Ke Ni

Epithelial-mesenchymal transition couples with cell cycle arrest at various stages

The paper shows that EMT paths are influenced by cell cycle phase coupling and highlights the limitations of low-dimensional representations in capturing transition dynamics.

GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells

GraphVelo extends RNA velocity inference to multimodal data by using graph-based machine learning to preserve vector information across different data representations.

AtlasAgent: Vision language model and Agent-guided Framework for Evaluation of Atlas-scale Single-cell Integration

AtlasAgent uses a vision-language model to rapidly evaluate large-scale single-cell data integration, outperforming traditional methods in speed and efficiency.

LivecellX: Corrective Deep Learning for Object-Oriented Single-Cell Analysis in Live-Cell Imaging

LivecellX corrects segmentation and tracking errors in live-cell imaging using deep learning and provides tools for lineage reconstruction and dynamic analysis.

Inferring Single-Cell RNA Kinetics from Various Biological Priors

This paper introduces scRNAkinetics, a method to estimate RNA kinetics parameters from scRNA-seq data using biological priors, showing accurate inference on simulated datasets and validation with existing studies.

Robust and Accurate Doublet Detection of Single-Cell Sequencing Data via Maximizing Area Under Precision-Recall Curve

This paper introduces RADO, a doublet detection algorithm for single-cell sequencing data that maximizes the area under the precision-recall curve, outperforming existing methods on multiple datasets.

Transiently increased intercommunity regulation characterizes concerted cell phenotypic transition

The paper analyzes single-cell RNA sequencing data using transition path theory to study gene regulation during cell phenotypic transitions, finding increased intercommunity regulation and GRN frustration.