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ORCIDJun Yu 0004
Person information
- affiliation: Chinese Academy of Sciences, Beijing Institute of Genomics, China
- affiliation (former): Zhejiang University, James D. Watson Institute of Genome Sciences, China
Other persons with the same name
- Jun Yu — disambiguation page
- Jun Yu 0001
![[0000-0002-3197-8103]](https://dblp.uni-trier.de/img/orcid-mark.12x12.png "0000-0002-3197-8103")
— University of Science and Technology of China, Department of Automation, Hefei, China - Jun Yu 0002 — Hangzhou Dianzi University, School of Computer Science, China (and 5 more)
- Jun Yu 0003 — Dalian University of Technology, Faculty of Electronic Information and Electrical Engineering, China
- Jun Yu 0005 — Umeå University, Umeå, Sweden
- Jun Yu 0006 — Singapore Management University, Singapore, Singapore
- Jun Yu 0007 — Kochi University of Technology, Kami, Japan
- Jun Yu 0008 — London School of Economics and Political Science, London, UK
- Jun Yu 0009 — Li Ka Shing Institute of Health Sciences, Hong Kong, China (and 1 more)
- Jun Yu 0010 — Fudan University, State Key Lab of ASIC & System, Shanghai, China
- Jun Yu 0011 — Zhengzhou University of Light Industry, College of Computer and Communication Engineering, China (and 1 more)
- Jun Yu 0012 — Niigata University, Institute of Science and Technology, Niigata-shi, Japan
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Journal Articles
- 2024
[j72]Ming Xiao, Rui Wei, Jun Yu, Chujie Gao, Fengyi Yang, Le Zhang:
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome. Genom. Proteom. Bioinform. 22(1) (2024)- 2023
- [j71]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): 501-514 (2023) - [j70]Jun Yu:
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology. Genom. Proteom. Bioinform. 21(5): 895-896 (2023) - [j69]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): 904-909 (2023) - [j68]Jingfa Xiao, Jun Yu:
T2T-YAO, T2T-SHUN, and More. Genom. Proteom. Bioinform. 21(6): 1081-1082 (2023) - 2022
- [j67]Shaochuan Li, Yuning Yang, Xin Wang, Jun Li, Jun Yu, Xiangtao Li, Ka-Chun Wong:
Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning. BioData Min. 15(1) (2022) - 2021
- [j66]Le Zhang, Zichun Dai, Jun Yu, Ming Xiao:
CpG-island-based annotation and analysis of human housekeeping genes. Briefings Bioinform. 22(1): 515-525 (2021) - [j65]Qingren Meng, Yanan Chu, Changjun Shao, Jing Chen, Jian Wang, Zhancheng Gao, Jun Yu, Yu Kang:
Roles of host small RNAs in the evolution and host tropism of coronaviruses. Briefings Bioinform. 22(2): 1096-1105 (2021) - [j64]Saifur Rahaman, Xiangtao Li, Jun Yu, Ka-Chun Wong:
CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA. Bioinform. 37(19): 3319-3327 (2021) - [j63]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): 1250-1261 (2021) - 2020
- [j62]Zhang Zhang, Shuhui Song, Jun Yu, Wenming Zhao, Jing-Fa Xiao, Yiming Bao:
The Elements of Data Sharing. Genom. Proteom. Bioinform. 18(1): 1-4 (2020) - [j61]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. Genom. Proteom. Bioinform. 18(3): 341-351 (2020) - [j60]Shan Chi, Guoliang Wang, Tao Liu, Xumin Wang, Cui Liu, Yuemei Jin, Hongxin Yin, Xin Xu, Jun Yu:
Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica. Genom. Proteom. Bioinform. 18(4): 415-429 (2020) - [j59]Jun Yu:
From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2. Genom. Proteom. Bioinform. 18(6): 627-639 (2020) - [j58]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): 648-663 (2020) - [j57]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): 2148-2154 (2020) - 2019
- [j56]Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori:
In Memory of Vladimir B. Bajic (1952-2019). Genom. Proteom. Bioinform. 17(5): 473-474 (2019) - [j55]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): 590-602 (2019) - 2018
- [j54]Le Zhang, Ming Xiao, Jingsong Zhou, Jun Yu:
Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA). Bioinform. 34(21): 3624-3630 (2018) - [j53]Jun Yu:
A Scientist Guerilla Fighter in the Frontiers of Bioinformatics - In Memory of Bailin Hao. Genom. Proteom. Bioinform. 16(5): 307-309 (2018) - [j52]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): 373-381 (2018) - [j51]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): 397-404 (2018) - [j50]Shuangyang Wu, Wanfei Liu, Hasan Awad Aljohi, Sarah A. Alromaih, Ibrahim O. Alanazi, Qiang Lin, Jun Yu, Songnian Hu:
REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results. J. Comput. Biol. 25(5): 509-516 (2018) - 2017
- [j49]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): 28-36 (2017) - [j48]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): 320 (2017) - [j47]Jun Yu:
A Piece of History that Cannot Be Missed for Precision Medicine. Genom. Proteom. Bioinform. 15(1): 1-2 (2017) - [j46]Jun Yu:
A Step Forward in Precision Medicine on "One Belt One Road". Genom. Proteom. Bioinform. 15(4): 219 (2017) - 2016
- [j45]Jun Yu:
Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences? Genom. Proteom. Bioinform. 14(1): 1-3 (2016) - [j44]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): 253-261 (2016) - 2015
- [j43]Dong Zou, Lina Ma, Jun Yu, Zhang Zhang:
Biological Databases for Human Research. Genom. Proteom. Bioinform. 13(1): 55-63 (2015) - [j42]Jing-Fa Xiao, Zhewen Zhang, Jiayan Wu, Jun Yu:
A Brief Review of Software Tools for Pangenomics. Genom. Proteom. Bioinform. 13(1): 73-76 (2015) - [j41]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): 187-192 (2015) - [j40]Dapeng Wang, Jun Yu:
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. Nucleic Acids Res. 43(Database-Issue): 990-995 (2015) - 2014
- [j39]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): 1297-1299 (2014) - [j38]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): S11 (2014) - [j37]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): 57-63 (2014) - [j36]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): 111-119 (2014) - [j35]Zhancheng Gao, Yu Kang, Jun Yu, Lufeng Ren:
Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections. Genom. Proteom. Bioinform. 12(3): 144-150 (2014) - [j34]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): 239-248 (2014) - [j33]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): 1222-1228 (2014) - 2013
- [j32]Zhang Zhang, Jun Yu:
Does the Genetic Code Have A Eukaryotic Origin? Genom. Proteom. Bioinform. 11(1): 41-55 (2013) - [j31]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): 72-75 (2013) - [j30]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): 1199-1205 (2013) - 2012
- [j29]Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu:
PGAP: pan-genomes analysis pipeline. Bioinform. 28(3): 416-418 (2012) - [j28]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: 43 (2012) - [j27]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): 4-10 (2012) - [j26]Peng Cui, Qiang Lin, Feng Ding, Songnian Hu, Jun Yu:
The Transcript-centric Mutations in Human Genomes. Genom. Proteom. Bioinform. 10(1): 11-22 (2012) - [j25]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): 74-81 (2012) - [j24]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): 82-93 (2012) - [j23]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): 175-180 (2012) - [j22]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): 186-196 (2012) - [j21]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): 326-335 (2012) - 2011
- [j20]Zhang Zhang, Jun Yu:
On the Organizational Dynamics of the Genetic Code. Genom. Proteom. Bioinform. 9(1-2): 21-29 (2011) - [j19]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): 238-244 (2011) - 2010
- [j18]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): 77-80 (2010) - [j17]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): 81-91 (2010) - [j16]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): 92-102 (2010) - [j15]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): 211-228 (2010) - [j14]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): 229-237 (2010) - 2009
- [j13]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): 107-115 (2009) - [j12]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): 116-127 (2009) - [j11]Yimei Cai, Xiaomin Yu, Songnian Hu, Jun Yu:
A Brief Review on the Mechanisms of miRNA Regulation. Genom. Proteom. Bioinform. 7(4): 147-154 (2009) - 2008
- [j10]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): 155-162 (2008) - 2007
- [j9]Jing-Fa Xiao, Jun Yu:
A Scenario on the Stepwise Evolution of the Genetic Code. Genom. Proteom. Bioinform. 5(3-4): 143-151 (2007) - [j8]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): 376-380 (2007) - 2006
- [j7]Zhang Zhang, Jun Yu:
Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates. Genom. Proteom. Bioinform. 4(3): 173-181 (2006) - [j6]Xiao-Qian Zhao, Jian-Fei Hu, Jun Yu:
Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits. Genom. Proteom. Bioinform. 4(4): 203-211 (2006) - [j5]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): 259-263 (2006) - 2005
- [j4]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): 399-402 (2005) - [j3]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): 438-441 (2005) - [j2]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) - 2004
- [j1]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): 377-382 (2004)
Conference and Workshop Papers
- 2022
- [c2]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: 319-333 - 2012
- [c1]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: 252-255
Coauthor Index
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