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Current Protocols|March 2, 2026
Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network VisualizationYuxuan Du, Yuqiu Wang, Fengzhu SunGenome Biology|January 31, 2026
Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C dataYuqiu Wang, Wenxuan Zuo, Jiawei Huang, et al.Genome Biology|March 1, 2022
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact mapsYuxuan Du, Fengzhu SunBioinformatics (Oxford, England)|April 28, 2022
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigsYuxuan Du, Fengzhu SunNature Communications|October 6, 2023
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C dataYuxuan Du, Fengzhu SunJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|September 9, 2024
Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with RestartYuxuan Du, Wenxuan Zuo, Fengzhu SunNature Communications|January 31, 2023
ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C dataYuxuan Du, Jed A Fuhrman, Fengzhu SunMicrobiome|July 24, 2025
Bidirectional subsethood of shared marker profiles enables accurate virus classificationChristopher Riccardi, Yuqiu Wang, Shibu Yooseph, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|January 12, 2022
Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial RegressionYuxuan Du, Sarah M Laperriere, Jed Fuhrman, et al.Patterns (New York, N.Y.)|May 27, 2024
DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq dataJiawei Huang, Yuxuan Du, Andres Stucky, et al.Pageof 40