Rujia Dai

Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-Cell/Nuclei RNA Sequencing Data

This study evaluates precision and accuracy in sc/snRNA-seq data, identifies factors affecting reproducibility, and introduces a tool to assess data quality and differential expression reliability.

Genetic Analysis of Psychosis Biotypes: Shared Ancestry-Adjusted Polygenic Risk and Unique Genomic Associations

The paper analyzes psychosis biotypes using ancestry-adjusted polygenic risk scores and identifies genomic associations with specific biotypes in brain transcriptomes.

Brain eQTLs of European, African American, and Asian ancestry improve interpretation of schizophrenia GWAS

This study identifies population-specific eQTLs in brain tissues from European, African American, and Asian ancestry individuals, revealing new schizophrenia risk genes and variants missed in European-only datasets.

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

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.

Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data

The paper evaluates deconvolution methods on human brain data, finding dtangle and bMIND perform best, and identifies decon-eQTLs that explain more schizophrenia heritability than bulk or single-cell eQTLs.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

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.

Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain

The paper constructs a cross-ancestry, cell-type-informed gene regulatory atlas of the developing human brain, identifying genetic regulation and linking it to neuropsychiatric disorders.

Analyses of the Autism-associated Neuroligin-3 R451C Mutation in Human Neurons Reveals a Gain-of-Function Synaptic Mechanism

The paper investigates the impact of the NLGN3 R451C mutation on human neurons, finding it reduces protein levels but enhances excitatory synapses, potentially contributing to ASD pathogenesis.

swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution

swCAM estimates subtype-specific expressions in individual samples using unsupervised deconvolution, revealing changes in cell proportions and gene expression in bipolar disorder.

Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development

The paper identifies correlated DNA methylation and gene expression pairs across tissues and brain development stages, finding most are tissue-specific and revealing novel regulatory mechanisms.

Agonal factors distort gene-expression patterns in human postmortem brains

This study identifies fever and infection as major agonal factors affecting gene expression in postmortem brains and recommends correcting for these factors using PEER or SVA.

Cell group analysis reveals changes in upper-layer neurons associated with schizophrenia

The paper uses cell-type deconvolution to analyze gene expression in schizophrenia and finds upper-layer neurons in the DLPFC are associated with SCZ risk.

csuWGCNA: a combination of signed and unsigned WGCNA to capture negative correlations

csuWGCNA combines signed and unsigned WGCNA to better detect negative correlations, improving module detection and biological interpretation in gene regulation.

Evaluating brain cell marker genes based on differential gene expression and co-expression

The paper evaluates brain cell marker genes using differential and co-expression data, identifying 22 gold standard and 16 novel candidates with improved specificity.

Positional effects revealed in Illumina Methylation Array and the impact on analysis

The paper identifies positional effects in Illumina Methylation Arrays and shows how they impact methylation measurements, recommending ComBat for correction.