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Alternative splicing links histone modifications to stem cell fate decision [Genome Biology 2018]

We profile the transcriptomes and epigenomes of human ESC and five types of differentiated cells. Exemplified by the splicing of transcription factor PBX1, we reveal the mechanism by which alternative splicing links histone modifications to stem cell fate decisions.

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scIGANs: single-cell RNA-seq imputation using generative adversarial networks [Nucleic Acids Research 2020]

A paragraph is a self-contained unit of a discourse in writing dealing with a particular point or idea. Paragraphs are usually an expected part of formal writing, used to organize longer prose.

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Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision [Nucleic Acids Research 2017]

We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network. When trained in different contexts, DeepCode can be expanded to a variety of biological and biomedical fields. 

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所有论著

谷歌学术：https://scholar.google.com/citations?user=AJza7rIAAAAJ&hl=en
参编英文专著
  1. 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
发表期刊论文列表 (#通讯作者)
（一）第一/通讯(#)作者（含共同，时间倒序）
  1. Li, Rufeng, Yuefeng Du, Kang Li, Xiaofan Xiong, Lingyu Zhang, Chen Guo, Shanfeng Gao, Yufei Yao, Yungang Xu#, and Juan Yang#. "Single-cell transcriptome profiling implicates the psychological stress-induced disruption of spermatogenesis." Molecular Therapy-Nucleic Acids (2024).
  2. Li Kang, Qiang Min, Xu Yungang#. Cell-type-specific alternative polyadenylation as a therapeutic biomarker in lung cancer progression. Molecular Therapy-Nucleic Acids, 2023;12;34. (SCI, IF 8.8, JCR rank Q1).​​​​​​​
  3. Li Y, Gao C, Song X, Wang X, Xu Y#, Han S#. Druggpt: A gpt-based strategy for designing potential ligands targeting specific proteins. bioRxiv, 2023; 2023-06.
  4. Duan Y#, Xu Y#. Explainable, trustworthy and responsive intelligent processing of biological resources integrating data, information, knowledge, and wisdom. Frontiers in Genetics; 4;13:1114441. (SCI, IF 3.7, JCR rank Q1).
  5. 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 (SCI, IF 8.786, JCR rank Q1)
  6. 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 (SCI, IF 5.738, JCR rank Q2)
  7. Rufeng Li, Lixin Li, Yungang Xu#, Juan Yang#, Machine learning meets omics: applications and perspectives, Briefings in Bioinformatics, 2021: bbab460 (SCI, IF 13.994, JCR rank Q1 top)
  8. 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. (SCI, IF 16.97, JCR rank Q1 top)
  9. 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. (SCI, IF 14.028, JCR Q1 top)
  10. 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. (SCI, IF 11.561, JCR rank Q1 top)
  11. 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. (SCI, IF 11.561, JCR rank Q1 top)
  12. 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. (SCI, IF 7.307, JCR rank Q1)
  13. 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. (SCI, IF: 4.599, JCR rank Q1)
  14. 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 (SCI, IF 4.015, JCR rank Q1)
  15. Yungang Xu, Maozu Guo#, Wenli Shi, Xiaoyan Liu, Chunyu Wang. (2013) A novel insight into Gene Ontology semantic similarity. Genomics 101(6): 368-375. (SCI, IF 2.910, JCR rank Q2)
  16. Yungang Xu, Yaguang Zhan#. (2009) Progress of the Research on Plant Drought-resistant Mechanism and Related Genes. Biotechnology Bulletin. 2009(2): 11-17.
（二）共同作者
  1. Wang, Tao, Hui Zhao, Yungang Xu, Yongtian Wang, Xuequn Shang, Jiajie Peng, and Bing Xiao. scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks. Briefings in Bioinformatics 24, no. 6 (2023): bbad384.
  2. Mao, Fengbiao, Husile Baiyin, Jinchen Li, Xiao Chen, Yungang Xu, Chenqi Wang, and Chang Li. Biomedical application of DNA modifications. Frontiers in Genetics 14 (2023): 1286185.
  3. 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. ​​​(SCI, IF 2.252, JCR rank Q3 )
  4. Mao, Fengbiao, Husile Baiyin, Jinchen Li, Xiao Chen, Yungang Xu, Chenqi Wang, and Chang Li. Biomedical application of DNA modifications. Frontiers in Genetics 14 (2023): 1286185.
  5. 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. (SCI, IF 10.502, JCR rank Q1 )
  6. 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. (SCI, IF 2.638, JCR Q2)
  7. 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. (SCI, IF 4.151, JCR Q1)
  8. 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 (SCI, IF 2.879, JCR rank Q2)
  9. Quan Zou#, Dariusz Mrozek, Qin Ma, Yungang Xu. (2017) Scalable Data Mining Algorithms in Computational Biology and Biomedicine. BioMed Research International (2017), 5652041. (SCI, IF 2.583, JCR Q2)
  10. 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.
  11. 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.
  12. 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.
  13. 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.