研究领域
研究内容： 我们主要以下几方面展开生物信息学研究：
(1) 发育和重编程大数据生命组学方面：通过将目前公共数据平台的高通量基因组、转录组、表观组等多组学数据与本实验室内部产生的数据进行整合分析，利用大数据生物信息学方法系统分析哺乳动物早期胚胎发育和体细胞多种重编程的分子差异，首次揭示了异种克隆动物胚胎发育受阻的关键转录因子调控网络（BMC Genomics. 2016 17:188; Brief Bioinform. 2017 18(4):712-721），筛选并探究一系列引起细胞编程和重编程阻滞的分子调控通路（Oncotarget, 2016 7(45): 74120-74131；Oncotarget, 2017），最近基于蛋白质家族序列保守性和选择进化压力，解析了DNA去甲基化关键蛋白TET家族功能发挥的序列基础（Brief Bioinform. 2018 bby053）。
(2) 计算生物学方面：自2009年起，较早地发展了基于DNA物理化学作为特征参数建立原核生物和植物启动子基因组区域预测模型的方法(Prog Biochem Biophys 2009 36(7): 863-871; Physica A 2010 389(19) 4217–4223; Genomics 2011 97(3): 112-120)，首次将离散增量算法与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, 38:859–867)和K 近邻最小离散增量算法KNN-ID(Amino Acids. 2013, 44(2):573-80; Mol Biosyst. 2015 11(3):950-7)，发展了基于蛋白质序列氨基酸约化(Reduced Amino Acids)用于蛋白质的功能分类的方法(Peptides. 2009, 30(10)1788–1793; Plos one, 2015 10(12):e0145541)，成功搭建了大数据蛋白质序列氨基酸约化与特征提取数据分析平台(Bioinformatics. 2017, 33(1):122-124)。
(3) 功能基因组学方面：开发了一套基于生物信息学方法的外源基因密码子优化和组织特异性表达调控元件改造方法，优化的人源化亚麻脂肪酸脱氢酶基因FAD3已经成功用于动物基因修饰育种(国家发明专利号：ZL201310344833.5)。通过筛选出具有组织特异的启动子和增强子序列转录因子结合位点调控Motif，该算法已成功构建了MRF4人工设计肌肉特异性表达启动子调控元件(国家发明专利号：ZL201410123506.1)，已在具有经济价值的动物基因编辑育种上进行了试验，效果明显。
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(62). 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 Biol. 2019, doi/10.1098/rsob.190054. (2018IF: 3.890).
(61). Shuai Liu, Mengye Lu, Hanshuang Li, Yongchun Zuo*, Prediction of Gene Expression Patterns with Generalized Linear Regression Model. Frontiers in Genetics, 2019, 10:120. (2017 IF: 4.151).
(60). 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).
(59). Dongqing Su, Qianzi Lu, Qi Zhang, Shiyuan Wang, Yi Pan, Yongchun Zuo*, Lei Yang, Characterization of human proteins with different subcellular localizations by topological and biological properties. Genomics, 2019, https://doi.org/10.1016/j.ygeno.2018.12.006. (2018 IF: 3.160).
(58). Yi Pan, Shiyuan Wang, Qi Zhang, Qianzi Lu, Dongqing Su, Yongchun Zuo*, Lei Yang. Analysis and prediction of animal toxins by various Chou’s pseudo components and reduced amino acid compositions. Journal of Theoretical Biology 462 (2019) 221–229.(2018 IF: 1.875).
(57). Wen Jin, Qianzhong Li, Yongchun Zuo, Yanni Cao, Luqiang Zhang, Rui Hou, Wenxia Su, The relationship between DNA methylation in key region and the differential expressions of genes in human breast tumor tissue, DNA and Cell Biology, 2019 38(1) 49-62. (2018 IF: 2.918).
(56). Qi Zhang, Shiyuan Wang, Yi Pan, Dongqing Su, Qianzi Lu, Yongchun Zuo*, Lei Yang*, Characterization of proteins in different subcellular localizations for Escherichia coli K12, Genomics, 2019, https://doi.org/10.1016/j.ygeno.2018.07.008. (2018 IF: 3.160).
(55). Liu DY, Li GP, Zuo YC*, Function determinants of TET proteins: the arrangements of sequence motifs with specific codes. Brief Bioinform. 2019, bby053, https://doi.org/10.1093/bib/bby053. (2018 IF: 9.101) .
(54). 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).
(53). Rongsong Luo, Chunling Bai, Lei Yang, Zhong Zheng, Guanghua Su, Guangqi Gao, Zhuying Wei, Yongchun Zuo*, Guangpeng Li, DNA methylation subpatterns at distinct regulatory regions in human early embryos, Open Biol. 2018, 8: 180131. (2017 IF: 3.286).
(52). Wang SY, Huo HY, Su DQ, Lu QZ, Chen XW, Yang L, Zuo YC*, Lv YL, Characterize the difference between TMPRSS2-ERG and non-TMPRSS2-ERG fusion patients by clinical and biological characteristics in prostate cancer, Gene, 2018 679:186-194. (2017 IF: 2.498).
(51). Lei Yang, Shiyuan Wang, Qi Zhang, Yi Pan, Yingli Lv, Xiaowen Chen, Yongchun Zuo* and Dapeng Hao, Clinical significance of immune microenvironment in ovarian cancer patients. Mol. Omics, 2018, 14, 341-351. (2016 IF: 2.781).
(50). Luqiang Zhang, Qianzhong Li, Wen Jin, Yongchun Zuo, Shuchun Guo. Genome-wide analysis of H3K36me3 and its regulations to cancer-related genes expression in human cell lines.Biosystems 2018, 171(2018) 59-65, (2017 IF: 1.619).
(49) Mengye Lu, Shuai Liu, Arun Kumarsangaiah, Yunpeng Zhou, Zheng Pan, Yongchun Zuo, Nucleosome Positioning with Fractal Entropy Increment of Diversity in Telemedicine. IEEE Access, 2018, 6：33451-33459. (2017 IF: 3.557)
(48) Zuo YC*, Su GH, Cheng L, Liu K, Feng Y, Wei ZY, Bai CL, Cao GF, Li GP*, Coexpression analysis identifies nuclear reprogramming barriers of somatic cell nuclear transfer embryos, Oncotarget, 2017, 8(39) 65847-65859 (2016 IF: 5.168).
(47) Huo HY, Li T, Wang SY, Lv YL, Zuo YC*, Yang L*, Prediction of presynaptic and postsynaptic neurotoxins by using Pseudo amino acid composition and motif features, Scientific Reports, 7: 5827 (2016 IF: 4.259).
(46) Yang L, Wang SY, Zhou M, Chen XW, Jiang W*, Zuo YC*, lv YL*, Molecular classification of prostate adenocarcinoma by the integrated somatic mutation profiles and molecular network. Scientific Reports, 2017, 7(1):738. (2016 IF: 4.259).
(45) Guo SC# , Zuo YC#, Zhang YF, Wu CY, Su WX, Jin W, Yu HF, An YL, Li QZ*. Large-scale transcriptome comparison of sunflower genes responsive to Verticillium dahliae. BMC Genomics. 2017. 18(1):42 (2015 IF: 3.867).
(44) Zuo YC*, Li Y, Chen YL, Li GP, Yan ZH, Yang L. 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.
(43) Che D, Wang Y, Bai W, Li L, Liu G, Zhang L, Zuo YC, Tao S, Hua J, Liao M*. Dynamic and modular gene regulatory networks drive the development of gametogenesis. Brief Bioinform. 2017 18(4):712-721. (2015 IF: 5.134)
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