曽 超 (Chao ZENG, Ph.D.)

Junior Researcher (Hamada Lab, Waseda University)

〒169-8555 新宿区大久保3-4-1 西早稲田キャンパス55号館N棟4階05B室

✎ chao.zeng{AT}aoni.waseda.jp

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News (archives)

• 2021/10/8: Our work on the impact of gene annotation choice on RNA-seq differential expression analyisis is published.
• 2021/9/27~28: IIBMP2021でポスター発表を行います。
• 2021/7/14: 「挑戦的研究(萌芽)」の科研費(分担)が採択されました。
• 2021/7/7~9: 第22回日本RNA学会年会(オンライン開催)でポスター発表を行います。
• 2021/04/13: Our collaborative study on the role of lncRNAs in drug resistance in lung cancer is published.
• 2021/04/01: I will be a junior reasearcher at Waseda University from today.
• 2021/03: I am happy to contribute as a reviewer editor in Frontier in Genetics.
• 2021/01/20: We're excited to share our study on repetative sequence & R-loop. This work is highlighted by preLights.

Experience

• 2021/04/01~present: Waseda University, Junior Researcher
• 2018/11/01~2021/03/31: CBBD-OIL (AIST), Postdoctoral Researcher
• 2018/05/01~2018/10/31: Waseda University, Research Associate
• 2016/12/01~2018/04/30: CBBD-OIL (AIST), Technical Staff
• 2016/04/01~2016/11/31: The University of Tokyo, Project Researcher

Education

• PhD in Science, The University of Tokyo, 2013~2016
• MSc in Informatics, Kyoto University, 2010~2013
• BSc in Information Processing, Tianjin University of Science & Technology, 2006~2010

Grants (2)

• 2021/07~2023/03: Grant-in-Aid for Challenging Exploratory Research (Co-Investigator) / 挑戦的萌芽研究・分担 (21K19402)
• 2020/04~2022/03: Grant-in-Aid for Early-Career Scientists / 若手研究 (20K15784)

Manuscripts in preparation

1. Katsuhisa Takahashi, Chao Zeng, Michiaki Hamada*
2. Chao Zeng, et al.
3. Chao Zeng*, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, Michiaki Hamada*, Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs, Methods in Molecular Biology (invited review, preprint)

Publications (Total 10・First author 5・*Corresponding 6)

1. Yu Hamaguchi*, Chao Zeng, Michiaki Hamada*, Impact of human gene annotations on RNA-seq differential expression analysis, BMC Genomics, 22:730, 2021. doi: 10.1186/s12864-021-08038-7 [preprint]
2. Masahiro Onoguchi, Chao Zeng, Ayako Matsumaru, Michiaki Hamada*, Binding patterns of RNA binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements, NAR Genomics and Bioinformatics, 3(3):lqab055, 2021. doi: 10.1093/nargab/lqab055. (bioRxiv)
3. Satoshi Takahashi, Rintaro Noro, Masahiro Seike*, Chao Zeng, Masaru Matsumoto, Akiko Yoshikawa, Shinji Nakamichi, Teppei Sugano, Mariko Hirao, Kuniko Matsuda, Michiaki Hamada, Akihiko Gemma, Long Non-Coding RNA CRNDE is Involved in Resistance to EGFR Tyrosine Kinase Inhibitor in EGFR-Mutant Lung Cancer via eIF4A3/MUC1/EGFR Signaling, International Journal of Molecular Sciences, 22(8):4005, 2021. doi: 10.3390/ijms22084005
4. Chao Zeng*, Masahiro Onoguchi, Michiaki Hamada*, Association analysis of repetitive elements and R-loop formation across species, Mobile DNA, 12(3), 2021. doi: 10.1186/s13100-021-00231-5. [bioRxiv] [preLights]
5. Chao Zeng, Michiaki Hamada*, Detection and characterization of ribosome-associated lncRNA, Methods in Molecular Biology, 2254:179-194, 2021. doi: 10.1007/978-1-0716-1158-6_11.
6. Chao Zeng*, Michiaki Hamada*, RNA-seq analysis reveals localization-associated alternative splicing across 13 cell lines, Genes, 11(7):820, 2020. doi: 10.3390/genes11070820. [bioRxiv]
7. Chao Zeng*, Michiaki Hamada*, Identifying sequence features that drive ribosomal association for lncRNA, BMC Genomics, 19(Suppl 10):906, 2018. doi: 10.1186/s12864-018-5275-8.
8. Chao Zeng*, Tsukasa Fukunaga and Michiaki Hamada*, Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data, BMC Genomics, 19:414, 2018. doi: 10.1186/s12864-018-4765-z.
9. Hu, Xiao-tong*, Chao Zeng*, Obstacle Avoidance and Path Planning Based on S-Type Double-Arc Insertion Method, 6th International Conference on Wireless Communications Networking and Mobile Computing (WiCOM), 2010. doi: 10.1109/WICOM.2010.5600668.
10. 胡晓彤*, 曽超*, 靶向穿刺自动进针障碍物规避路径规划的研究, 图像图形技术研究与应用, 2010.

Presentations (2012~2021)

Awards (2)

• 2017: 生命医薬情報学連合大会研究奨励賞
• 2008: National Scholarship by Ministry of Education of the People's Republic of China

Activities

• IIBMP2021 (chairman of the local organizing committee)
• Frontier in Genetics (reviewer editor in RNA section, 2021/3 ~ present)

Peer review experience

BMC Bioinformatics, Frontier in Genetics, Nature Methods