Andrew J. Chess

Single-cell genomics and regulatory networks for 388 human brains

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

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.

Schizophrenia-associated somatic copy number variants from 12,834 cases reveal contribution to risk and recurrent, isoform-specific NRXN1 disruptions

This study identifies somatic copy number variants (sCNVs) in schizophrenia cases, revealing their contribution to risk and specific NRXN1 disruptions.

DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

Population-level variation of enhancer expression identifies novel disease mechanisms in the human brain

The paper identifies population-level variation in enhancer expression in the human brain and links enhancer eQTL to schizophrenia heritability.

Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development

The paper evaluates brain somatic mosaicism in the adult human to identify rules governing cellular distribution during embryogenesis.

Enrichment of somatic mutations in schizophrenia brain targets prenatally active transcription factor bindings sites

The paper identifies prenatal mutational processes in schizophrenia brains linked to transcription factor binding sites and proposes a new term 'skiagenesis' for these mutations.

Sex differences in the human brain transcriptome of cases with schizophrenia

This study examines sex differences in schizophrenia gene expression using RNA-seq data from 437 controls and 341 cases, finding small effect sizes and reproducible signatures involving X/Y-linked genes and synaptic pathways.

Comprehensive identification of somatic nucleotide variants in human brain tissue

This study identifies somatic SNVs in non-cancerous human brain tissues and establishes best practices for detecting low-frequency variants.

EKLF/KLF1 expression defines a unique macrophage subset during mouse erythropoiesis

The paper identifies a unique macrophage subset in mouse erythropoiesis defined by EKLF/KLF1 expression and describes its transient role in erythroblastic islands.

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

The paper introduces a machine learning method to detect somatic L1 insertions in human brain tissue, revealing their widespread distribution in neurons and glia and potential role in neuropsychiatric diseases.

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

This paper performs a large-scale eQTL meta-analysis across cerebral cortical and cerebellar brain regions, identifying distinct eQTL patterns and demonstrating improved power over existing studies.

Functional annotation of rare structural variation in the human brain

The paper functionally annotates rare structural variants in the human brain by integrating SV calling with RNA-seq data to assess their regulatory effects and prioritize pathogenic deletions.

Dynamic landscape and genetic regulation of RNA editing in schizophrenia

The paper examines RNA editing changes in schizophrenia by analyzing postmortem brain samples and identifies genetic regulators and associations with schizophrenia GWAS loci.

Unperturbed Expression Bias of Imprinted Genes in Schizophrenia

The paper analyzes allelic expression bias in schizophrenia using RNA-seq data to assess imprinted gene expression and its relationship with age, ancestry, and disease.