Jun Yu

According to our database, Jun Yu authored at least 75 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome.

Ming Xiao, Rui Wei, Jun Yu, Chujie Gao, Fengyi Yang, Le Zhang

Genom. Proteom. Bioinform., 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, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu

Genom. Proteom. Bioinform., 2024

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, Xiang Zhang

Genom. Proteom. Bioinform., June, 2023

Toward a New Paradigm of Genomics Research - Celebration of the 20th Anniversary of Beijing Institute of Genomics.

Zhang Zhang, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2023

Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology.

Jun Yu

Genom. Proteom. Bioinform., 2023

T2T-YAO, T2T-SHUN, and More.

Jingfa Xiao, Jun Yu

Genom. Proteom. Bioinform., 2023

2022

Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning.

Shaochuan Li, Yuning Yang, Xin Wang, Jun Li, Jun Yu, Xiangtao Li, Ka-Chun Wong

BioData Min., 2022

Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes.

Ming Xiao, Ruiying Yin, Pengbo Gao, Jun Yu, Fubo Ma, Zichun Dai, Le Zhang

Proceedings of the Intelligent Computing Theories and Application, 2022

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, Le Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA.

Saifur Rahaman, Xiangtao Li, Jun Yu, Ka-Chun Wong

Bioinform., 2021

CpG-island-based annotation and analysis of human housekeeping genes.

Le Zhang, Zichun Dai, Jun Yu, Ming Xiao

Briefings Bioinform., 2021

Roles of host small RNAs in the evolution and host tropism of coronaviruses.

Qingren Meng, Yanan Chu, Changjun Shao, Jing Chen, Jian Wang, Zhancheng Gao, Jun Yu, Yu Kang

Briefings Bioinform., 2021

2020

CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study.

Ming Xiao, Xiangyu Yang, Jun Yu, Le Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2.

Jun Yu

Genom. Proteom. Bioinform., 2020

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.

Xufei Teng, Qianpeng Li, Zhao Li, Yuansheng Zhang, Guangyi Niu, Jing-Fa Xiao, Jun Yu, Zhang Zhang, Shuhui Song

Genom. Proteom. Bioinform., 2020

Genome Assembly and Pathway Analysis of Edible Mushroom <i>Agrocybe cylindracea</i>.

Yuan Liang, Dengxue Lu, Sen Wang, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng, Jianing Geng, Songnian Hu

Genom. Proteom. Bioinform., 2020

Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in <i>Saccharina japonica</i>.

Shan Chi, Guoliang Wang, Tao Liu, Xumin Wang, Cui Liu, Yuemei Jin, Hongxin Yin, Xin Xu, Jun Yu

Genom. Proteom. Bioinform., 2020

The Elements of Data Sharing.

Zhang Zhang, Shuhui Song, Jun Yu, Wenming Zhao, Jing-Fa Xiao, Yiming Bao

Genom. Proteom. Bioinform., 2020

2019

In Memory of Vladimir B. Bajic (1952-2019).

Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori

Genom. Proteom. Bioinform., 2019

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, Yu Kang, Jun Yu

Genom. Proteom. Bioinform., 2019

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, Songnian Hu

J. Comput. Biol., 2018

A <i>Scientist Guerilla Fighter</i> in the Frontiers of Bioinformatics - In Memory of Bailin Hao.

Jun Yu

Genom. Proteom. Bioinform., 2018

Rice Genomics: over the Past Two Decades and into the Future.

Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu

Genom. Proteom. 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, Xiaowei Zhang, Hasan Awad Aljohi, Jun Yu, Songnian Hu

Genom. Proteom. Bioinform., 2018

Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA).

Le Zhang, Ming Xiao, Jingsong Zhou, Jun Yu

Bioinform., 2018

2017

A Step Forward in Precision Medicine on "One Belt One Road".

Jun Yu

Genom. Proteom. Bioinform., 2017

A Piece of History that Cannot Be Missed for Precision Medicine.

Jun Yu

Genom. Proteom. Bioinform., 2017

ISVASE: identification of sequence variant associated with splicing event using RNA-seq data.

Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu

BMC Bioinform., 2017

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, Jing-Fa Xiao

Briefings Bioinform., 2017

2016

Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences?

Jun Yu

Genom. Proteom. Bioinform., 2016

Precision Medicine: What Challenges Are We Facing?

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

Genom. Proteom. Bioinform., 2016

2015

Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs.

Dapeng Wang, Jun Yu

Nucleic Acids Res., 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, Vladimir B. Bajic, Zhang Zhang

Nucleic Acids Res., 2015

Biological Databases for Human Research.

Dong Zou, Lina Ma, Jun Yu, Zhang Zhang

Genom. Proteom. Bioinform., 2015

A Brief Review of Software Tools for Pangenomics.

Jing-Fa Xiao, Zhewen Zhang, Jiayan Wu, Jun Yu

Genom. Proteom. Bioinform., 2015

2014

RiceWiki: a wiki-based database for community curation of rice genes.

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

Nucleic Acids Res., 2014

Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development.

Wei Xu, Chengqi Xin, Qiang Lin, Feng Ding, Wei Gong, Yuanyuan Zhou, Jun Yu, Peng Cui, Songnian Hu

Genom. Proteom. Bioinform., 2014

Ribogenomics: the Science and Knowledge of RNA.

Jiayan Wu, Jing-Fa Xiao, Zhang Zhang, Xumin Wang, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2014

A Comprehensive Transcriptomic Analysis of Infant and Adult Mouse Ovary.

Linlin Pan, Wei Gong, Yuanyuan Zhou, Xiaonuan Li, Jun Yu, Songnian Hu

Genom. Proteom. Bioinform., 2014

Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections.

Zhancheng Gao, Yu Kang, Jun Yu, Lufeng Ren

Genom. Proteom. 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, Jiayan Wu, Baoling Duan

BMC Genom., 2014

PanGP: A tool for quickly analyzing bacterial pan-genome profile.

Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jing-Fa Xiao

Bioinform., 2014

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

Nucleic Acids Res., 2013

Does the Genetic Code Have A Eukaryotic Origin?

Zhang Zhang, Jun Yu

Genom. Proteom. Bioinform., 2013

MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data.

Yuli Li, Shuhui Song, Cuiping Li, Jun Yu

Genom. Proteom. Bioinform., 2013

2012

The Pendulum Model for Genome Compositional Dynamics: from the Four Nucleotides to the Twenty Amino Acids.

Zhang Zhang, Jun Yu

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, Songnian Hu, Jun Yu

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, Shuhui Song, Min Sun, Jin Yang, Yadong Yang, Xiangdong Fang, Songnian Hu, Yongliang Zhao, Jun Yu

Genom. Proteom. Bioinform., 2012

Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis.

Peng Cui, Wanfei Liu, Yuhui Zhao, Qiang Lin, Daoyong Zhang, Feng Ding, Chengqi Xin, Zhang Zhang, Shuhui Song, Fanglin Sun, Jun Yu, Songnian Hu

Genom. Proteom. Bioinform., 2012

The Association Between H3K4me3 and Antisense Transcription.

Peng Cui, Wanfei Liu, Yuhui Zhao, Qiang Lin, Feng Ding, Chengqi Xin, Jianing Geng, Shuhui Song, Fanglin Sun, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2012

The Transcript-centric Mutations in Human Genomes.

Peng Cui, Qiang Lin, Feng Ding, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2012

Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes.

Peng Cui, Feng Ding, Qiang Lin, Lingfang Zhang, Ang Li, Zhang Zhang, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2012

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.

Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P. Townsend, Jun Yu

BMC Bioinform., 2012

PGAP: pan-genomes analysis pipeline.

Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu

Bioinform., 2012

BAsplice: Bi-direction alignment for detecting splice junctions.

Jingde Bu, Jiayan Wu, Meili Chen, Jing-Fa Xiao, Jun Yu, Xuebin Chi, Zhong Jin

Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

2011

On the Organizational Dynamics of the Genetic Code.

Zhang Zhang, Jun Yu

Genom. Proteom. Bioinform., 2011

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data.

Tongwu Zhang, Yingfeng Luo, Kan Liu, Linlin Pan, Bing Zhang, Jun Yu, Songnian Hu

Genom. Proteom. Bioinform., 2011

2010

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies.

Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, Jun Yu

Genom. Proteom. Bioinform., 2010

Evolutionary Transients in the Rice Transcriptome.

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

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, Gang Gao, Shuhui Song

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

Genom. Proteom. Bioinform., 2010

Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans.

Kaifu Chen, Lei Wang, Meng Yang, Jiucheng Liu, Chengqi Xin, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2010

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, Songnian Hu

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

Genom. Proteom. Bioinform., 2009

A Brief Review on the Mechanisms of miRNA Regulation.

Yimei Cai, Xiaomin Yu, Songnian Hu, Jun Yu

Genom. Proteom. Bioinform., 2009

2008

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

Genom. Proteom. Bioinform., 2008

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, Huanming Yang, Jun Yu, Jing Wang

Nucleic Acids Res., 2007

A Scenario on the Stepwise Evolution of the Genetic Code.

Jing-Fa Xiao, Jun Yu

Genom. Proteom. Bioinform., 2007

2006

Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits.

Xiao-Qian Zhao, Jian-Fei Hu, Jun Yu

Genom. Proteom. Bioinform., 2006

Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates.

Zhang Zhang, Jun Yu

Genom. Proteom. Bioinform., 2006

KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging.

Zhang Zhang, Jun Li, Xiao-Qian Zhao, Jun Wang, Gane Ka-Shu Wong, Jun Yu

Genom. Proteom. Bioinform., 2006

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, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang

PLoS Comput. Biol., 2005

SilkDB: a knowledgebase for silkworm biology and genomics.

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

Nucleic Acids Res., 2005

ChickVD: a sequence variation database for the chicken genome.

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

Nucleic Acids Res., 2005

2004

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.

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

Nucleic Acids Res., 2004