第一及通讯作者论著（# 第一作者，* 通讯作者）
1. Yinggai Song#, Songnian Hu, Sybren de Hoog, Xiao Liu, Xingye Meng, Ruoning Xue, Anne van Diepeningen, Fokkens Like, Ruoyu Li, Shenghan Gao*. Medical Fusarium: novel species or uncertain identifications?. mycosphere, 2023
2. Tao Yang#, Rong Liu#, Yingfeng Luo#, Songnian Hu#, Dong Wang#, Chenyu Wang, Manish K Pandey, Song Ge, Quanle Xu, Nana Li, Guan Li, Yuning Huang, Rachit K Saxena, Yishan Ji, Mengwei Li, Xin Yan, Yuhua He, Yujiao Liu, Xuejun Wang, Chao Xiang, Rajeev K Varshney*, Hanfeng Ding*, Shenghan Gao*, Xuxiao Zong*. Improved pea reference genome and pan - genome highlight genomic features and evolutionary characteristics. Nat Genet, 2022
3. Qinglan Sun#, Chang Shu#, Wenyu Shi, Yingfeng Luo, Guomei Fan, Jingyi Nie, Yuhai Bi, Qihui Wang, Jianxun Qi, Jian Lu, Yuanchun Zhou, Zhihong Shen, Zhen Meng, Xinjiao Zhang, Zhengfei Yu, Shenghan Gao*, Linhuan Wu*, Juncai Ma*, Songnian Hu*. VarEPS: an evaluation and prewarning system of known and virtual variations of SARS - CoV - 2 genomes. Nucleic Acids Res, 2022
4. Qianhui Zhu#, Shenghan Gao#, Binghan Xiao, Zilong He*, Songnian Hu*. Plasmer: an accurate and sensitive bacterial plasmid prediction tool based on machine - learning of shared k - mers and genomic features. Microbiology Spectrum, 2023
5. Wang Sen#, Gao Shenghan#, Nie Jingyi#, Tan Xinyu#, Xie Junhua, Bi Xiaochun, Sun Yan, Luo Sainan, Zhu Qianhui, Geng Jianing, Liu Wanfei, Lin Qiang, Cui Peng*, Hu Songnian*, Wu Shuangyang*. Improved 93 - 11 Genome and Time - Course Transcriptome Expand Resources for Rice Genomics. Frontiers in Plant Science, 2022
6. Yue Xie#, Sen Wang#, Shuangyang Wu#, Shenghan Gao#, Qingshu Meng#, Chengdong Wang, Jingchao Lan, Li Luo, Xuan Zhou, Jing Xu, Xiaobin Gu, Ran He, Zijiang Yang, Xuerong Peng, Songnian Hu*, Guangyou Yang*. Genome of the giant panda roundworm illuminates its host shift and parasitic adaptation. Genomics, Proteomics & Bioinformatics, 2021
7. Alice Easton#, Shenghan Gao#, Scott P Lawton, Sasisekhar Bennuru, Asis Khan, Eric Dahlstrom, Rita G Oliveira, Stella Kepha, Stephen F Porcella, Joanne Webster, Roy Anderson, Michael E Grigg, Richard E Davis*, Jianbin Wang*, Thomas B Nutman*. Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans. eLife, 2020
8. Wu Shuangyang#, Shenghan Gao#, Sen Wang, Jie Meng, Jacob Wickham, Sainan Luo, Xinyu Tan, Haiying Yu, Yujia Xiang, Songnian Hu, Lilin Zhao, and Jianghua Sun*. A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode. Genes, 2020
9. Peng Wang#, Yingfeng Luo#, Jianfeng Huang#, Shenghan Gao#, Guopeng Zhu, Zhiguo Dang, Jiangtao Gai, Meng Yang, Min Zhu, Huangkai Zhang, Xiuxu Ye, Aiping Gao, Xinyu Tan, Sen Wang, Shuangyang Wu, Edgar B. Cahoon, Beibei Bai, Zhichang Zhao, Qian Li, Junya Wei, Huarui Chen, Ruixiong Luo, Deyong Gong, Kexuan Tang, Bing Zhang, Zhangguang Ni, Guodi Huang, Songnian Hu*, Yeyuan Chen*. The genome evolution and domestication of tropical fruit mango. Genome Biology, 2020
10. Subramanian Balakrishnan#, Gao Shenghan#, Lercher Martin J, Hu Songnian*, Chen Wei - Hua*. Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. Nucleic Acids Research, 2019
11. Chunhui Li#, Wei Song#, Yingfeng Luo#, Shenghan Gao#, Ruyang Zhang, Zi Shi, Xiaqing Wang, Ronghuan Wang, Fengge Wang, Jidong Wang, Yanxin Zhao, Aiguo Su, Shuai Wang, Xin Li, Meijie Luo, Shuaishuai Wang, Yunxia Zhang, Jianrong Ge, Xinyu Tan, Ye Yuan, Xiaochun Bi, Hang He, Jianbing Yan, Yuandong Wang*, Songnian Hu*, Jiuran Zhao*. The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize. Molecular Plant, 2019
参与发表论著（非第一作者非通讯作者）
1. Qianhui Zhu#, Qi Chen#, Shenghan Gao, Zhenpeng Li, Haijian Zhou, Zhigang Cui, Guomei Fan, Xiao Liu, Xinmiao Wu, Juncai Ma, Biao Kan*, Songnian Hu*, Linhuan Wu*, Xin Lu*, PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes, Nucleic Acids Research, Volume 53, Issue D1, D169–D178, 2024
2. Ming Chen#, Lin Xia#, Xinyu Tan, Shenghan Gao, Sen Wang, Man Li, Yuansheng Zhang, Tianyi Xu, Yuanyuan Cheng, Yuan Chu, Songnian Hu*, Shuangyang Wu*, Zhang Zhang*. Seeing the unseen in characterizing RNA editome during rice endosperm development. Communication Biology, 2024
3. Qi Lu, Pengcheng Wang, Jiang Chang, De Chen, Shenghan Gao, Jacob Höglund, Zhengwang Zhang*. Population genomic data reveal low genetic diversity, divergence and local adaptation among threatened Reeves's Pheasant (Syrmaticus reevesii). Avian Research, 2024
4. Chang Shu#, Qinglan Sun#, Guomei Fan, Kesheng Peng, Zhengfei Yu, Yingfeng Luo, Shenghan Gao, Juncai Ma, Tao Deng, Songnian Hu*, Linhuan Wu*. VarEPS - Influ: an risk evaluation system of occurred and virtual variations of influenza virus genomes. Nucleic Acids Research, 2023
5. Hui Wang, Shenghan Gao, Yu Liu, Pengcheng Wang, Zhengwang Zhang, De Chen*. A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi - sample genomic data. Ecology and Evolution, 2022
6. Guan Li, Rong Liu, Rongfang Xu, Rajeev K. Varshney, Hanfeng Ding, Mengwei Li, Xin Yan, Shuxian Huang, Juan Li, Dong Wang, Yishan Ji, Chenyu Wang, Junguang He, Yingfeng Luo, Shenghan Gao, Pengcheng Wei*, Xuxiao Zong*, Tao Yang*. Development of an Agrobacterium - mediated CRISPR/Cas9 system in pea (Pisum sativum L.). The Crop Journal, 2022
7. Xiaolu Tang#, Ruochen Ying#, Xinmin Yao#, Guanghao Li, Changcheng Wu, Yiyuli Tang, Zhida Li, Bishan Kuang, Feng Wu, Changsheng Chi, Xiaoman Du, Yi Qin, Shenghan Gao, Songnian Hu, Juncai Ma, Tiangang Liu, Xinghuo Pang, Jianwei Wang, Guoping Zhao, Wenjie Tan*, Yaping Zhang*, Xuemei Lu*, Jian Lu*. Evolutionary analysis and lineage designation of SARS - CoV - 2 genomes. Science Bulletin, 2021
8. De Chen#, Yang Liu, Geoffrey Davison, Ding Li Yong, Shenghan Gao, Junhua Hu, Shou - Hsien Li, Zhengwang Zhang*. Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences. Molecular Phylogenetics and Evolution, 2020
9. Shuai Jin#, Hongyuan Fei#, Zixu Zhu#, Yingfeng Luo#, Jinxing Liu, Shenghan Gao, Feng Zhang, Yu - Hang Chen, Yanpeng Wang*, Caixia Gao*. Rationally Designed APOBEC3B Cytosine Base Editors with Improved Specificity. Molecular Cell, 2020
10. Yuan Liang#, Dengxue Lu#, Sen Wang#, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng*, Jianing Geng*, Songnian Hu*. Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe Cylindracea. Genomics, Proteomics & Bioinformatics, 2020
11. Julie Leclercq#, Shuangyang Wu#, Benoît Farinas, Stéphanie Pointet, Bénédicte Favreau, Hélène Vignes, Kuswanhadi Kuswanhadi, Enrique Ortega - Abboud, Jean - François Dufayard, Shenghan Gao, Gaëtan Droc, Songnian Hu, Chaorong Tang, Pascal Montoro*. Post - transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis. PeerJ, 2020
12. Wei Zhang#, Haiying Yu#, Yunxue Lv, Kathryn E. Bushley, Jacob D. Wickham, Shenghan Gao, Songnian Hu, Lilin Zhao, Jianghua Sun*. Gene family expansion of pinewood nematode to detoxify its host defence chemicals. Molecular Ecology, 2020
13. Fengchao Jiang#, Junhuan Zhang#, Sen Wang#, Li Yang, Yingfeng Luo, Shenghan Gao, Meiling Zhang, Shuangyang Wu, Songnian Hu, Haoyuan Sun*, Yuzhu Wang*. The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta - carotenoid synthesis. Horticulture Research, 2019
14. Wanfei Liu#, Shuangyang Wu#, Qiang Lin#, Shenghan Gao, Feng Ding, Xiaowei Zhang, Hasan Awad Aljohi*, Jun Yu*, Songnian Hu*. RGAAT: A Reference - Based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. Genomics, Proteomics & Bioinformatics, 2018
15. Jianbin Wang#, Shenghan Gao, Yulia Mostovoy, Yuanyuan Kang, Maxim Zagoskin, Yongqiao Sun, Bing Zhang, Laura K. White, Alice Easton, Thomas B. Nutman, Pui - Yan Kwok, Songnian Hu, Martin K. Nielsen, Richard E. Davis. Comparative genome analysis of programmed DNA elimination in nematodes. Genome Research, 2017
16. Chaorong Tang#, Meng Yang#, Yongjun Fang#, Yingfeng Luo#, Shenghan Gao, Xiaohu Xiao, Zewei An, Binhui Zhou, Bing Zhang, Xinyu Tan, Hoong - Yeet Yeang, Yunxia Qin, Jianghua Yang, Qiang Lin, Hailiang Mei, Pascal Montoro, Xiangyu Long, Jiyan Qi, Yuwei Hua, Zilong He, Min Sun, Wenjie Li, Xia Zeng, Han Cheng, Ying Liu, Jin Yang, Weimin Tian, Nansheng Zhuang, Rizhong Zeng, Dejun Li, Peng He, Zhe Li, Zhi Zou, Shuangli Li, Chenji Li, Jixiang Wang, Dong Wei, Chao - Qiang Lai, Wei Luo, Jun Yu, Songnian Hu*, Huasun Huang*. The rubber tree genome reveals new insights into rubber production and species adaptation. Nature Plants, 2016
17. Shuai Wang#, Sen Wang#, Yingfeng Luo, Lihua Xiao, Xuenong Luo, Shenghan Gao, Yongxi Dou, Huangkai Zhang, Aijiang Guo, Qingshu Meng, Junling Hou, Bing Zhang, Shaohua Zhang, Meng Yang, Xuelian Meng, Hailiang Mei, Hui Li, Zilong He, Xueliang Zhu, Xinyu Tan, Xing - quan Zhu, Jun Yu, Jianping Cai, Guan Zhu*, Songnian Hu*, Xuepeng Cai*. Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host. Nature Communications, 2016
18. Zilong He#, Huangkai Zhang#, Shenghan Gao, Martin J. Lercher, Wei - Hua Chen, Songnian Hu*. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Research, 2016
19. De Chen, Yang Liu, Geoffrey W. H. Davison, Lu Dong, Jiang Chang, Shenghan Gao, Shou - Hsien Li, Zhengwang Zhang*. Revival of the genus Tropicoperdix Blyth 1859 (Phasianidae, Aves) using multilocus sequence data. Zoological Journal of the Linnean Society, 2015

国家自然科学基金青年科学基金项目，《基于蛔科多物种比较基因组分析的程序性DNA消除研究》；2019/1–2021/12

第67批博后基金面上项目，《条斑紫菜共生微生物组动态变化及NRPS-PKS基因资源调研》；2020/8–2021/10

中国科学院微生物研究所青年探索项目，《基于可解释人工智能和基因组信息辅助的细菌培养条件推荐系统》；2023/10-2024/9