发表学术论文100余篇，其中SCI核心期刊60余篇。
1.《数量分类的方法与程序》 武汉大学出版社 1990
2.《水生植被研究的理论与方法》 华中师范大学出版社 1992
3.《分支分类的理论与方法》 科学出版社 1994
4.《简明生物信息学》 高等教育出版社 2001
5.《分子进化与系统发育》 高等教育出版社 2002
6.《生物信息学》 高等教育出版社 2003
7.《基因, 女郎, 伽莫夫》 上海科技教育出版社 2003
8.《基因计算》 上海科技教育出版社 2005
9.《林肯的DNA》 上海科技教育出版社 2005
10.《计算分子进化》 复旦大学出版社 2008
英文：
1. Jung, S., Perkins, S., Zhong, Y., Pramanik, S., Beaman, J. H. 1995. A new data model for biological classification. Computer Applications in Biosciences (CABIOS) 11: 237-246.
2. Zhong, Y., Jung, S, Pramanik, S, Beaman, J H. 1996. Data model and comparison and query methods for interacting classifications in a taxonomic database. Taxon 45(2): 223-241.
3. Zhong, Y., Meacham, C. A., Pramanik, S. 1997. A general method for tree-comparison based on subtree similarity and its use in a taxonomic database. BioSystems 42: 1-8.
4. Zhong, Y., Luo, Y., Pramanik, S., Beaman, J. H. 1999. HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees. Bioinformatics 15(2): 149-156.
5. Zhong, Y., Shi, S. H., Tang, X. H., Huang, Y. L., Tan, F. X., Zhang, X. Y. 2000. Testing relative evolutionary rates and estimating divergence times among six genera of Rhizophoraceae using cpDNA and nrDNA sequences. Chinese Science Bulletin 45: 1011-1015.
6. Shi, S., Jin, H., Zhong, Y., He, X., Huang, Y., Tan, F., Boufford, D. E. 2000. Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences. Theoretical and Applied Genetics 101: 925-930.
7. Sang, T., Zhong, Y. 2000. Testing hybridization hypotheses based on incongruent gene trees. Systematic Biology 49: 422-434.
8. Cui, X. H., Zhong, Y., Chen, J. K. 2000. Influence of a catastrophic flood on densities and biomasses of three plant species in Poyang Lake, China. Journal of Freshwater Ecology 15: 537-541.
9. He, Z. C., Zhang, X. Y., Zhong, Y., Ye, L. 2000. Phylogenetic relationships of Actinidia and related genera based on micromorphological characters of foliar trichomes. Genetic Resources and Crop Evolution 47: 627-639.
10. Wang, J. B., Wang, C., Shi, S. H., Zhong, Y. 2000. ITS regions in diploids of Aegilops (Poaceae) and their phylogenetic implications. Hereditas 132: 209-213.
11. Wang, J. B., Wang, C., Shi, S. H., Zhong, Y. 2000. Evolution of parental ITS regions of nuclear rDNA in allopolyploid Aegilops (Poaceae) species. Hereditas 133: 1-7.
12. Zhong, Y., Zhang, L., Su, D. M. 2000. Collaborations tailored for bioinformatics projects. Science 290: 2074. (Letter)
13. Shi, S., Huang, Y., Zhong, Y., Du, Y., Zhang, Q., Chang, H., Boufford, D.E. 2001. Phylogeny of the Altingiaceae based on cpDNA matK, PY-IGS and nrDNA ITS sequences. Plant Systematics and Evolution 230: 13-24.
14. Wu, J., Liang, Y., Zhong, Y., Fu, C., Chen, J. 2002. Advances in phylogenetic studies of Nematoda. Chinese Science Bulletin 47: 10-15.
15. Huang, Y., Shi, S., Zhong, Y., Tan, F. 2002. A new method for preparation of template DNA for PCR from special plant materials. Chinese Science Bulletin 47: 725-727.
16. Shi, S., Zhong, Y., Huang, Y., Du, Y., Qiu, X., Chang, H. 2002. Phylogenetic relationships of the Rhizophoraceae in China based on sequences of the chloroplast gene matK and the internal transcribed spacer regions of nuclear ribosomal DNA and combined data set. Biochemical Systematics and Ecology 30: 309-319.
