsheng Sun