截至目前，以第一/通讯作者累计在Nature Methods、Nucleic Acids Research、Research、Briefings in Bioinformatics等领域发表SCI论文100多篇（Google H指数34），论文被Nature、Nature Reviews Drug Discovery、Nature Reviews Molecular Cell Biology等国际顶级期刊引用超3700次，6篇入选ESI 1%全球高被引论文，获批国家发明专利和软件著作权20多项，先后主持承担国家高层次人才计划、国家重点研发计划、国家自然科学基金面上、青年等国家级项目8项，及省部级杰出青年基金、关键技术攻关等项目10多项。担任Current Gene Therapy、Scientific Reports期刊编委和Medinformatics期刊副主编等。

研究方法与兴趣：

多维度、跨尺度、跨时空、跨物种数字发育图谱绘制与数据库开发；时空多组学数据算法开发与生物信息学解析；多模态数据的精准医学与数智化家畜育种人工智能（AI）研发。

研究内容与科学发现：

1. 早期胚胎发育编程与体细胞重编程相关的“数字胚胎”研究：

        开发了空间多组学异构切片对齐算法3d-OT，构建了小鼠胚胎发育的3D时空轨迹 (Nature Methods, 2026)；提出基于定量描述“Waddington景观”哺乳动物早期胚胎发育和体细胞重编程过程细胞能量状态的方法 (Research, 2023，国家发明专利ZL 202211397106.0)，构建了最全面的哺乳动物多物种“数字发育”多组学资源库EmAtlas(Nucleic Acids Research, 2023；内蒙古新闻联播报道)和家畜繁育数据库LivestockDev (Zoological Research, 2025)，建立了细胞命运转变的人工智能预测平台EmPredictor(Bioinformatics, 2021; Brief Bioinform. 2021; 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、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 (Brief Bioinform. 2021)，提出模块化方法从中心法则(DNA-RNA-Protein)层面，解析了三种去甲基化酶家族TET、ALKBH、KDM非同源功能分化和特异性催化DNA，RNA和蛋白质底物适配性规律(Cell Mol Life Sci. 2021; Brief Bioinform. 2019, 2021; ESI 1% 高被引论文)。

2. 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)，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)。

部分代表性论文：

●Bingjie Dai, Litai Yi, Peizhuo Wang, Hanshuang Li, Pengwei Hu, Yancheng Song, Jixiang Xing, Zhenxing Feng, Zhiyuan Yuan*, Yongchun Zuo*, 3d-OT: A Deep Geometry-aware Framework for Heterogeneous Slices Alignment of Spatial Multi-omics, Nature Methods. 2026, DOI : 10.1038/s41592-026-03034-9. (中科院一区Top).

● PengCheng Song, YuChao Liang, Xiang He, QiYan Cheng, PengWei Hu, HanShuang Li, Yong Zhang, GuiFang Cao*, Yongchun Zuo*, LivestockDev: A multi-omics resource for exploring cross-species comparison of livestock embryogenesis, Zoological Research, 2025, DOI: 10.24272/j.issn.2095-8137.2025.328. (中科院一区Top).

● Bingjie Dai, Hanshuang Li, Peizhuo Wang, Pengwei Hu, Jixiang Xing, Yanan Hu, Qilemuge Xi, Yongchun Zuo*, DualNetM: an adaptive dual network framework for inferring functional-oriented markers. BMC Biology, (2025) 23:254. (中科院二区Top).

● Chunshen Long, Hanshuang Li, Zhifang Li, Jia Zhang, Qilemuge Xi, Yongchun Zuo*, Refining cell subpopulation identification and cell fate mapping using cell energy. Expert Systems with Applications, 2025 296 128999. (中科院一区Top).

● Jixiang Xing, Siqi Yang, Yuchao Liang, Pengwei Hu, Bingjie Dai, Hanshuang Li, Yongqiang Xing, Yongchun Zuo*, Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights from Machine Learning and the ZGAExplorer Platform. Cell Proliferation. 2025 e70039 (中科院一区Top).

● 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 (中科院一区Top).

● 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 (中科院二区).

● Zhihao Si, Hanshuang Li, Wenjing Shang, Yanan Zhao, Lingjiao Kong, Chunshen Long, Yongchun Zuo*, Zhenxing Feng*, SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network. Briefings in Bioinformatics. 2024 25(4):bbae259 (中科院计算生物学一区Top).

● Siqi Yang, Jixiang Xing, Dongyang Liu, Yancheng Song, Haoyu Yu, Shuhua Xu*, Yongchun Zuo*, Review and new insights into the catalytic structural domains of the Fe (ll) and 2-Oxoglutarate families, International Journal of Biological Macromolecules, 2024 278(Pt 4):134798. (中科院一区Top).

●  Lei Zheng, Pengfei Liang, Chunshen Long, Haicheng Li, Hanshuang Li, Yuchao Liang, Xiang He, Qilemuge Xi, Yongqiang Xing* and Yongchun Zuo*, EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis. Nucleic Acids Research, 2023, 51(D1), D924–D932 (中科院一区Top IF: 19.160).

●  Hanshuang Li, Chunshen Long, Yan Hong, Liaofu Luo*, Yongchun Zuo*, Characterizing Cellular Differentiation Potency and Waddington Landscape via Energy Indicator, Research, 2023, 6: 0118 (中科院一区Top IF: 11.036).

●  Hao Wang, Zhaoyue Zhang, Haicheng Li, ......, Yongqiang Xing*, Lei Yang*, Yongchun Zuo*, A cost-effective machine learning-based method for preeclampsia risk assessment and driver genes discovery. Cell & Bioscience, 2023, 13:41 (中科院二区Top IF: 9.584).

●  Jinzhao Li, Xiang He, Shuang Gao, Yuchao Liang, Zhi Qi, Qilemuge Xi, Yongchun Zuo*, Yongqiang Xing*, The Metal-binding Protein Atlas (MbPA): an integrated database for curating metalloproteins in all aspects, Journal of Molecular Biology, 2023 168117. (中科院二区 IF: 6.151).

●  Mingzhu Liu, Jian Zhou, Qilemuge Xi, Yuchao Liang, Haicheng Li, Pengfei Liang, Yuting Guo, Ming Liu, Temuqile Temuqile, Lei Yang*, Yongchun Zuo*, A computational framework of routine test data for the cost-effective chronic disease prediction, Briefings in Bioinformatics, 2023, 23: bbad054 (中科院计算生物学一区Top IF: 13.994).

●  Yuchao Liang, Siqi Yang, Lei Zheng, Hao Wang, Jian Zhou, Shenghui Huang, Lei Yang, Yongchun Zuo*, Research progress of reduced amino acid alphabets in protein analysis and prediction, Comput Struct Biotechnol J, 20, 2022, 3503-3510  (中科院二区 IF: 6.155).

●  Lei Zheng, Dongyang Liu, Yuan Alex Li, Siqi Yang, Yuchao Liang, Yongqiang Xing* and 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 (中科院一区Top IF: 19.160).

●  Yu Sun, Haicheng Li, Lei Zheng, Jinzhao Li, Yan Hong, Pengfei Liang, Lai-Yu Kwok, Yongchun Zuo*, Wenyi Zhang*, Heping Zhang*, iProbiotics: a machine learning platform for rapid identification of probiotic properties from whole-genome primary sequences. Briefings in Bioinformatics, 2022, 23(1) bbab477 (中科院计算生物学一区Top IF: 13.994).

●  Guoqing Liu*, Yu Sun, Lumeng Jia, Ruifeng Li, YongchunZuo*, Chromatin accessibility shapes meiotic recombination in mouse primordial germ cells through assisting double-strand breaks and loop formation, BBA-Gene Regulatory Mechanisms, 2022, 1865(5):194844. (中科院二区 IF:6.304)

●  Lemuge Chao, Siqi Yang, Hanshuang Li, Chunshen Long, Qilemuge Xi, Yongchun Zuo*. Competitive binding of TET1 and DNMT3A/B cooperates the DNA methylation pattern in human embryonic stem cells, BBA - Gene Regulatory Mechanisms, 2022, 1865 (7) 194861. (中科院二区 IF:6.304)

●  Hanshuang Li, Chunshen Long, Jinzhu Xiang, Pengfei Liang, Xueling Li*, Yongchun Zuo*, Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region, Briefings in Bioinformatics, 2021, 22(4):bbaa342. (中科院一区Top IF: 13.994).

●  Baofang Xu, Dongyang Liu, Zerong Wang, Ruixia Tian, Yongchun Zuo*, Multi-substrate Selectivity Based on Key Loops and Non-homologous Domains: New Insight into ALKBH Family, Cellular and Molecular Life Sciences, 2021, 78(1):129-141 (中科院一区Top IF: 9.261).

●  Pengfei Liang, Lei Zheng, Chunshen Long, Wuritu Yang, Lei Yang,*, Yongchun Zuo*, HelPredictor models single-cell transcriptome to predict human embryo lineage allocation, Briefings in Bioinformatics, 2021, 222(6):bbab196. (中科院一区Top IF: 13.994).

●  Shiyuan Wang, Qi Zhang, Chunlu Yu, Yiyin Cao, Yongchun Zuo*, Lei Yang*, Immune cell infiltration based signature for prognosis and immunogenomic analysis in breast cancer, Briefings in Bioinformatics, 2021, 22(2):2020-2031. (中科院一区Top IF: 11.622) ESI 1%高被引论文.

●  Hao Wang, Pengfei Liang, Lei Zheng, ChunShen Long, HanShuang Li, Yongchun Zuo*, eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition. Bioinformatics, 2021 37(15) 2157–2164. (2020 IF: 6.937).

●  Shiyuan Wang, Yuqiang Xiong, ......, Yongchun Zuo*, Lei Yang*,Clinical significance and immunogenomic landscape analyses of the immune cell signature based prognostic model for patients with breast cancer, Briefings in Bioinformatics, 2021, 22(4):bbaa311. (2020 IF: 11.622).

●  Zerong Wang, Dongyang Liu, Baofang Xu, Ruixia Tian, Yongchun Zuo*, Modular Arrangements of Sequence Motifs Determine the Functional Diversity of KDM Proteins, Briefings in Bioinformatics, 2021, 22(3):bbaa215 (2020 IF: 11.622).

●  Lei Zheng, Dongyang Liu, Wuritu Yang, Lei Yang*, Yongchun Zuo*,  RaacLogo: a new sequence logo generator by using reduced amino acid clusters, Briefings in Bioinformatics, 2021, 22(3):bbaa096 (2020 IF: 11.622) ESI 1%高被引论文.

●  Pengfei Liang, WurituYang, XingChen, ChunshenLong, LeiZheng ,HanshuangLi, YongchunZuo*, Machine Learning of Single-cell Transcriptome Highly Identify mRNA Signature by Comparing F-score Selection with Differential Expression Analysis, Molecular Therapy-Nucleic Acids, 2020, 20:155-163 (2019 IF: 7.032).

●  Hanshuang Li, Mingmin Song, Wuritu Yang, Pengbo, Cao, Lei, Zheng, Yongchun Zuo*, A comparative Analysis of Single-cell Transcriptome Identify Reprogramming Driver Factor for Efficiency Improvement, Molecular Therapy-Nucleic Acids, 2020, 19, 1053-1064 (2019 IF: 7.032).

●  Lei Zheng, Shenghui Huang, Nengjiang, Mu, Haoyue, Zhang, Jiayu Zhang, Yu Chang, Lei Yang*, Yongchun Zuo*, RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference, Database, 2019, baz131. (2019 IF: 2.593).

●  Hanshuang Li, Na Ta, Chunshen Long, Qiutang Zhang, Siyu Li, Shuai Liu, Lei Yang*, Yongchun Zuo*. The spatial binding model of the pioneer factor Oct4 with its target genes during cell reprogramming, Comput Struct Biotechnol J, 2019, 17, 1226-1233. (2018IF: 4.720).

●  Bosu Hu, Lei zheng, Chunshen Long, Mingmin Song, Tao Li, Lei Yang*, Yongchun Zuo*. EmExplorer：A database for exploring time activation of gene expression in mammalian embryos. Open Biology. 2019 9(6):190054.. (2018IF: 3.890).

●  Chunshen Long, Wei Li, Pengfei Liang, Shuai Liu, Yongchun Zuo*, Transcriptome Comparisons of Multi-species Identify Differential Genome Activation of Mammals Embryogenesis. 2019, IEEE Access, 2019, 7:7794-7802. (2018 IF: 4.098) ESI 1%高被引论文.

●  Dongyang Liu, Guangpeng Li*, Yongchun, Zuo*, Function determinants of TET proteins: the arrangements of sequence motifs with specific codes. Briefings in Bioinformatics. 2019, 20 (5), 1826-1835. (2018 IF: 9.101) ESI 1%高被引论文.

●  Guangqi Gao, Meng Xu, Chunling Bai, ......, Jun Yin*, Yongchun Zuo*, Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage colouration. GigaScience, 2018, 7(10) 1-14. (2017 IF: 7.267).

●  Yongchun Zuo*, Yuan Li, Yingli Chen, Guangpeng Li, Zhenhe Yan, Lei Yang. PseKRAAC: A flexible web server for generating pseudo K-tuple reduced amino acids composition. Bioinformatics. 2017, 33(1):122-124 (2016 IF:7.307).ESI 1%高被引论文.