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)

KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. - Zhang Zhang 002; Jun Li 051; Xiao-Qian Zhao; Jun Wang 004; Gane Ka-Shu Wong; Jun Yu 004 (Genom. Proteom. Bioinform., 2006)

Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates. - Zhang Zhang 002; Jun Yu 004 (Genom. Proteom. Bioinform., 2006)

Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits. - Xiao-Qian Zhao; Jian-Fei Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2006)

A Scenario on the Stepwise Evolution of the Genetic Code. - Jing-Fa Xiao; Jun Yu 004 (Genom. Proteom. Bioinform., 2007)

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)

Phylogenetic Analysis of Brine Shrimp (Artemia) in China Using DNA Barcoding. - Weiwei Wang; Qibin Luo; Haiyan Guo; Peter Bossier; Gilbert Van Stappen; Patrick Sorgeloos; Naihong Xin; Qishi Sun; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2008)

A Brief Review on the Mechanisms of miRNA Regulation. - Yimei Cai; Xiaomin Yu; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2009)

How Do Variable Substitution Rates Influence Ka and Ks Calculations? - Dapeng Wang; Song Zhang; Fuhong He; Jiang Zhu; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2009)

Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees. - Guoqiang Zhang; Lingxia Zhang; Mingcheng Zhang; Linlin Pan; Fengyu Wang; Jun Huang; Guoli Li; Jun Yu 004; Songnian Hu (Genom. Proteom. Bioinform., 2009)

Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans. - Kaifu Chen; Lei Wang; Meng Yang; Jiucheng Liu; Chengqi Xin; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2010)

The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome. - Ximiao He; Shu Tao; Jing Jin; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2010)

Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae. - Wanfei Liu; Dawei Huang; Kan Liu; Songnian Hu; Jun Yu 004; Gang Gao; Shuhui Song (Genom. Proteom. Bioinform., 2010)

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)

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. - Dapeng Wang; Yubin Zhang; Zhang Zhang 002; Jiang Zhu; Jun Yu 004 (Genom. Proteom. Bioinform., 2010)

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data. - Tongwu Zhang; Yingfeng Luo; Kan Liu; Linlin Pan; Bing Zhang 007; Jun Yu 004; Songnian Hu (Genom. Proteom. Bioinform., 2011)

On the Organizational Dynamics of the Genetic Code. - Zhang Zhang 002; Jun Yu 004 (Genom. Proteom. Bioinform., 2011)

BAsplice: Bi-direction alignment for detecting splice junctions. - Jingde Bu; Jiayan Wu; Meili Chen; Jing-Fa Xiao; Jun Yu 004; Xuebin Chi; Zhong Jin (ISB, 2012)

PGAP: pan-genomes analysis pipeline. - Yongbing Zhao; Jiayan Wu; Junhui Yang; Shixiang Sun; Jing-Fa Xiao; Jun Yu 004 (Bioinform., 2012)

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. - Zhang Zhang 002; Jun Li 051; Peng Cui 004; Feng Ding 003; Ang Li; Jeffrey P. Townsend; Jun Yu 004 (BMC Bioinform., 2012)

Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes. - Peng Cui 004; Feng Ding 003; Qiang Lin; Lingfang Zhang; Ang Li; Zhang Zhang 002; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2012)

The Transcript-centric Mutations in Human Genomes. - Peng Cui 004; Qiang Lin; Feng Ding 003; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2012)

The Association Between H3K4me3 and Antisense Transcription. - Peng Cui 004; Wanfei Liu; Yuhui Zhao; Qiang Lin; Feng Ding 003; Chengqi Xin; Jianing Geng; Shuhui Song; Fanglin Sun; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2012)

Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis. - Peng Cui 004; Wanfei Liu; Yuhui Zhao; Qiang Lin; Daoyong Zhang; Feng Ding 003; Chengqi Xin; Zhang Zhang 002; Shuhui Song; Fanglin Sun; Jun Yu 004; Songnian Hu (Genom. Proteom. Bioinform., 2012)

An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells. - Lina Ma; Linghu Nie; Jing Liu; Bing Zhang 007; Shuhui Song; Min Sun; Jin Yang; Yadong Yang; Xiangdong Fang; Songnian Hu; Yongliang Zhao; Jun Yu 004 (Genom. Proteom. Bioinform., 2012)

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition. - Hao Wu; Hongzhu Qu; Ning Wan; Zhang Zhang 002; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2012)

The Pendulum Model for Genome Compositional Dynamics: from the Four Nucleotides to the Twenty Amino Acids. - Zhang Zhang 002; Jun Yu 004 (Genom. Proteom. Bioinform., 2012)

MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data. - Yuli Li; Shuhui Song; Cuiping Li 004; Jun Yu 004 (Genom. Proteom. Bioinform., 2013)

Does the Genetic Code Have A Eukaryotic Origin? - Zhang Zhang 002; Jun Yu 004 (Genom. Proteom. Bioinform., 2013)

The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. - Dapeng Wang; Yan Xia; Xinna Li; Lixia Hou; Jun Yu 004 (Nucleic Acids Res., 2013)

PanGP: A tool for quickly analyzing bacterial pan-genome profile. - Yongbing Zhao; Xinmiao Jia; Junhui Yang; Yunchao Ling; Zhang Zhang 002; Jun Yu 004; Jiayan Wu; Jing-Fa Xiao (Bioinform., 2014)

Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. - Fu-Qiang Wang; Jun Zhong; Ying Zhao; Jing-Fa Xiao; Jing Liu; Meng Dai; Guizhen Zheng; Li Zhang; Jun Yu 004; Jiayan Wu; Baoling Duan (BMC Genom., 2014)

Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections. - Zhancheng Gao; Yu Kang 004; Jun Yu 004; Lufeng Ren (Genom. Proteom. Bioinform., 2014)

A Comprehensive Transcriptomic Analysis of Infant and Adult Mouse Ovary. - Linlin Pan; Wei Gong; Yuanyuan Zhou; Xiaonuan Li; Jun Yu 004; Songnian Hu (Genom. Proteom. Bioinform., 2014)

Ribogenomics: the Science and Knowledge of RNA. - Jiayan Wu; Jing-Fa Xiao; Zhang Zhang 002; Xumin Wang; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2014)

Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development. - Wei Xu; Chengqi Xin; Qiang Lin; Feng Ding 003; Wei Gong; Yuanyuan Zhou; Jun Yu 004; Peng Cui 004; Songnian Hu (Genom. Proteom. Bioinform., 2014)

RiceWiki: a wiki-based database for community curation of rice genes. - Zhang Zhang 002; Jian Sang; Lina Ma; Gang Wu; Hao Wu; Dawei Huang; Dong Zou; Siqi Liu; Ang Li; Lili Hao; Ming Tian; Chao Xu; et al. (Nucleic Acids Res., 2014)

A Brief Review of Software Tools for Pangenomics. - Jing-Fa Xiao; Zhewen Zhang; Jiayan Wu; Jun Yu 004 (Genom. Proteom. Bioinform., 2015)

Biological Databases for Human Research. - Dong Zou; Lina Ma; Jun Yu 004; Zhang Zhang 002 (Genom. Proteom. Bioinform., 2015)

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. - Lina Ma; Ang Li; Dong Zou; Xingjian Xu; Lin Xia; Jun Yu 004; Vladimir B. Bajic; Zhang Zhang 002 (Nucleic Acids Res., 2015)

Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. - Dapeng Wang; Jun Yu 004 (Nucleic Acids Res., 2015)

Precision Medicine: What Challenges Are We Facing? - Yu Xue 001; Eric-Wubbo Lameijer; Kai Ye 001; Kunlin Zhang; Suhua Chang; Xiaoyue Wang; Jianmin Wu; Ge Gao 004; Fangqing Zhao; Jian Li; Chunsheng Han; Shuhua Xu; et al. (Genom. Proteom. Bioinform., 2016)

Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences? - Jun Yu 004 (Genom. Proteom. Bioinform., 2016)

MTD: a mammalian transcriptomic database to explore gene expression and regulation. - Xin Sheng; Jiayan Wu; Qianqian Sun; Xue Li; Feng Xian; Manman Sun; Wan Fang; Meili Chen; Jun Yu 004; Jing-Fa Xiao (Briefings Bioinform., 2017)

ISVASE: identification of sequence variant associated with splicing event using RNA-seq data. - Hasan Awad Aljohi; Wanfei Liu; Qiang Lin; Jun Yu 004; Songnian Hu (BMC Bioinform., 2017)

A Piece of History that Cannot Be Missed for Precision Medicine. - Jun Yu 004 (Genom. Proteom. Bioinform., 2017)

A Step Forward in Precision Medicine on "One Belt One Road". - Jun Yu 004 (Genom. Proteom. Bioinform., 2017)

Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA). - Le Zhang 004; Ming Xiao; Jingsong Zhou; Jun Yu 004 (Bioinform., 2018)

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. - Wanfei Liu; Shuangyang Wu; Qiang Lin; Shenghan Gao; Feng Ding 009; Xiaowei Zhang; Hasan Awad Aljohi; Jun Yu 004; Songnian Hu (Genom. Proteom. Bioinform., 2018)

Rice Genomics: over the Past Two Decades and into the Future. - Shuhui Song; Dongmei Tian; Zhang Zhang 002; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2018)

A Scientist Guerilla Fighter in the Frontiers of Bioinformatics - In Memory of Bailin Hao. - Jun Yu 004 (Genom. Proteom. Bioinform., 2018)

REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results. - Shuangyang Wu; Wanfei Liu; Hasan Awad Aljohi; Sarah A. Alromaih; Ibrahim O. Alanazi; Qiang Lin; Jun Yu 004; Songnian Hu (J. Comput. Biol., 2018)

Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. - Xing Shi; Zhancheng Gao; Qiang Lin; Liping Zhao; Qin Ma 003; Yu Kang 004; Jun Yu 004 (Genom. Proteom. Bioinform., 2019)

In Memory of Vladimir B. Bajic (1952-2019). - Zhang Zhang 002; Jun Yu 004; Frank Eisenhaber; Xin Gao 001; Takashi Gojobori (Genom. Proteom. Bioinform., 2019)

The Elements of Data Sharing. - Zhang Zhang 002; Shuhui Song; Jun Yu 004; Wenming Zhao; Jing-Fa Xiao; Yiming Bao (Genom. Proteom. Bioinform., 2020)

Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica. - Shan Chi; Guoliang Wang; Tao Liu; Xumin Wang; Cui Liu; Yuemei Jin; Hongxin Yin; Xin Xu; Jun Yu 004 (Genom. Proteom. Bioinform., 2020)

Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea. - Yuan Liang; Dengxue Lu; Sen Wang; Yuhui Zhao; Shenghan Gao; Rongbing Han; Jun Yu 004; Weili Zheng; Jianing Geng; Songnian Hu (Genom. Proteom. Bioinform., 2020)

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. - Xufei Teng; Qianpeng Li; Zhao Li 008; Yuansheng Zhang; Guangyi Niu; Jing-Fa Xiao; Jun Yu 004; Zhang Zhang 002; Shuhui Song (Genom. Proteom. Bioinform., 2020)

From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2. - Jun Yu 004 (Genom. Proteom. Bioinform., 2020)

CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study. - Ming Xiao; Xiangyu Yang; Jun Yu 004; Le Zhang 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Roles of host small RNAs in the evolution and host tropism of coronaviruses. - Qingren Meng; Yanan Chu; Changjun Shao; Jing Chen 076; Jian Wang 065; Zhancheng Gao; Jun Yu 004; Yu Kang 004 (Briefings Bioinform., 2021)

CpG-island-based annotation and analysis of human housekeeping genes. - Le Zhang 004; Zichun Dai; Jun Yu 004; Ming Xiao (Briefings Bioinform., 2021)

CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA. - Saifur Rahaman; Xiangtao Li; Jun Yu 004; Ka-Chun Wong (Bioinform., 2021)

2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV. - Ming Xiao; Guangdi Liu; Jianghang Xie; Zichun Dai; Zihao Wei; Ziyao Ren; Jun Yu 004; Le Zhang 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes. - Ming Xiao; Ruiying Yin; Pengbo Gao; Jun Yu 004; Fubo Ma; Zichun Dai; Le Zhang 004 (ICIC (2), 2022)

Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning. - Shaochuan Li; Yuning Yang; Xin Wang; Jun Li 051; Jun Yu 004; Xiangtao Li; Ka-Chun Wong (BioData Min., 2022)

T2T-YAO, T2T-SHUN, and More. - Jingfa Xiao; Jun Yu 004 (Genom. Proteom. Bioinform., 2023)

Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology. - Jun Yu 004 (Genom. Proteom. Bioinform., 2023)

Toward a New Paradigm of Genomics Research - Celebration of the 20th Anniversary of Beijing Institute of Genomics. - Zhang Zhang 002; Songnian Hu; Jun Yu 004 (Genom. Proteom. Bioinform., 2023)

Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. - Jingqi Zhou; Ake Liu; Funan He; Yunbin Zhang; Libing Shen; Jun Yu 004; Xiang Zhang (Genom. Proteom. Bioinform., 2023)

Developing H5N1 Avian Influenza Mutation and Evolution Feature Analysis and Web Service. - Ming Xiao; Qichen Shang; Qiaozhen Zhang; Yi Xiao; Jun Yu 004; Le Zhang 004 (BIBM, 2024)

Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes. - Shuming Guo; Zhuo Huang; Yanming Zhang; Yukun He; Xiangju Chen; Wenjuan Wang; Lansheng Li; Yu Kang 004; Zhancheng Gao; Jun Yu 004; Zhenglin Du; Yanan Chu (Genom. Proteom. Bioinform., 2024)

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome. - Ming Xiao; Rui Wei; Jun Yu 004; Chujie Gao; Fengyi Yang; Le Zhang 004 (Genom. Proteom. Bioinform., 2024)

Single-cell RNA-seq Reveals the Inhibitory Effect of Methamphetamine on Liver Immunity with the Involvement of Dopamine Receptor D1. - Jin-Ting Zhou; Yungang Xu; Xiao-Huan Liu; Cheng Cheng; Jing-Na Fan; Xiaoming Li; Jun Yu 004; Shengbin Li (Genom. Proteom. Bioinform., 2024)

Precision oncology informatics for anticancer drug combination responses: A systematic review. - Saifur Rahaman; Peter Wang; Jun Yu 004; Tania Rahman; Muhammad Toseef; Ibrahim Mohammed Sayem; Xiangtao Li; Ka-Chun Wong (Comput. Biol. Medicine, 2025)