Vitae

Contact Information

Email: duan@songqi.org; Homepage: https://songqi.org; Twitter @duansongqi1999.

Research Interests

Single-cell RNA-seq; Data visualization; Immunology.

Education Background

Publications (# Co-first authors; * Co-corresponding authors)

See my Google Scholar page for a full list of publications.

  1. Yihao Liu#, Pengyi Liu#, Songqi Duan#, Jiayu Lin#, Wenxin Qi, Zhengwei Yu, Xia Gao, Xiuqiao Sun, Jia Liu, Jiewei Lin, Shuyu Zhai, Kai Qin, Yizhi Cao, Jingwei Li, Yang Liu, Mengmin Chen, Siyi Zou, Chenlei Wen, Jiao Wang, Da Fu, Jiancheng Wang, Haili Bao*, Keyan Sun*, Yu Jiang* and Baiyong Shen*. CTCF enhances pancreatic cancer progression via FLG-AS1-dependent epigenetic regulation and macrophage polarization. Cell Death & Differentiation, 2024. DOI: 10.1038/s41418-024-01423-1

  2. Shuang Zhao, Jie Li, Songqi Duan, Chang Liu, Hua Wang, Jiangtao Lu, Nannan Zhao, Xiaoyan Sheng, Yiwei Wu, Yanjun Li, Baofa Sun* and Lin Liu*. UBQLN1 links proteostasis and mitochondria function to telomere maintenance in human embryonic stem cells. Stem Cell Research & Therapy, 2024. DOI: 10.1186/s13287-024-03789-y

  3. Sai Xiao#, Shoubao Ma#, Baofa Sun#, Wenchen Pu, Songqi Duan, Jingjing Han, Yaqun Hong, Jianying Zhang, Yong Peng, Chuan He, Ping Yi*, Michael A. Caligiuri*, Jianhua Yu*. The tumor-intrinsic role of the m6A reader YTHDF2 in regulating immune evasion. Science Immunology, 2024. DOI: 10.1126/sciimmunol.adl2171

  4. Songqi Duan#, Hongyu Li#, Ziqi Wang#, Junqi Li, Weiming Huang, Chen Li, Zhenfeng Fang, Zhen Zen*, Baofa Sun, Yuntao Liu*. Tibetan tea consumption prevents obesity by modulating cellular composition and metabolic reprogramming of white adipose tissue. Food & Function, 2024. DOI: 10.1039/D3FO03506A

  5. Ziqi Wang, Hongyu Li, Weimin Huang, Songqi Duan, Yue Yan, Zhen Zeng*, Zhengfeng Fang, Cheng Li, Bin Hu, Wenjuan Wu, Xiguo Lan, Yuntao Liu*. Landscapes of the main components, metabolic and microbial signatures, and their correlations during pile-fermentation of Tibetan tea. Food Chemistry, 2024. DOI: 10.1016/j.foodchem.2023.136932

  6. Shoubao Ma#, Baofa Sun#, Songqi Duan#, Jingjing Han#, Tasha Barr, Jianying Zhang, Marc B Bissonnette, Marcin Kortylewski, Chuan He, Jianjun Chen, Michael A Caligiuri*, Jianhua Yu*. YTHDF2 orchestrates tumor-associated macrophage reprogramming and controls antitumor immunity through CD8+ T cells. Nature Immunology, 2023. DOI: 10.1038/s41590-022-01398-6

  7. Jianfeng Li*#, Benben Miao#, Shixiang Wang#, Wei Dong#, Houshi Xu#, Chenchen Si#, Wei Wang, Songqi Duan, Jiacheng Lou, Zhiwei Bao, Hailuan Zeng, Zengzeng Yang, Wenyan Cheng, Fei Zhao, Jianming Zeng, Xue-Song Liu*, Renxie Wu*, Yang Shen*, Zhu Chen*, Saijuan Chen*, Mingjie Wang*, Hiplot Consortium. Hiplot: A comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization. Breifings in Bioinformatics, 2022. DOI: 10.1093/bib/bbac261

  8. Yansu Yan#, Songqi Duan#, Huilan Zhang#, Yuntao Liu*, Cheng Li, Bin Hu, Aiping Liu, Dingtao Wu, Jialiang He, Wenjuan Wu. Preparation and characterization of Konjac glucomannan and pullulan composite films for strawberry preservation. Carbohydrate polymers, 2020. DOI: 10.1016/j.carbpol.2020.116446

  9. Yuntao Liu*#, Xiaoyu Duan#, Songqi Duan, Cheng Li, Bin Hu, Aiping Liu, Yinglong Wu, Hejun Wu, Hong Chen, Wenjuan Wu. Effects of in vitro digestion and fecal fermentation on the stability and metabolic behavior of polysaccharides from Craterellus cornucopioides. Food & function, 2020. DOI: 10.1039/D0FO01430C

  10. Yuntao Liu*#, Yuan Yuan#, Songqi Duan#, Cheng Li, Bin Hu, Aiping Liu, Dingtao Wu, Haiying Cui, Lin Lin*, Jialiang He, Wenjuan Wu. Preparation and characterization of chitosan films with three kinds of molecular weight for food packaging. International Journal of Biological Macromolecules, 2020. DOI: 10.1016/j.ijbiomac.2020.03.217

  11. Yuntao Liu*#, Tingting Tang#, Songqi Duan#, Zhizhi Qin, Cheng Li, Zhiqing Zhang, Aiping Liu, Dingtao Wu, Hong Chen, Guoquan Han, Bokun Lin, Jialiang He, Wenjuan Wu. Effects of sodium alginate and rice variety on the physicochemical characteristics and 3D printing feasibility of rice paste. LWT, 2020. DOI: 10.1016/j.lwt.2020.109360

  12. Yuntao Liu*#, Tingting Tang#, Songqi Duan#, Cheng Li, Qinlu Lin, Hejun Wu, Aiping Liu, Bin Hu, Dingtao Wu, Suqing Li, Li Shen, Wenjuan Wu. The purification, structural characterization and antidiabetic activity of a polysaccharide from Anoectochilus roxburghii. Food & function, 2020. DOI: 10.1039/C9FO00860H

  13. Yuntao Liu*#, Tingting Tang#, Songqi Duan#, Zhizhi Qin, Hui Zhao, Meiyan Wang, Cheng Li, Zhiqing Zhang, Aiping Liu, Guoquan Han, Dingtao Wu, Hong Chen, Li Shen, Wenjuan Wu, Yuping Dong. Applicability of rice doughs as promising food materials in extrusion-based 3D printing. Food and Bioprocess Technology, 2020. DOI: 10.1007/s11947-020-02415-y

Technical Skills

Programming Languages:

  • Python: Expertise in large-scale single-cell RNA-seq data analysis, data integration, and downstream bioinformatics workflows.

  • R: Proficient in bioinformatics data analysis, statistical analysis, and data visualization.

Bioinformatics & Data Analysis:

  • Single-cell Data Analysis: Experience in both upstream and downstream workflows. Skilled in aligning sequencing data in Linux to generate expression matrices and performing downstream analysis in Python and R, including custom analysis and public dataset integration.

  • Data Visualization: Advanced skills in creating publication-quality visualizations using ggplot2.

  • Molecular Docking & Virtual Screening: Experienced in performing molecular docking and virtual screening for drug discovery and protein-ligand interaction studies.

Server Management & Web Development:

  • Server Configuration and Management: Skilled in managing and configuring servers, particularly on Ubuntu systems, to support bioinformatics pipelines and data analysis.

  • Website Development: Experience in building and maintaining websites, proficient in front-end and back-end technologies.

Laboratory Skills

Molecular Biology Techniques:

  • Molecular Cloning: Skilled in gene cloning and vector construction, including overexpression in cell lines.

  • CRISPR Technology: Expertise in using CRISPR-Cas9 for gene knockout and performing CRISPR screens (knockout, activation, inhibition). Proficient in sgRNA design and CRISPR experiments, including large-scale functional screening.

  • PIPseq-based Single-cell Transcriptomics: Experience in sample preparation and library construction for single-cell RNA sequencing using PIPseq protocols.

Cell and Animal Work:

  • Cell Culture: Extensive experience with mammalian cell lines, including maintenance, transfection, and manipulation for molecular biology experiments.

  • Flow Cytometry and Sorting: Skilled in performing flow cytometry and cell sorting for various cellular assays.

  • Animal Handling & Experiments: Experience in conducting animal experiments, including genotyping (e.g., mouse tail DNA extraction), and handling animals for various research applications.

Operating Systems

  • MacOS (70%): Daily use for research, bioinformatics, and general productivity.
  • Ubuntu (30%): Expertise in configuring and managing Ubuntu servers, performing bioinformatics pipelines, and working in command-line environments.