Publications (underline: first authors, : corresponding authors, blue bold: lab members).
  1. Guole Liu, Tianyu Wang, Yingying Zhao, Quanyou Cai, Xiaotao Wang, Ziyi Wen, Lihui Lin, Yongbing Zhao, Ge Yang, Jiekai Chen
    SCARF: Single Cell ATAC-seq and RNA-seq Foundation model
    bioRxiv 2025
  2. Tianyu Wang, SiHoi Kou, Jinfeng Shao, Yongbing Zhao
    Deep Learning Applications in Single-Cell Transcriptomics (Invited Review in Chinese)
    Progress in Physiological Sciences 2025
  3. Jens Kalchschmidt, Tomoya Kanno, Solji Park, Wendy D Dubois, Yongbing Zhao, Pawel Trzaskoma, Craig J Thomas, Louis M Staudt, John J O’Shea, Seolkyoung Jung and Rafael Casellas
    Biphasic Control of the B cell Transcriptome by mTORC1 and GSK3
    Cell Reports 2025
  4. Zhi Nie, Yongbing Zhao, Shuhuan Yu, Jialin Mai, Hao Gao, Zhuojing Fan, Yiming Bao, Rujiao Lia, Jingfa Xiao
    NucMap 2.0: an updated database of genome-wide nucleosome positioning map across species
    Journal of Molecular Biology 2024
  5. Pawel Trzaskoma, SeolKyoung Jung, Aleksandra Pękowska, Christopher H. Bohrer, Xiang Wang, Faiza Naz, Stefania Dell'Orso, Wendy D. Dubois, Ana Olivera, Supriya V. Vartak, Yongbing Zhao, Subhashree Nayak, Andrew Overmiller, Maria I. Morasso, Vittorio Sartorelli, Daniel R. Larson, Carson C. Chow, Rafael Casellas, John J. O'Shea
    3D chromatin architecture, BRD4 and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network
    Science Advances 2024
  6. Chunhong Liu, Hiroyuki Nagashima, Nilisha Fernando, Victor Bass, Jaanam Gopalakrishnan, Sadie Signorella, Will Montgomery, Ai Ing Lim, Oliver Harrison, Lauren Reich, Chen Yao, Hong-Wei Sun, Stephen R. Brooks, Kan Jiang, Vijayaraj Nagarajan, Yongbing Zhao, Seol Kyoung Jung, Rachael Phillips, Yohei Mikami, Caleb A. Lareau, Yuka Kanno, Dragana Jankovic, Martin J. Aryee, Aleksandra Pekowska, Yasmine Belkaid, John O’Shea, Han-Yu Shih
    A Distal CTCF Binding Site Shapes Mdm1-Il22-Ifng Locus Regulation and is Essential for Early Th1 Differentiation and Specification
    Immunity 2024
  7. CNCB-NGDC Members and Partners (Yongbing Zhao is one of the joint first authors)
    Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024
    Nucleic Acids Research 2024
  8. Yongbing Zhao
    TFSyntax: a database of transcription factors binding syntax in mammalian genomes
    Nucleic Acids Research 2023
  9. Yongbing Zhao, Supriya V. Vartak, Andrea Conte, Xiang Wang, David A. Garcia, Evan Stevens, Seol Kyoung Jung, Kyong-Rim Kieffer-Kwon, Laura Vian, Timothy Stodola, Francisco Moris, Laura Chopp, Silvia Preite, Pamela L. Schwartzberg, Joseph M. Kulinski, Ana Olivera, Christelle Harly, Avinash Bhandoola, Elisabeth F. Heuston, David M. Bodine, Raul Urrutia, Arpita Upadhyaya, Matthew T. Weirauch, Gordon Hager and Rafael Casellas
    "Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes
    Molecular Cell 2022
  10. Yongbing Zhao, Jinfeng Shao, Yan W Asmann
    Assessment and Optimization of the Interpretability of Machine Learning Models Applied to Transcriptomic Data
    Genomics, Proteomics and Bioinformatics 2022
  11. Yadong Zhang, Zhewen Zhang, Hao Zhang, Yongbing Zhao, Zaichao Zhang, Jingfa Xiao
    PADS Arsenal: a database of prokaryotic defense systems related genes
    Nucleic Acids Research 2020
  12. Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W Asmann, Rujiao Li, Jingfa Xiao
    NucMap: a database of genome-wide nucleosome positioning map across species
    Nucleic Acids Research 2019
  13. Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You, Xinmiao Jia, Junhui Yang, Lingping Wang, Jinyue Wang, Haohuan Fu, Yu Kang, Fei Chen, Jun Yu, Jiayan Wu and Jingfa Xiao
    PGAP-X: Extension on pan-genome analysis pipeline
    BMC Genomics 2018
  14. Rujiao Li, Fang Liang, Mengwei Li, Dong Zou, Shixiang Sun, Yongbing Zhao, Wenming Zhao, Yiming Bao, Jingfa Xiao, and Zhang Zhang
    MethBank 3.0: a database of DNA methylomes across a variety of species
    Nucleic Acids Research 2018
  15. Xinyu Chen, Yadong Zhang, Zhewen Zhang, Yongbing Zhao, Chen Sun, Ming Yang, Jinyue Wang, Qian Liu, Baohua Zhang, Meili Chen, Jun Yu, Jiayan Wu, Zhong Jin, Jingfa Xiao
    PGAweb: A Web Server for Bacterial Pan-Genome Analysis
    Frontiers in microbiology 2018
  16. Gaihua Zhang, Yongbing Zhao, Yi Liu, Lipin Kao, Xiao Wang, Benjamin Skerry, and Zhaoyu Li
    FOXA1 Defines Cancer Cell Specificity
    Science Advances 2016
  17. Guoxiang Shi, Mingming Su, Junrong Liang, Ran Duan, Wenpeng Gu, Yuchun Xiao, Zhewen Zhang, Haiyan Qiu, Zheng Zhang, Yi Li, Xiaohe Zhang, Yunchao Ling, Lai Song, Meili Chen, Yongbing Zhao, Jiayan Wu, Huaiqi Jing, Jingfa Xiao, and Xin Wang
    Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica
    Archives of Microbiology 2016
  18. Yi Liu, Yongbing Zhao, Benjamin Skerry, Xiao Wang, Christelle Colin-Cassin, Derek C. Radisky and Zhaoyu Li
    Foxa1 is Essential for Mammary Duct Formation
    The Journal of Genetics and Development 2016
  19. Yongbing Zhao, Zhaoyu Li
    Interplay of estrogen receptors and FOXA factors in the liver cancer
    Molecular and Cellular Endocrinology 2015
  20. Yongbing Zhao, Jinlong Yin , Haiyan Guo, Yuyu Zhang, Wen Xiao, Chen Sun, Jiayan Wu, Xiaobo Qu, Jun Yu, Xumin Wang, Jingfa Xiao
    The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng
    Frontiers in Plant Science 2014
  21. Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jingfa Xiao
    PanGP:A tool for quickly analyzing bacterial pan-genome profile
    Bioinformatics 2014
  22. Zaichao Zhang, Zhong Jin, Yongbing Zhao, Zhewen Zhang, Rujiao Li, Jiayan Wu and Jingfa Xiao
    A systematic study on GPCR prototypes: did they really evolve from prokaryotic genes?
    IET Systems Biology 2014
  23. Yunchao Ling, Zhong Jin, Mingming Su, Jun Zhong, Yongbing Zhao, Jun Yu, Jiayan Wu, Jingfa Xiao
    VCGDB: a dynamic genome database of Chinese population.
    BMC Genomics 2014
  24. Siew Woh Choo, Wei Yee Wee, Yun Fong Ngeow, Mitchell Wayne, Joon Liang Tan, Guat Jah Wong, Yongbing Zhao and Jingfa Xiao
    Genomic reconnaissance of multiple, clinically derived isolates of the emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential
    Scientific Reports 2014
  25. Weili Liang, Yongbing Zhao, Chunxia Chen, Xiaoying Cui, Jun Yu, Jingfa Xiao, Biao Kan
    Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A
    PLoS ONE 2012
  26. Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao, Jun Yu
    PGAP: pan-genomes analysis pipeline
    Bioinformatics 2012
  27. Yongbing Zhao, Jingfa Xiao
    Homology modeling and molecular dynamics simulation studies of human type 1 3beta-hydroxysteroid dehydrogenase: Toward the understanding of cofactor specificity
    Journal of Computational Chemistry 2011
© 2025 Yongbing Zhao