以第一或通讯作者发表论文：
1.Chengwei Liang, Junyu Liu, Wenzhu Peng, Boyu Wang, Fan Yang, Weiwei You, Ying Wang*, AquaGS: An integrated GUI pipeline for genomic selection in aquaculture breeding, SoftwareX, Volume 27, 2024, 101770
.
2.Wenhao Zhang, Rui Jiang, Shengquan Chen, Ying Wang*, scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data. Genome Biology 24, 225 (2023).
3.王博宇,杨孜孜,SUN Fengzhu, 王颖*. 基于智能计算噬菌体的细菌宿主范围预测.微生物学报:1-24[2023-10-14].
4.Zhi Ma, Yang Young Lu*, Yiwen Wang, Renhao Lin, Zizi Yang, Fang Zhang, Ying Wang*; Metric learning for comparing genomic data with triplet Network. Briefings in Bioinformatics, 2022, bbac345
5.Yiluan Zheng#, Jianlu Shi#, Qi Chen, Chao Deng, Fan Yang, Ying Wang*; Identifying individual-specific microbial DNA fingerprints from skin microbiomes. Frontiers in Microbiology. 2022 Oct 6;13:960043.
6.Chao Deng#, Wenzhu Peng#, Zhi Ma, Caihuan Ke, Weiwei You*, Ying Wang*; AquaGWAS: a GWAS pipeline for aquatic animals and its application to reference-required and reference-free GWAS for abalone, Frontiers in Marine Science, 2022, Jan.
7.Yujie Hou#, Xiong Zhang#, Qinyan Zhou#, Ying Wang*, Hierarchical microbial functions prediction by graph aggregated embedding, Frontiers in Genetics, 2020, Nov.
8.Yang Young Lu#, Jiaxing Bai#, Yiwen Wang, Ying Wang*, Fengzhu Sun*，CRAFT: Compact genome Representati on toward large-scale Alignment-Free database, Bioinformatics, 2020, August
9.Ying Wang*, Qi Chen, Chao Deng, Yiluan Zheng, and Fengzhu Sun*, KmerGO: A Tool to Identify Group-Specific Sequences With k-mers. Frontiers in Microbiology, 2020 Nov.
10.Xingze Wang, Bin Tan, Xuan Luo, Caihuan Ke, Miaoqin Huang, Weiwei You*, Ying Wang*; Effects of temperature, diet and genotype-induced variations on the gut microbiota of abalone, Aquaculture, 2020, 524: 735269.
11.Ziye Wang, Ying Wang, Jed A Fuhrman, Fengzhu Sun, Shanfeng Zhu, Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences, Briefings in Bioinformatics, Volume 21, Issue 3, May 2020, Pages 777–790, bbz025, https://doi.org/10.1093/bib/bbz025
12.Zicheng Wang, Huazhe Lou, Ying Wang, Ron Shamir, Rui Jiang, Ting Chen, GePMI: A statistical model for personal intestinal microbiome identification[J]. npj Biofilms and Microbiomes, 2018, 4(1):20.
13.Ying Wang*, Lei Fu, Jie Ren, Zhaoxi Yu, Ting Chen, Fengzhu Sun*, Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures. Frontiers in Microbiology, 2018, 9:872. doi: 10.3389/fmicb.2018.00872
14.Ying Wang*, Kun Wang, Yang Young Lu and Fengzhu Sun*, Improving contig binning of metagenomic data using d2sBin oligonucleotide frequency dissimilarity. BMC Bioinformatics, 18:425(2017)
15.Weinan Liao, Jie Ren, Kun Wang, Shun Wang, Feng Zeng, Ying Wang*, Fengzhu Sun*, Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains. Scientific Reports, 2016, 6, 37243; doi: 10.1038/srep37243.
16.Ying Wang *, Xiaoye Lei, Shun Wang, Zicheng Wang, Nianfeng Song, Feng Zeng, Ting Chen, Effect of k-tuple length on sample-comparison with high-throughput sequencing data. Biochemical and Biophysical Research Communications, 2016, 469(4):1021-7.
17.Ying Wang*, Lina Chen, Nianfeng Song, Xiaoye Lei, GASS: genome structural annotation for Eukaryotes based on species similarity. BMC Genomics, 2015, 16:150
18.Lijuan Zhang, Tianci Guo, Bin Xi, Fan Yang, Kun Wang, Jiancheng Bi, Ying Wang* Automatic recognition of cardiac arrhythmias based on the geometric patterns of Poincaré plots. Physiological Measurement, 2015, 36, 283–301
19.Ying Wang*, Lin Liu, Lina Chen, Ting Chen, Fengzhu Sun*, Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies. PLoS ONE, 2014, 9(1): e84348. doi:10.1371/journal.pone.0084348
20.王颖, 刘麟. 一种基于RNA-Seq 的基因组注解评估方法. 科学通报, 2013, 58: 3471–3482, doi: 10.1360/972012-1038
21.Kai Feng, Ying Wang*, A Valid Method of Inverse R Wave Detection，Journal of Computational Information Systems ,vol.9,no. 3,2013.
22.Ying Wang*, Gaurang Mehta, Rajiv Mayani, Jingxi Lu, Tade Souaiaia, Yangho Chen, Andrew Clark, Oleg V. Evgrafov, James A. Knowles*, Ewa Deelman*, Ting Chen*, RseqFlow: Workflows for RNA-Seq data analysis, Bioinformatics. 2011 Sep 15;27(18):2598-600
发明专利
1.一种宏基组和宏转录组样本相异度的比较方法，ZL201610100159.X，授权日期：2018年7月17日
2.基于不同尺度tuple词频的微生物高通量测序数据分析协议，ZL201610577084.4，授权日期：2018年12月11日
3.一种基于k-tuple频度的核酸序列搜索方法及系统，ZL202010083043.6，授权日期：2022年4月29日
4.一种基于三元组神经网络的物种生物学分类方法及系统，ZL202010385660.1，授权日期：2022年4月29日
5.基于宏基因组的样本特异的物种互作网络构建方法及系统， ZL20221 0786638.7，授权日期：2023年5月23日
6.基于皮肤宏基因组数据的身份鉴定特征提取方法及系统，ZL20211 0158603.4，授权日期：2024年02月20日
