Jun Yu

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 22

Top Topics

Redescription Mining

Biological Databases

Gene Expression

Top Venues

Genom. Proteom. Bioinform.

Nucleic Acids Res.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Jingqi Zhou, Ake Liu, Funan He, Yunbin Zhang, Libing Shen, Jun Yu, Xiang Zhang
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. Genom. Proteom. Bioinform. 21 (3) (2023)
Zhang Zhang, Songnian Hu, Jun Yu
Toward a New Paradigm of Genomics Research - Celebration of the 20th Anniversary of Beijing Institute of Genomics. Genom. Proteom. Bioinform. 21 (5) (2023)
Jun Yu
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology. Genom. Proteom. Bioinform. 21 (5) (2023)
Ming Xiao, Ruiying Yin, Pengbo Gao, Jun Yu, Fubo Ma, Zichun Dai, Le Zhang
Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes. ICIC (2) (2022)
Ming Xiao, Guangdi Liu, Jianghang Xie, Zichun Dai, Zihao Wei, Ziyao Ren, Jun Yu, Le Zhang
2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Shan Chi, Guoliang Wang, Tao Liu, Xumin Wang, Cui Liu, Yuemei Jin, Hongxin Yin, Xin Xu, Jun Yu
. Genom. Proteom. Bioinform. 18 (4) (2020)
Zhang Zhang, Shuhui Song, Jun Yu, Wenming Zhao, Jing-Fa Xiao, Yiming Bao
The Elements of Data Sharing. Genom. Proteom. Bioinform. 18 (1) (2020)
Yuan Liang, Dengxue Lu, Sen Wang, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng, Jianing Geng, Songnian Hu
. Genom. Proteom. Bioinform. 18 (3) (2020)
Jun Yu
From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2. Genom. Proteom. Bioinform. 18 (6) (2020)
Xufei Teng, Qianpeng Li, Zhao Li, Yuansheng Zhang, Guangyi Niu, Jing-Fa Xiao, Jun Yu, Zhang Zhang, Shuhui Song
Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. Genom. Proteom. Bioinform. 18 (6) (2020)
Ming Xiao, Xiangyu Yang, Jun Yu, Le Zhang
CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (6) (2020)
Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. Genom. Proteom. Bioinform. 17 (6) (2019)
Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori
In Memory of Vladimir B. Bajic (1952-2019). Genom. Proteom. Bioinform. 17 (5) (2019)
Jun Yu
in the Frontiers of Bioinformatics - In Memory of Bailin Hao. Genom. Proteom. Bioinform. 16 (5) (2018)
Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu
Rice Genomics: over the Past Two Decades and into the Future. Genom. Proteom. Bioinform. 16 (6) (2018)
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. Genom. Proteom. Bioinform. 16 (5) (2018)
Jun Yu
A Step Forward in Precision Medicine on "One Belt One Road". Genom. Proteom. Bioinform. 15 (4) (2017)
Jun Yu
A Piece of History that Cannot Be Missed for Precision Medicine. Genom. Proteom. Bioinform. 15 (1) (2017)
Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data. BMC Bioinform. 18 (1) (2017)
Xin Sheng, Jiayan Wu, Qianqian Sun, Xue Li, Feng Xian, Manman Sun, Wan Fang, Meili Chen, Jun Yu, Jing-Fa Xiao
MTD: a mammalian transcriptomic database to explore gene expression and regulation. Briefings Bioinform. 18 (1) (2017)
Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jing-Fa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu
Precision Medicine: What Challenges Are We Facing? Genom. Proteom. Bioinform. 14 (5) (2016)
Jun Yu
Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences? Genom. Proteom. Bioinform. 14 (1) (2016)
Lina Ma, Ang Li, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic, Zhang Zhang
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res. 43 (Database-Issue) (2015)
Jing-Fa Xiao, Zhewen Zhang, Jiayan Wu, Jun Yu
A Brief Review of Software Tools for Pangenomics. Genom. Proteom. Bioinform. 13 (1) (2015)
Dong Zou, Lina Ma, Jun Yu, Zhang Zhang
Biological Databases for Human Research. Genom. Proteom. Bioinform. 13 (1) (2015)
Dapeng Wang, Jun Yu
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. Nucleic Acids Res. 43 (Database-Issue) (2015)
Zhang Zhang, Jian Sang, Lina Ma, Gang Wu, Hao Wu, Dawei Huang, Dong Zou, Siqi Liu, Ang Li, Lili Hao, Ming Tian, Chao Xu, Xumin Wang, Jiayan Wu, Jing-Fa Xiao, Lin Dai, Ling-Ling Chen, Songnian Hu, Jun Yu
RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Res. 42 (Database-Issue) (2014)
Fu-Qiang Wang, Jun Zhong, Ying Zhao, Jing-Fa Xiao, Jing Liu, Meng Dai, Guizhen Zheng, Li Zhang, Jun Yu, Jiayan Wu, Baoling Duan
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. BMC Genom. 15 (S-1) (2014)
Linlin Pan, Wei Gong, Yuanyuan Zhou, Xiaonuan Li, Jun Yu, Songnian Hu
A Comprehensive Transcriptomic Analysis of Infant and Adult Mouse Ovary. Genom. Proteom. Bioinform. 12 (5) (2014)
Wei Xu, Chengqi Xin, Qiang Lin, Feng Ding, Wei Gong, Yuanyuan Zhou, Jun Yu, Peng Cui, Songnian Hu
Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development. Genom. Proteom. Bioinform. 12 (3) (2014)
Jiayan Wu, Jing-Fa Xiao, Zhang Zhang, Xumin Wang, Songnian Hu, Jun Yu
Ribogenomics: the Science and Knowledge of RNA. Genom. Proteom. Bioinform. 12 (2) (2014)
Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jing-Fa Xiao
PanGP: A tool for quickly analyzing bacterial pan-genome profile. Bioinform. 30 (9) (2014)
Dapeng Wang, Yan Xia, Xinna Li, Lixia Hou, Jun Yu
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Res. 41 (Database-Issue) (2013)
Yuli Li, Shuhui Song, Cuiping Li, Jun Yu
MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data. Genom. Proteom. Bioinform. 11 (1) (2013)
Zhang Zhang, Jun Yu
Does the Genetic Code Have A Eukaryotic Origin? Genom. Proteom. Bioinform. 11 (1) (2013)
Peng Cui, Feng Ding, Qiang Lin, Lingfang Zhang, Ang Li, Zhang Zhang, Songnian Hu, Jun Yu
Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes. Genom. Proteom. Bioinform. 10 (1) (2012)
Lina Ma, Linghu Nie, Jing Liu, Bing Zhang, Shuhui Song, Min Sun, Jin Yang, Yadong Yang, Xiangdong Fang, Songnian Hu, Yongliang Zhao, Jun Yu
An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells. Genom. Proteom. Bioinform. 10 (6) (2012)
Hao Wu, Hongzhu Qu, Ning Wan, Zhang Zhang, Songnian Hu, Jun Yu
Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition. Genom. Proteom. Bioinform. 10 (4) (2012)
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu
PGAP: pan-genomes analysis pipeline. Bioinform. 28 (3) (2012)
Peng Cui, Qiang Lin, Feng Ding, Songnian Hu, Jun Yu
The Transcript-centric Mutations in Human Genomes. Genom. Proteom. Bioinform. 10 (1) (2012)
Peng Cui, Wanfei Liu, Yuhui Zhao, Qiang Lin, Feng Ding, Chengqi Xin, Jianing Geng, Shuhui Song, Fanglin Sun, Songnian Hu, Jun Yu
The Association Between H3K4me3 and Antisense Transcription. Genom. Proteom. Bioinform. 10 (2) (2012)
Peng Cui, Wanfei Liu, Yuhui Zhao, Qiang Lin, Daoyong Zhang, Feng Ding, Chengqi Xin, Zhang Zhang, Shuhui Song, Fanglin Sun, Jun Yu, Songnian Hu
Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis. Genom. Proteom. Bioinform. 10 (2) (2012)
Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P. Townsend, Jun Yu
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinform. 13 (2012)
Zhang Zhang, Jun Yu
The Pendulum Model for Genome Compositional Dynamics: from the Four Nucleotides to the Twenty Amino Acids. Genom. Proteom. Bioinform. 10 (4) (2012)
Jingde Bu, Jiayan Wu, Meili Chen, Jing-Fa Xiao, Jun Yu, Xuebin Chi, Zhong Jin
BAsplice: Bi-direction alignment for detecting splice junctions. ISB (2012)
Tongwu Zhang, Yingfeng Luo, Kan Liu, Linlin Pan, Bing Zhang, Jun Yu, Songnian Hu
BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data. Genom. Proteom. Bioinform. 9 (6) (2011)
Zhang Zhang, Jun Yu
On the Organizational Dynamics of the Genetic Code. Genom. Proteom. Bioinform. 9 (1-2) (2011)
Jun Wang, Jianguo Zhang, Ruiqiang Li, Hongkun Zheng, Jun Li, Yong Zhang, Heng Li, Peixiang Ni, Songgang Li, Shengting Li, Jingqiang Wang, Dongyuan Liu, Jason E. McDermott, Ram Samudrala, Siqi Liu, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong
Evolutionary Transients in the Rice Transcriptome. Genom. Proteom. Bioinform. 8 (4) (2010)
Kaifu Chen, Lei Wang, Meng Yang, Jiucheng Liu, Chengqi Xin, Songnian Hu, Jun Yu
Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans. Genom. Proteom. Bioinform. 8 (2) (2010)
Ximiao He, Shu Tao, Jing Jin, Songnian Hu, Jun Yu
The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome. Genom. Proteom. Bioinform. 8 (2) (2010)
Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, Jun Yu
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Genom. Proteom. Bioinform. 8 (1) (2010)
Wanfei Liu, Dawei Huang, Kan Liu, Songnian Hu, Jun Yu, Gang Gao, Shuhui Song
Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae. Genom. Proteom. Bioinform. 8 (4) (2010)
Yimei Cai, Xiaomin Yu, Songnian Hu, Jun Yu
A Brief Review on the Mechanisms of miRNA Regulation. Genom. Proteom. Bioinform. 7 (4) (2009)
Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu
How Do Variable Substitution Rates Influence Ka and Ks Calculations? Genom. Proteom. Bioinform. 7 (3) (2009)
Guoqiang Zhang, Lingxia Zhang, Mingcheng Zhang, Linlin Pan, Fengyu Wang, Jun Huang, Guoli Li, Jun Yu, Songnian Hu
Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees. Genom. Proteom. Bioinform. 7 (3) (2009)
Weiwei Wang, Qibin Luo, Haiyan Guo, Peter Bossier, Gilbert Van Stappen, Patrick Sorgeloos, Naihong Xin, Qishi Sun, Songnian Hu, Jun Yu
Phylogenetic Analysis of Brine Shrimp (Artemia) in China Using DNA Barcoding. Genom. Proteom. Bioinform. 6 (3-4) (2008)
Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu, Jing Wang
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 35 (Database-Issue) (2007)
Jing-Fa Xiao, Jun Yu
A Scenario on the Stepwise Evolution of the Genetic Code. Genom. Proteom. Bioinform. 5 (3-4) (2007)
Zhang Zhang, Jun Yu
Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates. Genom. Proteom. Bioinform. 4 (3) (2006)
Zhang Zhang, Jun Li, Xiao-Qian Zhao, Jun Wang, Gane Ka-Shu Wong, Jun Yu
KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. Genom. Proteom. Bioinform. 4 (4) (2006)
Xiao-Qian Zhao, Jian-Fei Hu, Jun Yu
Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits. Genom. Proteom. Bioinform. 4 (4) (2006)
Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. PLoS Comput. Biol. 1 (4) (2005)
Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, Jun Yu
SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res. 33 (Database-Issue) (2005)
Jing Wang, Ximiao He, Jue Ruan, Mingtao Dai, Jie Chen, Yong Zhang, Yafeng Hu, Chen Ye, Shengting Li, Lijuan Cong, Lin Fang, Bin Liu, Songgang Li, Jian Wang, David W. Burt, Gane Ka-Shu Wong, Jun Yu, Huanming Yang, Jun Wang
ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res. 33 (Database-Issue) (2005)
Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, Jun Wang
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res. 32 (Database-Issue) (2004)