About me
I am a fifth-year Ph.D. student, advised by Prof. Fengzhu Sun, from Department of Quantitative and Computational Biology at University of Southern California. My research focuses on the bioinformatics and biostatistics. I spent my entire childhood in Shanghai, China until my family moved to Wuhan, China when I stepped into the middle school. I came to America in 2019 and am now living in Los Angeles, USA.
Education
- Ph.D in Bioinformatics, University of Southern California, 2024 (expected)
- B.S. in Mathematics and Statistics, Wuhan University, 2019
- Secondary Degree in Computer Science, Wuhan University, 2019
Reseach interest
- Metagenomics and metagenomic Hi-C
- Single-cell omics
- High dimensional statistics
- Network analysis
Publication
[1] Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, and Fengzhu Sun. HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression. RECOMB 2021. [Paper] [Code] [Conference] [Video Record]
[2] Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, and Fengzhu Sun. Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. Journal of Computational Biology, 2022. [Paper] [Code]
[3] Yuxuan Du and Fengzhu Sun. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps. Genome Biology, 2022. [Paper] [Code]
[4] Yuxuan Du and Fengzhu Sun. HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs. Bioinformatics, 2022. [Paper] [Code]
[5] Yuxuan Du, Jed A. Fuhrman, and Fengzhu Sun. ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data. Nature Communications, 2023. [Paper] [Code]
[6] Jieli Ding, Jiaqian Zhang, Yanqin Feng, and Yuxuan Du. Quadratic upper bound algorithms for estimation under cox model in case-cohort studies. Statistics and Its Interface, 2023. [Paper]
[7] Yuxuan Du and Fengzhu Sun. MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data. Nature Communications, 2023. [Paper] [Code]
[8] Jiawei Huang, Yuxuan Du, Andres Stucky, Jiang F. Zhong and Fengzhu Sun. DeepDecon accurately estimates cell fractions in bulk RNA-seq data. ICIBM, 2023. [Code]
[9] Yuxuan Du, Wenxuan Zuo, and Fengzhu Sun. ImputeCC enhances integrative Hi-C-based metagenomic binning through constrained random-walk-based imputation. RECOMB 2024. [Code]
In Submission
[10] Wenxuan Zuo, Zifan Zhu, Yuxuan Du, Yingying Fan, Jinchi Lv, Fengzhu Sun. DeepLINK-T: Deep learning inference using knockoffs for feature selection in time series data. In submission
Professional Expericence
Oral presentation: HiCzin Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. RECOMB 2021, Augest 31st, Padova, Italy. [Video Record]
Reviewer: RECOMB 2021, RECOMB 2022, RECOMB 2023, Frontiers in Cellular and Infection Microbiology, Genome Biology, Communications Biology, ICIBM 2023.
Contact and Service
If you have any collaborations, service requests, or questions, welcome to contact me by email yuxuandu@usc.edu.