Manuscripts
Manuscripts
[5] Yuqiu Wang, Wenxuan Zuo, Jiawei Huang, Fengzhu Sun*, Yuxuan Du*. Benchmarking Alignment Strategies for Hi-C Reads in Metagenomic Hi-C Data. Under Review.
[4] Zixuan Wang, Athan Li, Shiyuan Wang, Yuxuan Du, and Ruishan Liu*. GenomicQA: A Benchmark Dataset for Question Answering on DNA Sequences and Genomic-Language Modeling. Under Review.
[3] Ni Zhao, Peiling Geng, Alejandro Gaher Perez, Anakha Chandramana Maya, Brijesh Yadav, Yuxuan Du, and Yong Ge*. Genomic and functional characterization of a Butyricicoccus strain isolated from human gut microbiota. Under Review.
[2] Jiawei Huang, Yuxuan Du, Kevin R. Kelly, Jiang F. Zhong*, and Fengzhu Sun*. DeepDeconUQ estimates malignant cell fractions in bulk RNA-seq tissue with valid prediction interval. Under Review.
[1] Wenxuan Zuo, Zifan Zhu, Yuxuan Du, Yi-Chun Yeh, Jed A. Fuhrman, Jinchi Lv, Yingying Fan*, and Fengzhu Sun*. DeepLINK-T: deep learning inference for time series data using knockoffs and LSTM. Under Review.
[9] Chentong Sun, Zhen Qin, Ruishan Liu, Yuanxiong Guo, Yong Ge, and Yuxuan Du*. MetaHiCNet: A web-based platform for normalizing and visualizing microbial Hi-C interactions. Nucleic Acids Research. [Code]
[8] Yuxuan Du, Wenxuan Zuo, Fengzhu Sun. Imputing Metagenomic Hi-C contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart. Journal of Computational Biology.
[7] Jiawei Huang, Yuxuan Du, Andres Stucky, Jiang F. Zhong and Fengzhu Sun. DeepDecon accurately estimates cell fractions in bulk RNA-seq data. Patterns.[Paper] [Code]
[6] 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]
[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]
[4] 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]
[3] Yuxuan Du and Fengzhu Sun. HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs. Bioinformatics, 2022. [Paper] [Code]
[2] Yuxuan Du and Fengzhu Sun. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps. Genome Biology, 2022. [Paper] [Code]
[1] 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, Wenxuan Zuo, and Fengzhu Sun. ImputeCC enhances integrative Hi-C-based metagenomic binning through constrained random-walk-based imputation. RECOMB 2024. [Code]
[2] 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]
[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]