Zhe Zhang

A multimodal foundation model to integrate histology with spatial molecular programs

SQUALL integrates histology and spatial transcriptomics to enable virtual spatial gene expression profiling and clinical prediction across cancers and platforms.

Inhibition of integrin αvβ8-mediated TGFβ activation and active-TGFβ blockade promote anti-tumor immunity through distinct biological mechanisms

The paper shows that blocking integrin αvβ8 suppresses TGFβ in tumor-draining lymph nodes and enhances DC-T cell activation, offering a new immunotherapy strategy distinct from TGFβ ligand blockade.

Single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation

This study creates a single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation using a new platform and integrates transcriptomic and morphological data to identify temporal shifts in gene expression.

Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors

The paper presents an integrative spatial multi-omics atlas of female genital tumors, identifying prognostic tumor niches and developing a model to predict their abundance from histopathology.

LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD

This study shows that LINE1 RNA dysregulation impairs chromatin accessibility in ALS/FTD, leading to transcriptional changes and neuronal dysfunction.

5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins

This study shows that 5-ethynyluridine (5EU) causes nuclear accumulation of TDP-43 and other RNA-binding proteins by altering RNA metabolism and splicing.

Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms

The paper benchmarks five high-throughput subcellular spatial transcriptomics platforms using multi-omics data from cancer samples, evaluating performance across multiple metrics.

Spatial organization of PI3K-PI(3,4,5)P3-AKT signaling by focal adhesions

This study identifies focal adhesions as the subcellular hubs organizing PI3K-PI(3,4,5)P3-AKT signaling, showing localized lipid production and AKT activation, and demonstrates that combined inhibition of PI3K and FAK enhances cancer cell suppression.

A longitudinal resource for population neuroscience of school-age children and adolescents in China

The paper introduces a longitudinal dataset of school-age children and adolescents in China, detailing its design, sampling, and neuroimaging measurements.

Temporal and spatial dynamics mapping reveals follicle development regulated by different stromal cell populations

The paper maps temporal and spatial dynamics of follicle development in mice by analyzing single-cell and spatial transcriptomes, revealing distinct stromal cell populations with specific roles in follicle development.

CTCF blocks anti-sense transcription initiation at divergent gene promoters

The paper shows CTCF suppresses antisense transcription at divergent promoters without affecting sense transcription, using a combination of genetic and molecular techniques.

Generating Templates and Growth Charts for School-Aged Brain Development

The paper develops a pipeline to generate age-specific MRI brain templates and growth charts for children and adolescents, revealing neurodevelopmental differences between Chinese and US populations.

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

The paper develops PETAL, a library of 62,208 mAbs against 15,199 peptides, enabling proteome-scale antibody generation and target discovery across species.

Genome sequencing analysis identifies high-risk Epstein-Barr virus subtypes for nasopharyngeal carcinoma

The paper identifies two EBV variants in BALF2 associated with increased NPC risk through genome sequencing and association studies in China.