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Tianyi Xu
Tianyi Xu

Senior Engineer

Gene Expression Nebulas

Email: xuty (AT) big.ac.cn

Tel: +86 84097845

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. Guan D, Bai Z, Zhu X, Zhong C, Hou Y, Zhu D, Chicken G C, Li H, Lan F, Diao S, Yao Y, Zhao B, Li X, Pan Z, Gao Y, Wang Y, Zou D, Wang R, Xu T, Sun C, Yin H, Teng J, Xu Z, Lin Q, Shi S, Shao D, Degalez F, Lagarrigue S, Wang Y, Wang M, Peng M, Rocha D, Charles M, Smith J, Watson K, Buitenhuis A J, Sahana G, Lund M S, Warren W, Frantz L, Larson G, Lamont S J, Si W, Zhao X, Li B, Zhang H, Luo C, Shu D, Qu H, Luo W, Li Z, Nie Q, Zhang X, Xiang R, Liu S, Zhang Z, Zhang Z, Liu G E, Cheng H, Yang N, Hu X, Zhou H and Fang L. Genetic regulation of gene expression across multiple tissues in chickens. Nature Genetics. 2025, 57, 1298-1308. [PMID:40200121]

  2. Xu T# as co-first author in CNCB-NGDC Members & Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Res. 2025, 53, D30-D44. [PMID:39530327]

  3. Zhu T, Chu Y, Niu G, Pan R, Chen M, Cheng Y, Zhang Y, Li Z, Jiang S, Hao L, Zou D*, Xu T*, Zhang Z*. Editome Disease Knowledgebase v2.0: an updated resource of editome-disease associations through literature curation and integrative analysis. Bioinform Adv. 2025, 5(1):vbaf012. [PMID:39968378]

  4. Liu J,  Yuan Q,  Cai R,  Zhao J,  Chen J,  Zhang M, Wang Y, Zhuang M, Xu T*, Song X*, Wu J*. Investigating full-length circRNA transcripts to reveal circRNA-mediated regulation of competing endogenous RNAs in gastric cancer. Current Bioinformatics. 2025, 20(2), 164-178.

  5. Chen M, Xia L, Tan X, Gao S, Wang S, Li M, Zhang Y, Xu T, Cheng Y, Chu Y, Hu S, Wu S, Zhang Z*. Seeing the unseen in characterizing RNA editome during rice endosperm development. Communications biology. 2024, 7(1), 1314. [PMID:39397073]

  6. 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]

  7. Xu T# as co-first author in CNCB-NGDC Members & Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res. 2024, 52, D18-D32. [PMID:38018256]

  8. 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]

  9. 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]

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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]

  15. 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]

  16. 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]

  17. 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]

  18. 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] 

  19. 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] 

  20. 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]

  21. 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]

  22. 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]

  23. 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. 

  24. 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]

  25. 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]

  26. 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]

  27. 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]

  28. 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]

  29. 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]