研究方向
欢迎访问内蒙古大学生物信息学实验室,我们的研究方向主要集中于:
早期胚胎发育编程与体细胞重编程相关的“数字胚胎”研究:
提出一种基于能量指标定量描述沃丁顿景观中哺乳动物早期胚胎发育和体细胞重编程过程细胞状态的方法 (Research, 2023,国家发明专利ZL 202211397106.0),构建完成了哺乳动物早期发育时空调控多组学数据资源库与云平台EmAtlas(Nucleic Acids Research, 2023 内蒙古新闻联播报道)和多物种胚胎发育时序性激活数据库EmExplorer (Open Biol. 2019; 软著2019SR0463259),建立了细胞命运转变的人工智能预测平台EmPredictor(Bioinformatics, 2021; Brief Bioinform. 2021; 软著2019SR0463259; 科技日报报道),筛选了全面的体细胞重编程过程胚胎基因组激活(ZGA)的分子屏障(J Cell Mol Med, 2022; Mol Ther Nucleic Acids. 2020)、R-loop与组蛋白修饰协同调控等表观调控障碍 (BBA-Gene Regulatory Mechanisms. 2022a,b; Theriogenology, 2020; Int J Mol Sci. 2021,2022),完成先锋转录因子竞争性和协同靶向调控细胞重编程的理论生物学描述 (Comput Struct Biotechnol J, 2019; Brief Bioinform. 2021),改进了物种特异性胚胎基因组激活比较转录组方法 ( Mol Ther Nucleic Acids. 2020; ESI 1% 高被引论文),基于序列保守性和选择进化压力,解析了去甲基化关键蛋白TET、ALKBH、KDM家族功能发挥的序列基础(Cell Mol Life Sci. 2021; Brief Bioinform. 2019, 2021; ESI 1% 高被引论文)。
单细胞组学与时空组学多模态数据生物信息学算法研究:
提出一种基于最小离散增量的时序性单细胞轨迹推断的方法IDTI(Fundamental Research. 2024),提出了一种基于EfficientNet卷积神经网络开展时空转录组空间域的方法EfNST(Communications Biology. 2024),构建了首个基于人工智能模型的预测益生菌的方法及平台(Brief Bioinform. 2021, 国家发明专利ZL202211397170.9)针对能否用较少氨基酸类别开展蛋白质序列、结构及功能的分析和从头设计?先后开发了基于氨基酸约化字母表 (RAAC)进行蛋白质功能的人工智能(AI)研究 (Peptides. 2009),搭建了分析与特征提取平台RaacBook (Bioinformatics. 2017; ESI 1% 高被引论文; Database, 2019; 软著2019SR0467812),开发了RaacLogo (Brief Bioinform. 2021; ESI 1% 高被引论文)和RaacFold (Nucleic Acids Research, 2022; 内蒙古人民政府官网报道)。早期工作还包括:发展了基于DNA空间几何描述参数建立启动子机器学习预测模型的方法 (Prog Biochem Biophys 2009; Physica A 2010; Genomics 2011),将离散增量(ID)与K紧邻算法有机结合,先后提出了K 近邻平均离散增量算法K-MID (Amino Acids 2010)和K 近邻最小离散增量算法KNN-ID (Amino Acids. 2013; Mol Biosyst. 2015)等。
最新成果
Yanan Zhao, Chunshen Lon, Wenjing Shang, Zhihao Si, Zhigang Liu*, Zhenxing Feng*, Yongchun Zuo*. A composite scaling network of EfficientNet for improving spatial domain identification performance.Communications Biology.2024 7(1):1567(2023 IF:5.2).
Yan Hong, Hanshuang Li, Chunshen Long, Pengfei Liang, Jian Zhou, Yongchun Zuo*.An increment of diversity method for cell state trajectory inference of time-series scRNA-seq data.Fundamental Research. 2024 4(4):770-776 (2023 IF:6.2).
Hanshuang Li, Chunshen Long, Yan Hong, Liaofu Luo, Yongchun Zuo*. Characterizing Cellular Differentiation Potency and Waddington Landscape via Energy Indicator,Research, 2023, 6: 0118 (2021 IF: 11.036).
Lei Zheng, Pengfei Liang, Chunshen Long, Haicheng Li, Hanshuang Li, Yuchao Liang, Xiang He, Qilemuge Xi, Yongqiang Xing*, Yongchun Zuo*. EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis.Nucleic Acids Research, 2023, 51(D1), D924-D932 (2021 IF: 19.160).
Lei Zheng, Dongyang Liu, Yuan Alex Li, Siqi Yang, Yuchao Liang, Yongqiang Xing*, Yongchun Zuo*.RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets.Nucleic Acids Research, 2022, 50(W1), W633-W638 (2021 IF: 19.160).