Zechuan Shi

FORGE is a configurable Nextflow pipeline for snMultiome analysis that integrates snRNA-seq and snATAC-seq data through latent-variable models and enables regulatory network inference and differential testing.

The paper constructs a single-nucleus transcriptomic atlas of Alzheimer's disease and identifies cell-type-specific molecular subtypes and therapeutic targets using a new framework.

This paper shows that spinal cord oligodendrocyte metabolic changes after injury lead to β-amyloid production and chronic pain.

The paper identifies age-related dysregulation of transcription networks in oligodendrocyte differentiation using single-nucleus RNA and ATAC sequencing in mice, with parallels in MS lesions.

This study uses single-nucleus multi-omics to identify shared and distinct regulatory pathways in Pick's and Alzheimer's disease, revealing disease-specific enhancers and TF binding patterns.

The paper investigates how the APOE Christchurch variant affects microglial responses to amyloid and tau pathology in mouse models, finding it enhances plaque-related responses but suppresses tau-related inflammation.

This study uses spatial transcriptomics and single-nucleus RNA-seq to compare genetic and sporadic Alzheimer's Disease, finding similar spatial and cell-type specific changes between sporadic AD and AD in Down Syndrome.

The paper identifies the cellular origins and functional changes of astrocytes forming protective borders around CNS injuries, showing their role in neuroprotection.