Thomas M. Hyde

The paper uses spatial transcriptomics to analyze molecular differences in mood disorders and biological sex in the human prefrontal cortex, identifying sex- and disorder-specific gene expression patterns.

This study maps the spatiomolecular organization of the human habenula using multi-omic approaches, identifying molecular signatures and spatial domains linked to psychiatric disorders.

This paper develops a 3D spatial genomics framework to reconstruct the molecular and cellular organization of the human nucleus accumbens across anatomical axes.

This study creates a spatial transcriptomic atlas of the human amygdala, revealing distinct cell types and genetic risk localization across its subnuclei.

This study creates a spatiomolecular atlas of the human nucleus accumbens using spatial transcriptomics and single-nucleus RNA sequencing, revealing spatial gradients and conserved features across species.

The paper uses a novel 'liquidity' metric to analyze gene expression trajectories across lifespan, revealing delayed maturation and perinatal GABA switch in schizophrenia risk without detectable neuropathology.

The paper integrates spatial transcriptomics and single-nucleus RNA-seq data from the human dACC to define molecular profiles, spatial domains, and functional insights.

This study maps molecular and genetic signatures of schizophrenia in human prefrontal cortex across spatial scales, revealing altered BDNF-TrkB signaling and inhibitory circuit dysfunction.

The paper introduces co-expression-based models to improve eQTL predictions and identifies novel schizophrenia-associated genes using brain RNA-seq data.

spaTransfer transfers cell type or spatial domain labels between single-cell and spatial transcriptomics datasets using non-negative matrix factorization and a multinomial model.

The paper investigates how APOE genotype affects gene expression in the human entorhinal cortex, identifying an oligodendrocyte subtype as a potential mediator of Alzheimer's disease risk.

The paper performs transcriptomic analysis of the human habenula and identifies molecular changes associated with schizophrenia risk and illness state.

The paper analyzes the transcriptomic landscape of the human locus coeruleus in relation to Alzheimer's disease risk factors and neuromelanin content using spatially-resolved transcriptomics.

The paper analyzes transcriptomic diversity in amygdalar subdivisions across humans and nonhuman primates using single-nucleus RNA sequencing and identifies distinct neuronal subtypes and transcriptional specializations.

The paper compares gene expression in immature neurons across species to identify human-specific features and shared biological processes.

The paper integrates single-nucleus and spatial transcriptomics data to map the molecular landscape of the human hippocampus, identifying cell types and spatial domains.

The paper benchmarks cellular deconvolution methods using a multi-assay dataset from human prefrontal cortex, finding Bisque and hspe to be the most accurate.

This study analyzes age-related changes in gene expression in the human dentate gyrus, identifying shifts in neurogenesis, maturation, and neuroinflammation across the lifespan.

The paper examines FKBP5 DNA methylation in schizophrenia and finds lower methylation in a proximal enhancer linked to higher gene expression and age.

The paper performs snRNA-seq on human lateral septum tissue to identify cell types and marker genes, finding conserved and species-specific expression patterns.

The paper introduces visiumStitched, a tool for stitching Visium spatial transcriptomics data across multiple capture areas, enabling seamless analysis without data loss.

The paper identifies a specific APOE transcript and functional SNP associated with Alzheimer's disease using integrated genomic data from human postmortem brains.

This study identifies Reelin as a marker of cocaine-activated neuronal ensembles in the rat nucleus accumbens and shows its role in cocaine reward and neuronal excitability.

The paper analyzes transcriptomic and proteomic data from specific brain regions to identify molecular changes in schizophrenia, showing superior regional discrimination in transcriptomic and proteomic data.

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

The paper analyzes repeat expression across the human lifespan in the neurotypical brain, identifying age-dependent upregulation of HERV-K in older adults.

The paper re-analyzes RNA sequencing data comparing gene expression in living and postmortem human brain tissue, finding that living samples had lower quality, and questions the validity of previous conclusions about postmortem studies.

The paper uses spatial proteogenomics to analyze gene expression changes in Alzheimer's disease brains linked to amyloid-beta and tau pathology.