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Tianyi Xu
Tianyi Xu

Engineer

Gene Expression Nebulas

Email: xuty (AT) big.ac.cn

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WORK EXPERIENCE

  • Engineer, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation CNCB, China, 2021 - Present

EDUCATION

  • Visiting Scholar, The University of Texas Health Science Center at Houston (UTHealth), USA, 2018-2019

  • Ph.D. in Instrument Science and Technology, Nanjing University of Aeronautics and Astronautics, China, 2021

  • M.S. in Biology, Shanghai Ocean University, China, 2015

  • B.S. in Plant Protection, Jiangxi Agricultural University, China, 2012

RESEARCH INTERESTS

  • Molecular function and regulation of non-coding RNA in human disease

  • Functional genomics data integration and analytics

  • Transcriptional and post-transcriptional regulation

DATA RESOURCES

ACADEMIC ACTIVITIES

  • Poster: A Structured Metadata Curation Model and Standardized Analysis Pipeline for RNA-seq Data on both Bulk and Single-cell Levels. Qingdao, Oct. 28-30, 2023.

  • Poster: Gene Expression Nebulas (GEN) and GENToolkit. GPB Omics & Bioinformatics Frontiers Symposium 2023, Aug. 2-4, Beijing.

  • Talk: Gene Expression Nebulas (GEN) and GENToolkit. 2023 Bioinformatics and Intelligent Information Processing Conference. Jinan, Jun. 18-20, 2023.

  • Poster: Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. The 10th National Conference on Bioinformatics and System Biology of China. Chengdu, Oct. 25-28, 2021. (Third Prize Award)

  • Talk: Genome-wide analysis of the expression of circular RNA full-length trans and construction of the circRNA‑miRNA‑mRNA network in cervical cancer. The fifth CCF Bioinformatics Conference CBC2020. Harbin, Oct. 16-18, 2020.

  • Poster: VISDB: a manually curated database of viral integration sites in the human genome. The American Society of Human Genetics annual conference ASHG 2019. Houston, Oct. 15-19, 2019.

  • Poster: Circular RNA expression profiles and features in human tissues. International Conference on Intelligent Biology and Medicine ICIBM 2016. Houston, Dec. 8-10, 2016.

  • Reviewer: NAR, GPB, Science of The Total Environment, BIB, Bioinformatics, BMC Genomics, Heliyon, Functional & Integrative Genomics, Molecular and Cellular Biochemistry, etc.

PUBLICATIONS #Co-first author, *Corresponding author

  1. Bu C#, Zheng X#, Zhao X#, Xu T#, Bai X#, Jia Y, Chen M, Hao L, Xiao J, Zhang Z, Zhao W, Tang B*, Bao Y*. GenBase: A Nucleotide Sequence Database. Genomics, Proteomics & Bioinformatics. 2024, qzae047. [PMID:38913867]

  2. Wang Y#, Wu J#, Zhao J#, Xu T#, Zhang M, Liu J, Wang Y, Wang Q*, Song X*. Global characterization of RNA editing in genetic regulation of multiple ovarian cancer subtypes. Mol Ther Nucleic Acids. 2024, 35(1):102127. [PMID:38352860]

  3. Tian D#, Xu T#, Kang H, Luo H, Wang Y, Chen M, Li R, Ma L, Wang Z, Hao L, Tang B, Zou D, Xiao J, Zhao W, Bao Y, Zhang Z*, Song S*. Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications. aBIOTECH. 2024, 5(1):94-106.  [PMID:38576435]

  4. Wang Y, Zhao J, Wu J, Liu J, Wang Y, Xu T, Zhang M, Zhuang M, Zou L, Sun W*, Han P*, Song X*. Genome-wide perturbations of A-to-I RNA editing dysregulated circular RNAs promoting the development of cervical cancer. Computers in biology and medicine. 2023, 166:107546. [PMID:37826952]

  5. Bu C, Zheng X, Mai J, Nie Z, Zeng J, Qian Q, Xu T, Sun Y, Bao Y*, Xiao J*. CCLHunter: An efficient toolkit for cancer cell line authentication. Comput Struct Biotechnol J. 2023, 21:4675-4682. [PMID:37841327]

  6. Zhu M#, Xu T#, Zhang H, Fan X, Wang Y, Zhang J, Yu F*. Characterization of prognosis and immune infiltration by a novel glutamine metabolism-related model in cutaneous melanoma. Biocell. 2023, 9:1931-1945.

  7. Zhang X, Chen X, Liu J, Li Y, Wu J, Chen M, Zhang R, Xu X, Xu T*, Sun Q*. A novel metabolism-related prognostic gene development and validation in gastric cancer. Clin Transl Oncol. 2023, 25(2):447-459. [PMID:36168087]

  8. Xu T# as co-first author in CNCB-NGDC Members and Partners: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Research, 2023, 51(D1):D18-D28. [PMID:36420893]

  9. Zhang Y#, Zou D#, Zhu T#, Xu T#, Chen M#, Niu G, Zong W, Pan R, Jing W, Sang J, Liu C, Xiong Y, Sun Y, Zhai S, Chen H, Zhao W, Xiao J, Bao Y, Hao L*, Zhang Z*. Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. Nucleic Acids Research, 2022, 50(D1):D1016-D1024. [PMID: 34591957]

  10. Wang Y, Kang H, Xu T, Hao L, Bao Y*, Jia P*. CeDR Atlas: a knowledgebase of cellular drug response. Nucleic Acids Research, 2022, 50(D1):D1164-D1171. [PMID: 34634794]

  11. Liu L, Zhang Y, Niu G, Li Q, Li Z, Zhu T, Feng C, Liu X, Zhang Y, Xu T, Chen R, Teng X, Zhang R, Zou D, Ma L*, Zhang Z*. BrainBase: a curated knowledgebase for brain diseases. Nucleic Acids Research, 2022, 50(D1):D1131-D1138. [PMID: 34718720]

  12. Xu T# as co-first author in CNCB-NGDC Members and Partners: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research, 2022, 50(D1):D27-D38. [PMID:34718731]

  13. Xu T, Wang L, Jia P, Song X*, Zhao Z*. An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change. Biomedicines, 2021; 9(6):657. [PMID: 34201256] 

  14. Wang Y, Song X*, Xu T. Identification and analysis of RNA editing events in ovarian serous cystadenoma using RNA-seq Data. Current Gene Therapy, 2021,21(3):258-269. [PMID: 33573552] 

  15. Xu T, Song X*, Wang Y, Fu S*, Han P*. Genome-wide analysis of the expression of circular RNA full-length transcripts and construction of the circRNA‑miRNA‑mRNA network in cervical cancer. Front Cell Dev Biol., 2020, 8:603516. [PMID: 33330502]

  16. Zhao J, Song X*, Xu T, Yang Q, Liu J, Jiang B, Wu J*. Identification of potential prognostic competing triplets in high-grade serous ovarian cancer. Frontiers in Genetics, 2021, 11:607722. [PMID: 33519912]

  17. Tang D, Li B, Xu T, Hu R, Tan D, Song X, Jia P, Zhao Z*. VISDB: a manually curated database of viral integration sites in the human genome. Nucleic Acids Research, 2020, 48(D1): D633–D641. [PMID: 31598702]

  18. Yang Q, Wu J, Zhao J, Xu T, Han P*, Song X*. The Expression Profiles of lncRNAs and Their Regulatory Network during Smek1/2 Knockout Mouse Neural Stem Cells Differentiation. Current Bioinformatics, 2020, 151:77-78. 

  19. Wu J, Li Y, Wang C, Cui Y, Xu T, Wang C, Wang X, Sha J, Jiang B, Wang K, Hu Z*, Guo X*, Song X*. CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs. Genomics, Proteomics & Bioinformatics, 2019, 175:522–534. [PMID: 32007626]

  20. Liu J, Wu J, Lin J, Zhao J, Xu T, Yang Q, Zhao J*, Zhao Z*, Song X*. Changes in the Microbial Community Diversity of Oil Exploitation. Genes (Basel), 2019, 108:556. [PMID: 31344878]

  21. Wei J, Xu T, Wu J, Song X*. Molecular mechanisms of recursive splicing events in long introns of eukaryotes. Hereditas, 2019,412:89-97. [PMID: 30803940]

  22. Zhao J, Wu J, Xu T, Yang Q, He J, Song X*. IRESfinder: Identifying RNA Internal Ribosome Entry Site in Eukaryotic Cell using Framed K-mer Features. Journal of Genetics and Genomics, 2018, 45:403-406. [PMID: 30054216]

  23. Yang Q, Wu J, Zhao J, Xu T, Zhao Z*, Song X*, Han P*. Circular RNA expression profiles during the differentiation of mouse neural stem cells. BMC Systems Biology, 2018, 12(S8):128. [PMID: 30577840]

  24. Xu T, Wu J, Han P, Zhao Z*, Song X*. Circular RNA expression profiles and features in human tissues: A study using RNA-seq data. BMC Genomics, 2017, 18(S6):680. [PMID: 28984197]