Yuqi Cheng

Hi! I’m a PhD student in the Computational Science and Engineering program at Georgia Tech College of Computing, advised by Dr. Xiuwei Zhang. Before starting my PhD, I did my Master’s degree in computational biology at Weill Cornell Medicine (’22) and my bachelor’s double majored in biology and data science at China Agricultural University (’20).

My research interest currently lies in the intersection of single-cell genomics/epigenetics and deep learning methods: (1) Integrating and annotating heterogeneous single-cell ATAC-seq data with deep generative models, and (2) Combining other epigenetic information (Hi-C, CNV, etc) to infer tumor cell composition.

Selected Publications

scBalance

A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data

Yuqi Cheng, Xingyu Fan, Jianing Zhang, and Yu Li

Communications Biology, 2023

Bib HTML

@article{cheng2023scalable,
  title = {A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data},
  author = {Cheng, Yuqi and Fan, Xingyu and Zhang, Jianing and Li, Yu},
  journal = {Communications Biology},
  volume = {6},
  number = {1},
  pages = {545},
  year = {2023},
  publisher = {Nature Publishing Group UK London},
}

CLEAR

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis

Wenkai Han*, Yuqi Cheng*, Jiayang Chen*, Huawen Zhong, and 6 more authors

Briefings in Bioinformatics, 2022

Bib HTML

@article{han2022self,
  title = {Self-supervised contrastive learning for integrative single cell RNA-seq data analysis},
  author = {Han*, Wenkai and Cheng*, Yuqi and Chen*, Jiayang and Zhong, Huawen and Hu, Zhihang and Chen, Siyuan and Zong, Licheng and King, Irwin and Gao, Xin and Li, Yu},
  journal = {Briefings in Bioinformatics},
  volume = {23},
  number = {5},
  year = {2022},
}