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SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers
Xiao-Xuan Cai, Jing-Shan Liao, Jia-Jun Ma, Yu-Xuan Pang, Yi-Gang Chen, Yang-Chi-Dung Lin, Yi-Dan Chen, Xin Cao, Yi-Cheng Zhang, Tao-Sheng Xu, Tzong-Yi Lee, Hsi-Yuan Huang, Hsien-Da Huang
https://arxiv.org/abs/2508.05692

SiCmiR Atlas: Single-Cell miRNA Landscapes Reveals Hub-miRNA and Network Signatures in Human Cancers
microRNA are pivotal post-transcriptional regulators whose single-cell behavior has remained largely inaccessible owing to technical barriers in single-cell small-RNA profiling. We present SiCmiR, a two-layer neural network that predicts miRNA expression profile from only 977 LINCS L1000 landmark genes reducing sensitivity to dropout of single-cell RNA-seq data. Proof-of-concept analyses illustrate how SiCmiR can uncover candidate hub-miRNAs in bulk-seq cell lines and hepatocellular carcinoma, …