Research

Our work focuses on three major research topics

  • Genomics of neuropsychiatric disease from post mortem brain collections
  • Statistical methods for single cell and integrative genomics
  • Statistically rigorous, open source software

Ongoing work includes

  • Statistical methods to identify differentially expressed genes from single cell transcriptomics data across 100s-1000s of individuals
  • Characterizing genetic regulation of chromatin accessibility in the human brain and its role in mediating risk of neuropsychiatric disease
  • Understanding effects of genetic regulation and Alzheimer’s disease on gene expression and chromatin accessibility in human microglia

Data: Single cell/nucleus RNA-seq, bulk RNA-seq and ATAC-seq, genotyping, WGS

Selected Publications

(2024). Genetic regulation of cell type–specific chromatin accessibility shapes brain disease etiology. Science 384(6698).

PDF Dataset

(2023). Comment on: What genes are differentially expressed in individuals with schizophrenia? A systematic review. Molecular Psychiatry 28, 523–525.

PDF

(2022). Genetics of the human microglia regulome refines Alzheimer’s disease risk loci. Nature Genetics 54, 1145–1154.

PDF Code Project

(2022). Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits. Nature Genetics 54, 161–169.

PDF Code Project

(2022). Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia. Biological Psychiatry 91(1):92-101.

PDF Code Dataset

(2021). Analysis framework and experimental design for evaluating synergy-driving gene expression. Nature Protocols. 16: 812–840.

PDF Code

(2020). decorate: Differential Epigenetic Coregulation Test. Bioinformatics. 36(9): 2856–2861.

PDF Project

(2019). Functional Interpretation of Genetic Variants Using Deep Learning Predicts Impact on Epigenome. Nucleic Acids Research, 47(20): 10597–10611.

PDF Project

(2019). New considerations for hiPSC-based models of neuropsychiatric disorders. Molecular Psychiatry. 24, 49–66.

PDF

(2017). Mapping regulatory variants in hiPSC models. Nature Genetics 50, 1–2.

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(2017). Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. Cell Stem Cell, 20(4): 518–532.

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(2013). PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data. PLoS Comput Biol 9(6): e1003101.

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Software

dreamlet

Efficient differential expression analysis of large-scale single cell transcriptomics data

decorate

decorate: Differential Epigenetic Coregeulation Test

dream

dream: Powerful differential expression analysis for repeated measures designs

Brain eQTL meta-analysis

Joint fine-mapping of large-scale post-mortem brain resource with many public GWAS datasets

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder

Public resource of functional genomic data from the dorsolateral prefrontal cortex (DLPFC; Brodmann areas 9 and 46): RNA-seq and SNP genotypes on 980 individuals, and ATAC-seq on 269 individuals from 4 separate brain banks.

DeepFIGV

Functional Interpretation of Genetic Variants Using Deep Learning Predicts Impact on Epigenome.

variancePartition

Interpreting drivers of variation in complex gene expression studies with linear mixed models

Data and code resources for an hiPSC model

RNA-seq data from hiPSC-derived neural progenitor cells and neurons from controls and patients with childhood onset schizophrenia

Design hiPSC experiments

Design powerful transcriptome experiments given cost constraints

Referance map of human brain epigenome

Data from ChIP-seq for H3K4me3 (promoters) and H3K27ac (enhancers and promoters) from 2 brain regions from 17 individuals

Epigenomics

PsychENCODE

lrgpr

Interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R

Resources

dreamlet

Efficient differential expression analysis of large-scale single cell transcriptomics data

decorate

decorate: Differential Epigenetic Coregeulation Test

dream

dream: Powerful differential expression analysis for repeated measures designs

Brain eQTL meta-analysis

Joint fine-mapping of large-scale post-mortem brain resource with many public GWAS datasets

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder

Public resource of functional genomic data from the dorsolateral prefrontal cortex (DLPFC; Brodmann areas 9 and 46): RNA-seq and SNP genotypes on 980 individuals, and ATAC-seq on 269 individuals from 4 separate brain banks.

DeepFIGV

Functional Interpretation of Genetic Variants Using Deep Learning Predicts Impact on Epigenome.

variancePartition

Interpreting drivers of variation in complex gene expression studies with linear mixed models

Data and code resources for an hiPSC model

RNA-seq data from hiPSC-derived neural progenitor cells and neurons from controls and patients with childhood onset schizophrenia

Design hiPSC experiments

Design powerful transcriptome experiments given cost constraints

Referance map of human brain epigenome

Data from ChIP-seq for H3K4me3 (promoters) and H3K27ac (enhancers and promoters) from 2 brain regions from 17 individuals

Epigenomics

PsychENCODE

lrgpr

Interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R

Contact