BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. - Wenming Zhao; Jing Wang 003; Ximiao He; Xiaobing Huang; Yongzhi Jiao; Mingtao Dai; Shulin Wei; Jian Fu; Ye Chen; Xiaoyu Ren; Yong Zhang 036; Peixiang Ni; et al. (Nucleic Acids Res., 2004)

ChickVD: a sequence variation database for the chicken genome. - Jing Wang 003; Ximiao He; Jue Ruan; Mingtao Dai; Jie Chen; Yong Zhang 036; Yafeng Hu; Chen Ye; Shengting Li; Lijuan Cong; Lin Fang; Bin Liu; et al. (Nucleic Acids Res., 2005)

SilkDB: a knowledgebase for silkworm biology and genomics. - Jing Wang 003; Qingyou Xia; Ximiao He; Mingtao Dai; Jue Ruan; Jie Chen; Guo Yu; Haifeng Yuan; Yafeng Hu; Ruiqiang Li; Tao Feng; Chen Ye; et al. (Nucleic Acids Res., 2005)

ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. - Ruiqiang Li; Jia Ye; Songgang Li; Jing Wang 003; Yujun Han; Chen Ye; Jian Wang 065; Huanming Yang; Jun Yu 004; Gane Ka-Shu Wong; Jun Wang 004 (PLoS Comput. Biol., 2005)

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. - Suhua Chang; Jiajie Zhang; Xiaoyun Liao; Xinxing Zhu; Dahai Wang; Jiang Zhu; Tao Feng; Baoli Zhu; George F. Gao; Jian Wang 065; Huanming Yang; Jun Yu 004; et al. (Nucleic Acids Res., 2007)

MethyCancer: the database of human DNA methylation and cancer. - Ximiao He; Suhua Chang; Jiajie Zhang; Qian Zhao; Haizhen Xiang; Kanthida Kusonmano; Liu Yang; Zhong Sheng Sun; Huanming Yang; Jing Wang 003 (Nucleic Acids Res., 2008)

DNA Copy Number Aberrations in Breast Cancer by Array Comparative Genomic Hybridization. - Jian Li; Kai Wang; Shengting Li; Vera Timmermans-Wielenga; Fritz Rank; Carsten Wiuf; Xiuqing Zhang; Huanming Yang; Lars Bolund (Genom. Proteom. Bioinform., 2009)

The YH database: the first Asian diploid genome database. - Guoqing Li; Lijia Ma; Chao Song; Zhentao Yang; Xiulan Wang; Hui Huang; Yingrui Li; Ruiqiang Li; Xiuqing Zhang; Huanming Yang; Jian Wang 065; Jun Wang 004 (Nucleic Acids Res., 2009)

Evolutionary Transients in the Rice Transcriptome. - Jun Wang 004; Jianguo Zhang; Ruiqiang Li; Hongkun Zheng; Jun Li 051; Yong Zhang 036; Heng Li 002; Peixiang Ni; Songgang Li; Shengting Li; Jingqiang Wang; Dongyuan Liu; et al. (Genom. Proteom. Bioinform., 2010)

BS-SNPer: SNP calling in bisulfite-seq data. - Shengjie Gao; Dan Zou; Likai Mao; Huayu Liu; Pengfei Song; Youguo Chen; Shancen Zhao; Changduo Gao; Xiangchun Li; Zhibo Gao; Xiaodong Fang; Huanming Yang; et al. (Bioinform., 2015)

Whole genome synthesis: from poliovirus to synthetic yeast. - Junbiao Dai; Yizhi Cai; Yinjing Yuan; Huanming Yang; Jef D. Boeke (Quant. Biol., 2017)

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. - Jia Ye; Yong Zhang 036; Huihai Cui; Jiawei Liu; Yuqing Wu; Yun Cheng; Huixing Xu; Xingxin Huang; Shengting Li; An Zhou; Xiuqing Zhang; Lars Bolund; et al. (Nucleic Acids Res., 2018)

A new massively parallel nanoball sequencing platform for whole exome research. - Yu Xu; Zhe Lin; Chong Tang 005; Yujing Tang; Yue Cai; Hongbin Zhong; Xuebin Wang; Wenwei Zhang; Chongjun Xu; Jingjing Wang; Jian Wang 065; Huanming Yang; et al. (BMC Bioinform., 2019)

Prophage Hunter: an integrative hunting tool for active prophages. - Wenchen Song; Hai-Xi Sun; Carolyn Zhang; Li Cheng; Ye Peng; Ziqing Deng; Dan Wang; Yun Wang; Ming Hu; Wenen Liu; Huanming Yang; Yue Shen; et al. (Nucleic Acids Res., 2019)

PIRD: Pan Immune Repertoire Database. - Wei Zhang 178; Longlong Wang; Ke Liu; Xiaofeng Wei; Kai Yang; Wensi Du; Shiyu Wang; Nannan Guo; Chuanchuan Ma; Lihua Luo; Jinghua Wu; Liya Lin; et al. (Bioinform., 2020)

SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. - Yong Zhang 036; Yongsheng Chen; Huixin Xu; Junbin Fang; Zijian Zhao; Weipeng Hu; Xiaoqin Yang; Jia Ye; Yun Cheng; Jiayin Wang; Weiqiang Sun; Jian Wang 065; et al. (BMC Bioinform., 2020)

Genomic basis for RNA alterations in cancer. - Claudia Calabrese; Natalie R. Davidson; Deniz Demircioglu; Nuno A. Fonseca; Yao He; André Kahles; Kjong-Van Lehmann; Fenglin Liu; Yuichi Shiraishi; Cameron M. Soulette; Lara Urban; Liliana Greger; et al. (Nat., 2020)

Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios. - Mengyang Xu; Lidong Guo; Xiao Du; Lei Li; Brock A. Peters; Li Deng; Ou Wang; Fang Chen; Jun Wang 004; Zhesheng Jiang; Jinglin Han; Ming Ni; et al. (Bioinform., 2021)

The international Human Genome Project: A milestone for life sciences and humanity-The three stages and three major impacts of the HGP, and three contributions by China. - Wei Dong; Boqing Qiang; Huanming Yang (Quant. Biol., 2021)

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes. - Zhuye Jie; Chen Chen; Lilan Hao; Fei Li; Liju Song; Xiaowei Zhang; Jie Zhu; Liu Tian; Xin Tong; Kaiye Cai; Zhe Zhang; Yanmei Ju; et al. (Genom. Proteom. Bioinform., 2022)

Over 50, 000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. - Jie Zhu; Liu Tian; Peishan Chen; Mo Han; Liju Song; Xin Tong; Xiaohuan Sun; Fangming Yang; Zhipeng Lin; Xing Liu; Chuan Liu; Xiaohan Wang; et al. (Genom. Proteom. Bioinform., 2022)

Contrastive learning enables rapid mapping to multimodal single-cell atlas of multimillion scale. - Meng Yang; Yueyuxiao Yang; Chenxi Xie; Ming Ni; Jian Liu; Huanming Yang; Feng Mu; Jian Wang 065 (Nat. Mach. Intell., 2022)

Towards practical and robust DNA-based data archiving using the yin-yang codec system. - Zhi Ping; Shihong Chen; Guangyu Zhou; Xiaoluo Huang; Sha Joe Zhu; Haoling Zhang; Henry H. Lee; Zhaojun Lan; Jie Cui; Tai Chen; Wenwei Zhang; Huanming Yang; et al. (Nat. Comput. Sci., 2022)

AI/ML-Derived Whole-Genome Predictor Prospectively and Clinically Predicts Survival and Response to Treatment in Brain Cancer. - Sri Priya Ponnapalli; Penelope Miron; Kristy L. S. Miskimen; Kristin A. Waite; Nadiya Sosonkina; Sara E. Coppens; Anthony C. Bryan; Estevan P. Kiernan; Huanming Yang; Jay Bowen; Ghunwa A. Nakouzi; Jill S. Barnholtz-Sloan; et al. (SC Workshops, 2023)

Self-play reinforcement learning guides protein engineering. - Yi Wang 121; Hui Tang; Lichao Huang; Lulu Pan; Lixiang Yang; Huanming Yang; Feng Mu; Meng Yang (Nat. Mac. Intell., 2023)

Author Correction: Self-play reinforcement learning guides protein engineering. - Yi Wang 121; Hui Tang; Lichao Huang; Lulu Pan; Lixiang Yang; Huanming Yang; Feng Mu; Meng Yang (Nat. Mac. Intell., 2023)

Towards interpretable imaging genomics analysis: Methodological developments and applications. - Xiaoping Cen; Wei Dong; Wei Lv; Yi Zhao; Fred Dubee; Alexios-Fotios A. Mentis; Dragomirka Jovic; Huanming Yang; Yixue Li (Inf. Fusion, 2024)