Jun Yu

80 papers Journal 77Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics.
Genom. Proteom. Bioinform.
Guangya Duan, Sisi Zhang, Bixia Tang, Jing-Fa Xiao, Zhang Zhang, Peng Cui, Jun Yu, Wenming Zhao
2025 J jnl
Precision oncology informatics for anticancer drug combination responses: A systematic review.
Comput. Biol. Medicine
Saifur Rahaman, Peter Wang, Jun Yu, Tania Rahman, Muhammad Toseef, Ibrahim Mohammed Sayem, Xiangtao Li, Ka-Chun Wong
2024 J jnl
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome.
Genom. Proteom. Bioinform.
Ming Xiao, Rui Wei, Jun Yu, Chujie Gao, Fengyi Yang, Le Zhang
2024 — conf
Developing H5N1 Avian Influenza Mutation and Evolution Feature Analysis and Web Service.
BIBM
Ming Xiao, Qichen Shang, Qiaozhen Zhang, Yi Xiao, Jun Yu, Le Zhang
2024 J jnl
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes.
Genom. Proteom. Bioinform.
Shuming Guo, Zhuo Huang, Yanming Zhang, Yukun He, Xiangju Chen, Wenjuan Wang, Lansheng Li, Yu Kang, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu
2024 J jnl
Single-cell RNA-seq Reveals the Inhibitory Effect of Methamphetamine on Liver Immunity with the Involvement of Dopamine Receptor D1.
Genom. Proteom. Bioinform.
Jin-Ting Zhou, Yungang Xu, Xiao-huan Liu, Cheng Cheng, Jing-Na Fan, Xiaoming Li, Jun Yu, Shengbin Li
2023 J jnl
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation.
Genom. Proteom. Bioinform.
Jingqi Zhou, Ake Liu, Funan He, Yunbin Zhang, Libing Shen, Jun Yu, Xiang Zhang
2023 J jnl
T2T-YAO, T2T-SHUN, and More.
Genom. Proteom. Bioinform.
Jingfa Xiao, Jun Yu
2023 J jnl
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology.
Genom. Proteom. Bioinform.
Jun Yu
2023 J jnl
Toward a New Paradigm of Genomics Research - Celebration of the 20th Anniversary of Beijing Institute of Genomics.
Genom. Proteom. Bioinform.
Zhang Zhang, Songnian Hu, Jun Yu
2022 J jnl
Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning.
BioData Min.
Shaochuan Li, Yuning Yang, Xin Wang, Jun Li, Jun Yu, Xiangtao Li, Ka-Chun Wong
2022 — conf
Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes.
ICIC (2)
Ming Xiao, Ruiying Yin, Pengbo Gao, Jun Yu, Fubo Ma, Zichun Dai, Le Zhang
2021 J jnl
2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ming Xiao, Guangdi Liu, Jianghang Xie, Zichun Dai, Zihao Wei, Ziyao Ren, Jun Yu, Le Zhang
2021 J jnl
A fine-scale map of genome-wide recombination in divergent
Briefings Bioinform.
Yu Kang, Lina Yuan, Xing Shi, Yanan Chu, Zilong He, Xinmiao Jia, Qiang Lin, Qin Ma, Jian Wang, Jingfa Xiao, Songnian Hu, Zhancheng Gao, Fei Chen, Jun Yu
2021 J jnl
CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA.
Bioinform.
Saifur Rahaman, Xiangtao Li, Jun Yu, Ka-Chun Wong
2021 J jnl
CpG-island-based annotation and analysis of human housekeeping genes.
Briefings Bioinform.
Le Zhang, Zichun Dai, Jun Yu, Ming Xiao
2021 J jnl
Roles of host small RNAs in the evolution and host tropism of coronaviruses.
Briefings Bioinform.
Qingren Meng, Yanan Chu, Changjun Shao, Jing Chen, Jian Wang, Zhancheng Gao, Jun Yu, Yu Kang
2020 J jnl
CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ming Xiao, Xiangyu Yang, Jun Yu, Le Zhang
2020 J jnl
Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.
Genom. Proteom. Bioinform.
Xufei Teng, Qianpeng Li, Zhao Li, Yuansheng Zhang, Guangyi Niu, Jing-Fa Xiao, Jun Yu, Zhang Zhang, Shuhui Song
2020 J jnl
From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2.
Genom. Proteom. Bioinform.
Jun Yu
2020 J jnl
Genome Assembly and Pathway Analysis of Edible Mushroom
Genom. Proteom. Bioinform.
Yuan Liang, Dengxue Lu, Sen Wang, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng, Jianing Geng, Songnian Hu
2020 J jnl
The Elements of Data Sharing.
Genom. Proteom. Bioinform.
Zhang Zhang, Shuhui Song, Jun Yu, Wenming Zhao, Jing-Fa Xiao, Yiming Bao
2020 J jnl
Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in
Genom. Proteom. Bioinform.
Shan Chi, Guoliang Wang, Tao Liu, Xumin Wang, Cui Liu, Yuemei Jin, Hongxin Yin, Xin Xu, Jun Yu
2019 J jnl
In Memory of Vladimir B. Bajic (1952-2019).
Genom. Proteom. Bioinform.
Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori
2019 J jnl
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients.
Genom. Proteom. Bioinform.
Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu
2018 J jnl
A
Genom. Proteom. Bioinform.
Jun Yu
2018 J jnl
Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA).
Bioinform.
Le Zhang, Ming Xiao, Jingsong Zhou, Jun Yu
2018 J jnl
REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results.
J. Comput. Biol.
Shuangyang Wu, Wanfei Liu, Hasan Awad Aljohi, Sarah A. Alromaih, Ibrahim O. Alanazi, Qiang Lin, Jun Yu, Songnian Hu
2018 J jnl
RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
Genom. Proteom. Bioinform.
Wanfei Liu, Shuangyang Wu, Qiang Lin, Shenghan Gao, Feng Ding, Xiaowei Zhang, Hasan Awad Aljohi, Jun Yu, Songnian Hu
2018 J jnl
Rice Genomics: over the Past Two Decades and into the Future.
Genom. Proteom. Bioinform.
Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu
2017 J jnl
A Piece of History that Cannot Be Missed for Precision Medicine.
Genom. Proteom. Bioinform.
Jun Yu
2017 J jnl
A Step Forward in Precision Medicine on "One Belt One Road".
Genom. Proteom. Bioinform.
Jun Yu
2017 J jnl
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data.
BMC Bioinform.
Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu
2017 J jnl
MTD: a mammalian transcriptomic database to explore gene expression and regulation.
Briefings Bioinform.
Xin Sheng, Jiayan Wu, Qianqian Sun, Xue Li, Feng Xian, Manman Sun, Wan Fang, Meili Chen, Jun Yu, Jing-Fa Xiao
2016 J jnl
Precision Medicine: What Challenges Are We Facing?
Genom. Proteom. Bioinform.
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
2016 J jnl
Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences?
Genom. Proteom. Bioinform.
Jun Yu
2015 J jnl
A Brief Review of Software Tools for Pangenomics.
Genom. Proteom. Bioinform.
Jing-Fa Xiao, Zhewen Zhang, Jiayan Wu, Jun Yu
2015 J jnl
Biological Databases for Human Research.
Genom. Proteom. Bioinform.
Dong Zou, Lina Ma, Jun Yu, Zhang Zhang
2015 J jnl
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.
Nucleic Acids Res.
Lina Ma, Ang Li, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic, Zhang Zhang
2015 J jnl
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs.
Nucleic Acids Res.
Dapeng Wang, Jun Yu
2014 J jnl
A Comprehensive Transcriptomic Analysis of Infant and Adult Mouse Ovary.
Genom. Proteom. Bioinform.
Linlin Pan, Wei Gong, Yuanyuan Zhou, Xiaonuan Li, Jun Yu, Songnian Hu
2014 J jnl
Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development.
Genom. Proteom. Bioinform.
Wei Xu, Chengqi Xin, Qiang Lin, Feng Ding, Wei Gong, Yuanyuan Zhou, Jun Yu, Peng Cui, Songnian Hu
2014 J jnl
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum.
BMC Genom.
Fu-Qiang Wang, Jun Zhong, Ying Zhao, Jing-Fa Xiao, Jing Liu, Meng Dai, Guizhen Zheng, Li Zhang, Jun Yu, Jiayan Wu, Baoling Duan
2014 J jnl
Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections.
Genom. Proteom. Bioinform.
Zhancheng Gao, Yu Kang, Jun Yu, Lufeng Ren
2014 J jnl
PanGP: A tool for quickly analyzing bacterial pan-genome profile.
Bioinform.
Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jing-Fa Xiao
2014 J jnl
Ribogenomics: the Science and Knowledge of RNA.
Genom. Proteom. Bioinform.
Jiayan Wu, Jing-Fa Xiao, Zhang Zhang, Xumin Wang, Songnian Hu, Jun Yu
2014 J jnl
RiceWiki: a wiki-based database for community curation of rice genes.
Nucleic Acids Res.
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
2013 J jnl
Does the Genetic Code Have A Eukaryotic Origin?
Genom. Proteom. Bioinform.
Zhang Zhang, Jun Yu
2013 J jnl
MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data.
Genom. Proteom. Bioinform.
Yuli Li, Shuhui Song, Cuiping Li, Jun Yu
2013 J jnl
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.
Nucleic Acids Res.
Dapeng Wang, Yan Xia, Xinna Li, Lixia Hou, Jun Yu
2012 J jnl
An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells.
Genom. Proteom. Bioinform.
Lina Ma, Linghu Nie, Jing Liu, Bing Zhang, Shuhui Song, Min Sun, Jin Yang, Yadong Yang, Xiangdong Fang, Songnian Hu, Yongliang Zhao, Jun Yu
2012 — conf
BAsplice: Bi-direction alignment for detecting splice junctions.
ISB
Jingde Bu, Jiayan Wu, Meili Chen, Jing-Fa Xiao, Jun Yu, Xuebin Chi, Zhong Jin
2012 J jnl
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.
BMC Bioinform.
Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P. Townsend, Jun Yu
2012 J jnl
Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis.
Genom. Proteom. Bioinform.
Peng Cui, Wanfei Liu, Yuhui Zhao, Qiang Lin, Daoyong Zhang, Feng Ding, Chengqi Xin, Zhang Zhang, Shuhui Song, Fanglin Sun, Jun Yu, Songnian Hu
2012 J jnl
Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes.
Genom. Proteom. Bioinform.
Peng Cui, Feng Ding, Qiang Lin, Lingfang Zhang, Ang Li, Zhang Zhang, Songnian Hu, Jun Yu
2012 J jnl
PGAP: pan-genomes analysis pipeline.
Bioinform.
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu
2012 J jnl
Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition.
Genom. Proteom. Bioinform.
Hao Wu, Hongzhu Qu, Ning Wan, Zhang Zhang, Songnian Hu, Jun Yu
2012 J jnl
The Association Between H3K4me3 and Antisense Transcription.
Genom. Proteom. Bioinform.
Peng Cui, Wanfei Liu, Yuhui Zhao, Qiang Lin, Feng Ding, Chengqi Xin, Jianing Geng, Shuhui Song, Fanglin Sun, Songnian Hu, Jun Yu
2012 J jnl
The Pendulum Model for Genome Compositional Dynamics: from the Four Nucleotides to the Twenty Amino Acids.
Genom. Proteom. Bioinform.
Zhang Zhang, Jun Yu
2012 J jnl
The Transcript-centric Mutations in Human Genomes.
Genom. Proteom. Bioinform.
Peng Cui, Qiang Lin, Feng Ding, Songnian Hu, Jun Yu
2011 J jnl
BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data.
Genom. Proteom. Bioinform.
Tongwu Zhang, Yingfeng Luo, Kan Liu, Linlin Pan, Bing Zhang, Jun Yu, Songnian Hu
2011 J jnl
On the Organizational Dynamics of the Genetic Code.
Genom. Proteom. Bioinform.
Zhang Zhang, Jun Yu
2010 J jnl
Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae.
Genom. Proteom. Bioinform.
Wanfei Liu, Dawei Huang, Kan Liu, Songnian Hu, Jun Yu, Gang Gao, Shuhui Song
2010 J jnl
Evolutionary Transients in the Rice Transcriptome.
Genom. Proteom. Bioinform.
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
2010 J jnl
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies.
Genom. Proteom. Bioinform.
Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, Jun Yu
2010 J jnl
Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans.
Genom. Proteom. Bioinform.
Kaifu Chen, Lei Wang, Meng Yang, Jiucheng Liu, Chengqi Xin, Songnian Hu, Jun Yu
2010 J jnl
The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome.
Genom. Proteom. Bioinform.
Ximiao He, Shu Tao, Jing Jin, Songnian Hu, Jun Yu
2009 J jnl
A Brief Review on the Mechanisms of miRNA Regulation.
Genom. Proteom. Bioinform.
Yimei Cai, Xiaomin Yu, Songnian Hu, Jun Yu
2009 J jnl
How Do Variable Substitution Rates Influence Ka and Ks Calculations?
Genom. Proteom. Bioinform.
Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu
2009 J jnl
Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees.
Genom. Proteom. Bioinform.
Guoqiang Zhang, Lingxia Zhang, Mingcheng Zhang, Linlin Pan, Fengyu Wang, Jun Huang, Guoli Li, Jun Yu, Songnian Hu
2008 J jnl
Phylogenetic Analysis of Brine Shrimp (Artemia) in China Using DNA Barcoding.
Genom. Proteom. Bioinform.
Weiwei Wang, Qibin Luo, Haiyan Guo, Peter Bossier, Gilbert Van Stappen, Patrick Sorgeloos, Naihong Xin, Qishi Sun, Songnian Hu, Jun Yu
2007 J jnl
A Scenario on the Stepwise Evolution of the Genetic Code.
Genom. Proteom. Bioinform.
Jing-Fa Xiao, Jun Yu
2007 J jnl
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.
Nucleic Acids Res.
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
2006 J jnl
Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits.
Genom. Proteom. Bioinform.
Xiao-Qian Zhao, Jian-Fei Hu, Jun Yu
2006 J jnl
Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates.
Genom. Proteom. Bioinform.
Zhang Zhang, Jun Yu
2006 J jnl
KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging.
Genom. Proteom. Bioinform.
Zhang Zhang, Jun Li, Xiao-Qian Zhao, Jun Wang, Gane Ka-Shu Wong, Jun Yu
2005 J jnl
ChickVD: a sequence variation database for the chicken genome.
Nucleic Acids Res.
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
2005 J jnl
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun.
PLoS Comput. Biol.
Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang
2005 J jnl
SilkDB: a knowledgebase for silkworm biology and genomics.
Nucleic Acids Res.
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
2004 J jnl
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
Nucleic Acids Res.
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