Python pipeline

This project was conducted in collaboration with the Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, and aims to systematically characterize the cellular composition and spatial organization of hippocampal subregions across species.

This study revealed that transport stress (TS) suppresses immune function and exacerbates Mycobacterium tuberculosis (Mtb) infection. TS induced anxiety-like behaviors, disrupted HPA axis homeostasis, and disturbed hormone secretion and stress-related gene expression.

This study developed a recombinant adeno-associated virus strategy for controllable expression of the N-terminal gasdermin domain and demonstrated that it can induce tumor cell pyroptosis, activate antitumor immunity, and effectively inhibit tumor growth.

This project utilized single-cell transcriptomics and antigen receptor sequencing to systematically characterize the molecular features of immune cells before and after COVID-19 inactivated vaccine administration. We identified a clonal population of CD8⁺ T cells enriched in both vaccinated individuals and COVID-19 patients, which interact with monocytes and dendritic cells to participate in the immune response.

During my one-year visiting program at UNSW, I collaborated with Hannah Long’s group at the University of Edinburgh on identifying the zebrafish ortholog of the human EC1.45 enhancer, employing a combination of sequence alignment, transcription factor motif quantification, machine learning approaches, and genome synteny analysis to systematically characterize conserved regulatory elements.

This project developed SPIDER-Seq, a single-cell multi-modal sequencing approach integrating projectome, transcriptome, anatomy, and spatial-omics, to map the mouse PFC, reveal coordinated organizational principles and projection patterns, characterize neurotransmitter/receptor networks, and predict neuron projections including fear engram neurons.

This project generated a spatiotemporal single-cell atlas of the mouse prefrontal cortex (PFC) during early postnatal development, revealing dynamic molecular and cellular changes, particularly in intratelencephalic (IT) neurons. Our analyses identified time-specific gene expression programs, neuron–glia interactions, and signaling pathways underlying IT neuron maturation, providing a valuable resource for understanding PFC development and related neurological disorders.

spatialDE-pipeline packages the SpatialDE method, allowing rapid detection of spatially variable genes (SVGs) in spatial transcriptomics data with a single command.

STAGATE-pipeline is a workflow that packages the existing STAGATE method, enabling rapid computation and visualization of spatial domains in spatial transcriptomics data with a single command.