CV

Education

B.S. in Bioinformatics, Huazhong University of Science and Technology, 2018
- visiting student, University of California, Berkeley, 2016
M.S. in Computer Science, Huazhong University of Science and Technology, 2021
Ph.D in Computer Science, Vanderbilt University, 2026 (expected)

Publications

Text mining of gene–phenotype associations reveals new phenotypic profiles of autism-associated genes

Li, S., Guo, Z., Ioffe, J.B. et al. Text mining of gene–phenotype associations reveals new phenotypic profiles of autism-associated genes. Sci Rep 11, 15269 (2021).

An ensemble deep learning framework to refine large deletions in linked-reads

Y. Hu, S. V. Mangal, L. Zhang, X. Zhou. An ensemble deep learning framework to refine large deletions in linked-reads. The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2021)

Automated filtering of genome-wide large deletions through an ensemble deep learning framework

Yunfei Hu, Sanidhya Mangal, Lu Zhang, Xin Zhou, Automated filtering of genome-wide large deletions through an ensemble deep learning framework, Methods, Volume 206, 2022, Pages 77-86.

Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads

Hu, Y., Yang, C., Zhang, L., Zhou, X. (2023). Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads. In: Peters, B.A., Drmanac, R. (eds) Haplotyping. Methods in Molecular Biology, vol 2590.

ADEPT: Autoencoder with Differentially Expressed Genes and Imputation for a Robust Spatial Transcriptomics Clustering

Y. Hu, Y. Zhao, C. T. Schunk, Y. Ma, T. Derr*, X. M. Zhou*. ADEPT: autoencoder with differentially expressed genes and imputation for a robust spatial transcriptomics clustering. (Recomb-seq 2023).

MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning

Hu, Yunfei, et al. "MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning." bioRxiv (2024): 2024-02.

CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data.

Yuan, W., Luo, C., Hu, Y., Zhang, L., Wen, Z., Liu, Y. H., ... & Zhou, X. M. (2024). CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data. bioRxiv, 2024-02.

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

Hu, Yunfei, et al. "Benchmarking clustering, alignment, and integration methods for spatial transcriptomics." Genome Biology 25.1 (2024): 212.

Yunfei

CV

Education

Publications

Text mining of gene–phenotype associations reveals new phenotypic profiles of autism-associated genes

An ensemble deep learning framework to refine large deletions in linked-reads

Automated filtering of genome-wide large deletions through an ensemble deep learning framework

Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads

ADEPT: Autoencoder with Differentially Expressed Genes and Imputation for a Robust Spatial Transcriptomics Clustering

MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning

CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data.

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

Talks

BIBM2021 oral presentation

RECOMB-seq2023 oral presentation

RECOMB-seq2024 oral presentation

Teaching

Mentoring Activities

Teaching Assistant

Teaching Assistant

Teaching Assistant