Publications

Selected Publications

scIGANs: single-cell RNA-seq imputation using generative adversarial networks

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We propose the generative adversarial networks (GANs) for scRNA-seq imputation (scIGANs), which uses generated cells rather than observed cells to avoid these limitations and balances the performance between major and rare cell populations. 

 

Alternative splicing links histone modifications to stem cell fate decision

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We analyze 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.

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision

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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. 

Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data

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We introduce PAIRADISE (Paired Replicate Analysis of Allelic Differential Splicing Events), a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. PAIRADISE provides a useful computational tool for elucidating the genetic variation and phenotypic association of alternative splicing in populations.

Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks

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We proposed the pseudo-3D clustering algorithm, which starts from extracting initial non-hierarchically organized modules and then iteratively deciphers the hierarchical organization of modules according to a bottom-up strategy.

Full Publications

 
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Journal Articles

  (1)First-author/Correspondence

  1. 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)

  2. 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)

  3. Rufeng Li, Lixin Li, Yungang Xu#, Juan Yang#. (2021) Machine learning meets omics: applications and perspectives. Briefings in Bioinformatics, bbab460, https://doi.org/10.1093/bib/bbab460 (SCI, IF 11.662, JCR rank Q1 top)

  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. (SCI, IF 16.971, JCR rank Q1 top)

  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. (SCI, IF 14.028, JCR Q1 top)

  6. 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)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. Yungang Xu, Yaguang Zhan#. (2009) Progress of the Research on Plant Drought-resistant Mechanism and Related Genes. Biotechnology Bulletin. 2009(2): 11-17.

  (2) Co-authors

  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 sogdianaIn Vitro Cellular & Developmental Biology-Plant, 57(2), 307-318. (SCI, IF 2.252, JCR rank Q3 )

  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 (AJHG) 107, 3 (2020): 461-472. (SCI, IF 10.502, JCR rank Q1 )

  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. (SCI, IF 2.638, JCR Q2)

  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. (SCI, IF 4.151, JCR Q1)

  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 (SCI, IF 2.879, JCR rank Q2)

  6. 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)

  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.

Books & Chapters

  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