(1.)Basic Information

Name:           Yungang Xu (In Chinese: 徐云刚)​​​​​​​

 

Title:             Professor

Affiliation:    School of Basic Medical Sciences, Xi’an Jiaotong University, China

 

Address:      76 W Yanta Rd., Xi’an, Shaanxi 710069, China

Mobile:         +86-195****6380

Skype name: yungang.xu

E-mail:           yungang.xu【at】xjtu.edu.cn; yungang.xu【at】hotmail.com

Homepage:  www.xu-bioinfo.com  

Links: Google Scholar, Research Gate, PubMed, ORCID, ResearcherID

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(2.)Positions

  1. 2021.03-Current: Professor, School of Basic Medical Sciences, Xi’an Jiaotong University (XJTU), Xi’an, China
  2. 2019.04-2021.02: Postdoctoral Research Fellow, Children’s Hospital of Philadelphia (CHOP), University of Pennsylvania (UPenn), USA
  3. 2018.09-2019.03: Assistant Professor, School of Biomedical Informatics, University of Texas Health Science Center at Houston (UT Health), USA.
  4. 2017.07-2018.08: Faculty Associate (aka. Instructor), School of Biomedical Informatics, University of Texas Health Science Center at Houston (UT Health), USA.
  5. 2015.04-2017.06: Postdoctoral Research Fellow, School of Medicine (aka. Wake Forest Baptist Medical Center, WFBMC), Wake Forest University, USA.
  6. 2014.11-2015.03, Research Assistant, School of Computer Science and Technology, Harbin Institute of Technology (HIT), China.

(3.)Education

  1. 2010.09-2014.10: Ph.D. in Bioinformatics, School of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology (HIT), China.
  2. 2007.09-2010.07: Master's degree in Biology, School of Life Science, Northeast Forestry University (NEFU), China.
  3. 2003.09 -2007.07: Bachelor's degree in Biology, School of Life Science, Northeast Forestry University (NEFU), China.

(4.)Projects

  1. Computational studies of splicing epigenetic code on lineage tree for stem cell fate decision (NSFC) (2022-2025) (PI: Xu, YG)
  2. Deciphering the splicing (epi)genetic code. National Institutes of Health (NIH) (2018-2023). NO. R01 GM129644-01 (Co-investigator; PI: Zhou, XB);
  3. Integrative approach to studying lncRNA functions. National Institutes of Health (NIH) (2017-2022). NO. 1R01GM123037-01 (Co-investigator; PI: Zhou, XB);
  4. Methods of construction and analysis of miRNA-gene bilayer network. National Natural Science Foundation of China (NSFC) (2016-2019). NO. 61571163 (Co-investigator; PI: Guo, MZ);
  5. Methods of Reconstruction and Overlapping Community Detection in Functional Gene Network. National Natural Science Foundation of China (NSFC) (2013-2016). NO. 61271346 (Co-investigator; PI: Guo, MZ);
  6. Research on the symmetric prediction of protein-protein interactions and gene-gene functional associations. National Natural Science Foundation of China (NSFC) (2012-2015). NO. 61172098 (Co-investigator; PI: Guo, MZ);
  7. Research on information processing and analysis methods of Soybean RNA structure and evolution. National Natural Science Foundation of China (NSFC) (2010-2013). NO. 60932008 (Co-investigator; PI: Guo, MZ).

(5.)Scientific Research

Research Area

  1. Bioinformatics/Computational biology;
  2. Computational epigenomics;
  3. Transcriptional regulations and Alternative splicing;
  4. Stem cell fate decision/cell lineage modeling;
  5. Cancer genomics; Multi-omics informatics
  6. Molecular biology, functional genomics;
  7. Biological network; Systems Biology;
  8. Machine learning (in multi-omics).

(7.)Publications

As first-author (# correspondence)

  1. Rufeng Li, Lixin Li, Yungang Xu#, Juan Yang#, Machine learning meets omics: applications and perspectives, Briefings in Bioinformatics, 2021: bbab460
  2. Qi Wang, Hanmin Tang, Xuehui Luo, Jie Chen, Xinyue Zhang, Xinyue Li, Yuesen Li, Yuetong Chen, Yungang Xu#, Suxia Han#, Immune-Associated Gene Signatures Serve as a Promising Biomarker of Immunotherapeutic Prognosis for Renal Clear Cell Carcinoma, Frontiers in immunology, 2022, 24;13:890150 
  3. Jun Zhu, Tenghui Han, Shoujie Zhao, Yejing Zhu, Shouzheng Ma, Fenghua Xu, Bai Tingting, Yuxin Tang, Yungang Xu#, Lei Liu#, Computational Characterizing Necroptosis Reveals Implications for Immune Infiltration and Immunotherapy of Hepatocellular Carcinoma, Frontiers in Oncology, 2022, 12:933210 
  4. Yungang Xu#, Zhigang Zhang, Lei You, Jiajia Liu#, Zhiwei Fan, and Xiaobo Zhou#. (2020) scIGANs: single-cell RNA-seq imputation using generative adversarial networks." Nucleic acids research 48, 15 (2020): e85-e85.
  5. Yungang Xu, Weiling Zhao, Scott D. Olson, Karthik S. Prabhakara, Xiaobo Zhou#. (2018) Alternative splicing links histone modifications to stem cell fate decision. Genome Biology 19(1):133.
  6. Yungang Xu#, Xiaobo Zhou (2018) Applications of Single-Cell Sequencing for Multiomics. In: Huang T. (eds) Computational Systems Biology. 1754: 327-374. Springer Press, New York, NY. DOI:10.1007/978-1-4939-7717-8_19
  7. Yungang Xu#, Yongcui Wang, Jiesi Luo, Weilin Zhao, Xiaobo Zhou#. (2017) Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision. Nucleic Acids Research 45 (21), 12100-12112.
  8. Yungang Xu#, Maozu Guo#, Chunyu Wang, Yang Liu, Guojun Liu. (2016) Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks. Nucleic Acids Research 44 (20), e152.
  9. Yungang Xu, Maozu Guo#, Xiaoyan Liu, Chunyu Wang, Yang Liu. (2014) Inferring the Soybean (Glycine max) microRNA functional network based on target gene network. Bioinformatics 30 (1):94-103.
  10. Yungang Xu, Maozu Guo#, Xiaoyan Liu, Chunyu Wang, Yang Liu. (2014) SoyFN: a knowledge database of soybean functional networks. Database-The Journal of Biological Databases and Curation, 2014: bau019.
  11. Yungang Xu#, Maozu Guo#, Xiaoyan Liu, Chunyu Wang, Yang Liu. (2014) System-level insights into the cellular interactome of a non-model organism: inferring, modeling, and analyzing functional gene network of Glycine max. PLOS ONE (2014) 9(11): e113907.
  12. Yungang Xu, Maozu Guo#, Wenli Shi, Xiaoyan Liu, Chunyu Wang. (2013) A novel insight into Gene Ontology semantic similarity. Genomics 101(6): 368-375.
  13. Yungang Xu, Yaguang Zhan#. (2009) Progress of the Research on Plant Drought-resistant Mechanism and Related Genes. Biotechnology Bulletin. 2009(2): 11-17.

As co-author

  1. Liming He, Yungang Xu, Fansuo Zeng, Hongmei Tian, Ying Xiao, Hualing Liu, Lei Yu, Yaguang Zhan. (2021) Establishment of a micropropagation supporting technology for the Fraxinus mandshurica × Fraxinus sogdiana. In Vitro Cellular & Developmental Biology-Plant, 57(2), 307-318. 
  2. Levon Demirdjian, Yungang Xu, Emad Bahrami-Samani, Yang Pan, Shayna Stein, Zhijie Xie, Eddie Park, Ying Nian Wu, and Yi Xing#. (2020) Detecting Allele-Specific Alternative Splicing from population-scale RNA-Seq Data. The American Journal of Human Genetics 107, 3 (2020): 461-472.
  3. Zhijin Li, Hua Tan, Weiling Zhao, Yungang Xu, Zhigang Zhang, Maode Wang, Xiaobo Zhou#. Integrative analysis of DNA methylation and gene expression profiles identifies MIR4435-2HG as an oncogenic lncRNA for glioma progression. Gene 75 (2019): 144012.
  4. Liu, Changan, Jacqueline Chyr, Weiling Zhao, Yungang Xu, Zhiwei Ji, Hua Tan, Claudio Soto, and Xiaobo Zhou#. (2018) Genome-Wide Association and Mechanistic Studies Indicate that Immune Response Contributes to Alzheimer’s Disease Development. Frontiers in Genetics 9 (2018): 410.
  5. Quan Zou#, Lei Chen, Tao Huang, Yungang Xu. (2017) Machine Learning and Graph Analytics in Computational Biomedicine. Artificial Intelligence in Medicine. Doi: 10.1016/j.artmed.2017.09.003.
  6. Quan Zou#, Dariusz Mrozek, Qin Ma, Yungang Xu. (2017) Scalable Data Mining Algorithms in Computational Biology and Biomedicine. BioMed Research International (2017), 5652041.
  7. Ruida Guo, Fansuo, Yaguang Zhan#, Shujuan Li, Huijie Geng, Guiqin Zhang, Shengzhi Yao, Yungang Xu. (2013).Variation Analysis of Traits of Seed on Interspecific Hybrid F1 of Fraxinus. Forest Engineering, 29(5): 39-43.
  8. Bo Li, Yaguang Zhan#, Yungang Xu, Fansuo Zeng, Guiqin Zhang. (2012) Photosynthetic Physiological Characteristics in F1 Progeny of Fraxinus mandshurica and Fraxinus Americana under Drought Stress. Acta Botanica Boreali-Occidentalia Sinica. 32(11): 2313-2320.
  9. Shujuan Li, Yaguang Zhan#, Chuanping Yang, Yungang Xu. (2009) Response Surface Methodology to Determine the Optimal Medium for Pollen Germination for Ash. Bulletin of Botany. 44(2):223-229.
  10. Lei Wang, Shujuan Li, Yungang Xu, Yaguang Zhan#. (2008) Establishment of Propagation System of Mature Embryo and Stem Segment of Fraxinus velutina. Forestry Science & Technology. 33(3): 1-3.

Note: The citation number comes from Google Scholar.