Jiaqi Zhang

The paper introduces eccDNAMamba, a model for ultra-long eccDNA sequences, showing improved performance in cancer discrimination and copy-number prediction.

scMultiNODE integrates gene expression and chromatin accessibility data across timepoints to recover developmental dynamics and annotations for weak modalities.

scNODE predicts single-cell gene expression at unobserved timepoints using a deep learning model combining VAE and ODEs, improving trajectory inference and perturbation analysis.

This study evaluates gene co-expression estimation methods on simulated and experimental single-cell datasets, finding high false discovery rates and limited improvement from preprocessing.