Engineer
Gene Expression Nebulas
Email: xuty (AT) big.ac.cn
Tel:
Gene Expression Nebulas
Email: xuty (AT) big.ac.cn
Tel:
PROFESSIONAL EXPERIENCE
Engineer, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation CNCB, China, 2021 - Present
Visiting Scholar, The University of Texas Health Science Center at Houston (UTHealth), USA, 2018-2019
EDUCATION
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
RNA editing
DATA RESOURCES
Gene Expression Nebulas : a data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species
ACADEMIC ACTIVITIES
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, Bioinformatics, BMC Genomics, Heliyon, Functional & Integrative Genomics, Molecular and Cellular Biochemistry, Frontiers in Series Journal.
PUBLICATIONS #Co-first author, *Corresponding author
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. Comput Biol Med. 2023, 166:107546. [PMID:37826952]
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]
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.
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]
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]
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]
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]
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]
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]
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]
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]
Xu T, Song X*, Wang Y, Fu S*, Han P*. Genome-wide analysis of the expression of circular RNA full-length trans and construction of the circRNA‑miRNA‑mRNA network in cervical cancer. Frontiers in Cell and Developmental Biology, 2020, 8:603516. [PMID: 33330502]
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]
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]
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.
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]
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]
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]
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]
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]
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]