Faculty
Email：kaiyuanzhu@sjtu.edu.cn
Address：上海市闵行区东川路800号电院3-315
Institute：Institute of Artificial General Intelligence
MainPage：https://sjtu-cg.github.io/
Brief Introduction
长聘教轨副教授，博士生导师，国家级海外青年人才，上海市海外高层次青年人才。主要研究方向为计算基因组学、癌症基因组学，聚焦基因组数据的高效存储、检索与分析，具体研究内容包括但不限于：（1）癌症基因组局部扩增与复杂结构变异（如染色体外DNA）重建；（2）基因组数据压缩与索引；（3）宏基因组、泛基因组与肿瘤微生物组分析；（4）三维基因组与染色质结构解析；（5）隐私保护基因组数据分析。我们致力于以算法创新推动基因组学研究，从海量基因组数据中挖掘生物学新规律，加深对癌症等疾病发生、发展机制的理解，加速肿瘤精准诊疗的实现。欢迎具有计算机科学、数学、统计学、生物信息学等背景的优秀学生与学者加入团队，共同开拓计算基因组学前沿。
Education
2014.09 - 2021.05 Indiana University Bloomington, Luddy School of Informatics, Computing, and Engineering, 计算机科学, 博士
2010.09 - 2014.06 山东大学, 泰山学堂, 计算机科学与技术, 本科
Professional Experience
2026.01 - 至今 kaiyun官网入口, kaiyun官网入口, 长聘教轨副教授
2021.09 - 2025.12 UC San Diego, Department of Computer Science and Engineering, Postdoctoral Scholar
2021.03 - 2021.09 Indiana University Bloomington, Luddy School of Informatics, Computing, and Engineering, Visiting Research Associate
2019.08 - 2020.12 National Cancer Institute, Cancer and Data Science Laboratory, Graduate Fellow
Publications
Some papers:
1. Chowdhury, B., Zhu, K., Li, C., Alsing, J., Luebeck, J., Stefanova, M. E., Chapman, O. S., Kraft, K., Zhang, S., Lim, J. Y. S., Xie, Y., Kim, Y. J., Wu, S., Chavez, L., Nir, G., Henssen, A. G., Mischel, P. S., Chang, H. Y., & Bafna, V. (2026). Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D. Nature Communications, 17(1), 894
2. Zhu, K., Jones, M. G., Luebeck, J., Bu, X., Yi, H., Hung, K. L., Wong, I. T. L., Zhang, S., Mischel, P. S., Chang, H. Y., & Bafna, V. (2024). CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. Genome Research, 34(9), 1344-1354.
3. Zhu, K., Robinson, W., Schäffer, A. A., Xu, J., Ruppin, E., Ergun, A. F., Ye, Y., & Sahinalp, S. C. (2022). Strain level microbial detection and quantification with applications to single cell metagenomics. Nature Communications, 13(1), 6430
4. Kockan, C., Zhu, K., Dokmai, N., Karpov, N., Kulekci, M. O., Woodruff, D. P., & Sahinalp, S. C. (2020). Sketching algorithms for genomic data analysis and querying in a secure enclave. Nature Methods, 17(3), 295-301.
5. Ginart, A. A., Hui, J., Zhu, K., Numanagic, I., Courtade, T. A., Sahinalp, S. C., & Tse, D. N. (2018). Optimal compressed representation of high throughput sequence data via light assembly. Nature Communications, 9(1), 566
Academic Service
Journal Review: Genome Research; iScience; Genome Biology; Bioinformatics; PLOS Computational Biology; IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB); BMC Bioinformatics
Conference Refree: RECOMB 2025; RECOMB 2024; ISMB/ECCB 2023; RECOMB 2023; ICALP 2022; RECOMB 2022; RECOMB 2021; SIAM SOSA 2021; RECOMB 2020; RECOMB 2019; RECOMB 2018; CPM 2017
Program Committee: RECOMB-Seq 2026
Posters Chair: RECOMB 2026
Organizing Committee: RECOMB 2022
Address: No. 800 Dongchuan Road, Shanghai
Email: https://www.safaricomp.com
Postal Code: 200240
Tel: +86-21-34205058 / 34204728
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