PT  - JOURNAL ARTICLE
AU  - Liang, Shaoheng
AU  - Wang, Fang
AU  - Han, Jincheng
AU  - Chen, Ken
TI  - Latent periodic process inference from single-cell RNA-seq data
AID  - 10.1101/625566
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 625566
4099  - http://biorxiv.org/content/early/2019/05/02/625566.short
4100  - http://biorxiv.org/content/early/2019/05/02/625566.full
AB  - Convoluted biological processes underlie the development of multicellular organisms and diseases. Advances in scRNA-seq make it possible to study these processes from cells at various developmental stages. Achieving accurate characterization is challenging, however, particularly for periodic processes, such as cell cycles. To address this, we developed Cyclum, a novel AutoEncoder approach that characterizes circular trajectories in the high-dimensional gene expression space. Cyclum substantially improves the accuracy and robustness of cell-cycle characterization beyond existing approaches. Applying Cyclum to removing cell-cycle effects leads to substantially improved delineations of cell subpopulations, which is useful for establishing various cell atlases and studying tumor heterogeneity. Cyclum is available at https://github.com/KChen-lab/cyclum.