Ziqing Deng

This study uses spatial transcriptomics and snRNA-seq to identify 25 forebrain regions and characterize dynamic changes in the human fetal cortex and striatum during late first and early second trimesters.

OmniCell integrates single-cell and spatial transcriptomics to model tissue context, revealing how gene programs operate in different anatomical environments.

OneGenome-Rice (OGR) is a genomic foundation model for rice pre-trained on 422 genomes, outperforming existing models in 11 tasks and enabling downstream applications like trait analysis and gene expression prediction.

STID provides a standardized framework for analyzing spatial transcriptomic data in infectious diseases, enabling pathogen background correction, niche identification, and multi-sample comparative analyses.

RegFormer improves single-cell RNA sequencing analysis by integrating gene regulatory networks with Mamba-based modeling, outperforming existing models in clustering, integration, and annotation.

BiOmics introduces an AI agent that improves multi-omics interpretation by combining reasoning and embedding spaces, outperforming existing methods in variant discovery, cell annotation, and drug repurposing.

DynPerturb models spatiotemporal perturbation dynamics in single-cell and spatial transcriptomics, outperforming existing methods in regulatory link prediction and uncovering dynamic regulatory rewiring in biological systems.

This study identifies a Mg-Fe-PmrAB regulatory circuit that mediates polymyxin tolerance in Enterobacteriaceae under phosphate starvation and shows that targeting this circuit can reverse tolerance.

UniCell improves cell type annotation and cross-dataset harmonization by combining Cell Ontology with transcriptomic data, outperforming existing tools in accuracy and rare cell detection.

Stereopy provides a framework for analyzing multi-sample spatial transcriptomics data to model comparative and spatiotemporal cellular heterogeneity through three key algorithms.

This study uses spatial transcriptomics to show that cerebral vasculatures, particularly meninges, drive inflammation and tissue damage in Japanese encephalitis by forming a feedback loop involving immune cells and cell death mechanisms.

The paper analyzes the pathogen infectome of small mammals in southern China, identifying new pathogens and factors influencing their distribution and diversity.

The paper analyzes wildlife infectomes to identify zoonotic pathogens, finding 62 novel pathogens including a new coronavirus genus and highlighting high pathogen diversity in Carnivora and Rodentia.

This study characterizes intra-host SARS-CoV-2 genomic variants and their evolutionary dynamics in COVID-19 patients using deep sequencing data.

This study compares SARS-CoV-2 viral populations in COVID-19 patients to show narrow transmission bottlenecks and stochastic dynamics in intra-host and inter-host evolution.

This paper compares amplicon, hybrid capture, and metatranscriptomic sequencing methods for directly sequencing SARS-CoV-2 genomes from clinical samples, finding differences in bias, sensitivity, and accuracy.