Jianhua Xing

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.

Protrusion force and cell-cell adhesion-induced polarity alignment govern collective migration modes

This paper develops a computational model to study how protrusion force and cell-cell adhesion influence collective migration modes in microtumors under hypoxia.

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.

Long-range genomic loci stochastically assemble into hierarchical chromosome structures

The paper identifies long-range chromosomal loops spanning over 100 Mb and shows they form via multivalent binding, independent of known nuclear structures, suggesting a distributed mechanism for chromosome organization.

Mapping Transcriptomic Vector Fields of Single Cells

The paper introduces dynamo, a framework for estimating RNA velocities and predicting cell fates using single-cell RNA-seq data, applied to various biological processes.

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.

Live cell imaging and analysis reveal cell phenotypic transition dynamics inherently missing in snapshot data

The paper develops a live-cell imaging platform to study phenotypic transitions, revealing dynamics missed by snapshot data.

Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in

This paper develops a modular Gibson assembly method for efficient and cost-effective CRISPR donor DNA construct generation, showing improved assembly efficiency compared to conventional methods.

Pathway crosstalk enables cells to interpret TGF-β duration

The paper shows that TGF-β signaling duration is interpreted through pathway crosstalk that controls SNAIL1 expression.

Targeting temporal dynamics of microenvironmental factors halts tumor migration and alleviates effects of dynamic tumor heterogeneity

This study shows that targeting the temporal dynamics of microenvironmental factors can halt tumor migration and overcome tumor heterogeneity.