截至目前，以第一/通讯作者累计在Nucleic Acids Research (IF: 19.160)、Research (IF: 11.036)、Cellular and Molecular Life Sciences (IF: 9.261)、Briefings in Bioinformatics( IF: 13.994)、Bioinformatics (IF:7.307)等领域内知名期刊上发表SCI论文80多篇（谷歌H指数31），其中6篇成果入选ESI 1%全球高被引论文，相关数据技术方法获批国家发明专利和软件著作权20多项，成果先后被人民日报、科技日报、内蒙古自治区人民政府官网、内蒙古科技厅官网、创新内蒙古等媒体报道转载，个人杰青事迹作为“先锋”模范被内蒙古科技厅专题报道；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7项，及省部级杰出青年基金、重点研发计划等项目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：

多维度跨尺度调控图谱绘制与数据库开发；多组学联合技术的生物信息学解析；多模态数据的人工智能建模。

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：

        提出了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)。

2. 关键核酸/蛋白质调控因子功能发挥相关的计算生物学研究：

        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)，将多样性增量算法(ID)与K紧邻算法有机结合，先后提出了K 近邻平均多样性增量算法K-MID (Amino Acids 2010)和K 近邻最小多样性增量算法KNN-ID (Amino Acids. 2013; Mol Biosyst. 2015)。构建了一种基于人工智能模型的预测微生物益生潜力的方法及其装置（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)进行蛋白质功能分类的人工智能(AI)建模研究 (Peptides. 2009)，搭建了蛋白质序列分析与特征提取平台RaacBook (Bioinformatics. 2017; ESI 1% 高被引论文; Database, 2019; 软著2019SR0467812)，开发了可视化蛋白质功能域的模体(motif)分析方法RaacLogo (Brief Bioinform. 2021; ESI 1% 高被引论文)和结构生物信息分析工具RaacFold (Nucleic Acids Research, 2022; 内蒙古人民政府官网报道)。

部分代表性论文：

● 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).

● 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. (2023 IF:8.2).

● 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 (2021 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 (2021 IF: 11.036).

● Hao Wang, Zhaoyue Zhang, Haicheng Li, Jinzhao Li, Hanshuang Li, Mingzhu Liu, Pengfei Liang, Qilemuge Xi, 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 (2021 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. (2021 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 (2021 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  (2021 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 (2021 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 (2021 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. (2021 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. (2021 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. (2021 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 (2020 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. (2021 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. (2020 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, Qi Zhang, Dongqing Su, Chunlu Yu, Yiyin Cao, Yi Pan, Qianzi Lu, 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, Yulan Yang, Guangpeng Li, Junyang Xu ,Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, 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.