Jonathan Flint C

This study creates a 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons, revealing lineage-specific 3D genomic dynamics and regulatory programs associated with neuropsychiatric disease risk.

The paper shows genotype- and phenotype-based genetic instruments explain largely independent components of liability to psychiatric disorders, supported by theoretical analysis and simulations.

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

This study identifies synergistic sets of genetic risk variants in psychiatric disorders, suggesting subtypes and reinterpreting shared genetic effects.

Family-based GWAS meta-analysis of 34 phenotypes shows standard GWAS effects carry sizeable confounding uncorrelated with direct genetic effects, while assortative mating likely inflates SNP heritability and genetic correlations.

The paper identifies causal genes at QTLs associated with fear-related behavior using complementation testing and finds six genes, including four with known synaptic roles and one long non-coding RNA.

AutoComplete improves phenotype imputation in biobank data, enhancing GWAS power and genetic discovery.

The paper investigates dominance and additivity in mammalian genetics, finding dominance accounts for 25% of heritable variance and reveals novel dominance QTLs and trans-acting effects in gene expression.

The paper introduces PA-FGRS, a method to estimate genetic liability from family records, and shows it improves MDD classification and GWAS power when combined with genotypes.

This paper introduces PACA, a contrastive learning method for subphenotype subtyping, which outperforms existing methods by capturing weak subphenotypic variation in complex diseases.

This paper shows that cross-trait assortative mating explains genetic correlations between traits, suggesting many reported genetic similarities may be overestimated.

This paper improves genetic studies of MDD by integrating shallow and deep phenotypes, enhancing GWAS power and PRS accuracy while preserving specificity.

This study performs a GWAS on creativity using 241,736 individuals, identifying 25 loci and showing genetic overlap with several psychiatric disorders.

The paper combines data from two independent mouse studies to identify genetic loci for traits, finds poor replication rates, and proposes a method to assess confidence in associations.

This paper introduces a statistical method to identify tissue-specific genetic contributions to complex traits at the individual level using eQTLs and applies it to BMI and WHRadjBMI in the UK Biobank.

The paper introduces JEPEGMIX2-P, a TWAS pathway method that improves computational efficiency and performance for psychiatric disorder GWAS, showing increased power over existing methods like MAGMA.

The paper introduces V-seq, a cost-effective method for viral genome sequencing that uses multiplexed RT primers to improve coverage and reduce costs.

This paper improves psychiatric GWAS by re-imputing summary statistics using a larger, more diverse reference panel, revealing new signals from rare variants.

This study benchmarks WGS-based structural variant callers using a PCR-confirmed gold standard, finding wide performance variation and identifying tools best suited for low and ultra-low pass data.

This paper introduces GxEMM, a mixed model for gene-environment interactions, showing it improves heritability estimates and reveals stress reduces heritability of major depression.

This paper shows that GWAS using minimal phenotyping for depression identifies non-specific genetic factors shared with other psychiatric conditions, not specific to major depressive disorder.

The paper assesses the installability and archival stability of computational biology tools, finding many are inaccessible or hard to install, and recommends policy changes to improve these aspects.

This paper introduces Reverse GWAS (RGWAS) to identify and validate phenotypic subtypes using genetics, finding three novel metabolic subtypes and showing differential treatment effects.

The paper identifies coping-style behaviors in rats with enhanced parent-of-origin heritability and confirms these effects through reciprocal crosses.

This study presents a comprehensive catalog of genetic variation in Han Chinese using whole-genome sequencing, revealing population structure, admixture, and loci under local adaptation.

This paper evaluates methods for estimating heritability and genetic correlation in case-control studies, finding that PCGC-s accurately handles non-genetic risk factors and provides unbiased estimates for schizophrenia and bipolar disorder.

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

The paper uses GWAS data to identify polygenic risk scores for drug metabolism pathways, finding that the GO:17144 pathway is significantly predictive of recurrent depressive disorder.