Nicholas Mancuso

Inferring causal cell types of human diseases and risk variants from candidate regulatory elements

This paper introduces CT-FM and CT-FM-SNP methods to identify causal cell types and variants for diseases, finding most SNPs affect traits via a single cell type set.

Highly efficient genotype compression leveraging genealogical relatedness

The paper introduces a lossless compression method for genotype data using genealogical relatedness, achieving significant size reduction and speedup in genetic analyses.

Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression

The paper presents an isoform-level lung cell atlas using single-cell long-read RNA-sequencing, revealing genetic effects on isoform regulation that improve cell-type classification and identify novel variants associated with lung cancer risk.

Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology

The paper constructs a single-cell eQTL dataset from Asian never-smokers, identifying alveolar cell-specific genes linked to lung cancer susceptibility.

Integrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traits

The paper integrates perturbational screens, eQTL, and GWAS data to identify mediating genes for complex traits, finding 546 significant genes enriched for immune response and cellular signaling.

The impact of Indigenous American-like ancestry on risk of acute lymphoblastic leukemia in Hispanic/Latino children

This study investigates the impact of Indigenous American-like ancestry on acute lymphoblastic leukemia risk in Hispanic/Latino children, finding no global association but significant local haplotype effects.

traceax: a JAX-based framework for stochastic trace estimation

traceax provides a scalable framework for stochastic trace estimation, offering efficient and accurate trace computation with reduced memory and runtime compared to direct methods.

A likelihood-based framework for demographic inference from genealogical trees

This paper introduces a likelihood-based framework called gLike to infer demographic history from genealogical trees, showing improved accuracy in estimating population parameters compared to existing methods.

Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping

jaxQTL improves sc-eQTL mapping by using count-based models, identifying more eGenes and explaining more SNP-heritability than bulk-eQTLs.

Multi-ancestry GWAS of severe pregnancy nausea and vomiting identifies risk loci associated with appetite, insulin signaling, and brain plasticity

Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk

The paper introduces SuShiE, a model that improves multi-ancestry fine-mapping of cis-molQTLs, identifying more genes and prioritizing functionally enriched variants.

Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data

The paper introduces aFC-n, a method to improve eQTL effect size estimation and gene expression prediction, revealing significant residual allelic imbalance in many genes.

Tree-based QTL mapping with expected local geneticrelatedness matrices

This paper introduces a QTL mapping method using expected local genetic relatedness matrices derived from ancestral recombination graphs, improving detection of QTLs in populations with limited imputation resources.

Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics

This paper introduces HAMSTA, a method to estimate heritability from admixture mapping summary statistics while adjusting for ancestral stratification bias, and applies it to African American datasets.

Fetally-encoded GDF15 and maternal GDF15 sensitivity are major determinants of nausea and vomiting in human pregnancy

This study identifies fetal and maternal GDF15 as key factors in pregnancy-related nausea and vomiting, showing their roles in disease risk and severity.

A rigorous benchmarking of alignment-based HLA callers for RNA-seq data

This study benchmarks 12 HLA callers on RNA-seq data across 682 samples to evaluate accuracy, computational cost, and performance differences by ancestry.

The motif composition of variable-number tandem repeats impacts gene expression

The paper identifies VNTR motifs linked to gene expression using a repeat-pangenome graph, showing motif variation explains more associations than VNTR length.

Novel insight into the etiology of ischemic stroke gained by integrative transcriptome-wide association study

This study identifies 136 genes/eRNA/proteins associated with ischemic stroke risk using integrative transcriptome-wide association analysis across multiple tissues and finds potential therapeutic candidates.

A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics

FactorGo identifies pleiotropic components across thousands of human diseases and traits using GWAS summary statistics, outperforming existing methods in capturing latent factors.

Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies

This paper introduces MA-FOCUS, a multi-ancestry fine-mapping framework that improves the identification of causal genes in TWAS by leveraging ancestry-specific LD and eQTL patterns.

A genealogical estimate of genetic relationships

This paper introduces an eGRM framework that estimates genetic relationships using coalescent theory and ancestral recombination graphs, showing improved population structure detection compared to traditional GRMs.

Ancestry-specific maps of GRCh38 linkage disequilibrium blocks for human genome research

The paper creates ancestry-specific linkage disequilibrium block maps for GRCh38, providing updated LD blocks for four populations.

H3k27ac-HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility

The paper uses HiChIP to link prostate cancer GWAS risk variants to target genes, finding new associations not detected by eQTL methods and validating them with CRISPRi.

Genome-wide transethnic meta-analysis identifies novel susceptibility loci for childhood acute lymphoblastic leukemia

This study identifies five novel genetic loci associated with childhood acute lymphoblastic leukemia through a trans-ethnic meta-analysis across four ethnic groups.

Leveraging expression from multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests improves the power of transcriptome-wide association studies (TWAS)

This paper improves transcriptome-wide association study (TWAS) power by integrating multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests, identifying more gene-trait associations.

A Hierarchical Approach Using Marginal Summary Statistics for Multiple Intermediates in a Mendelian Randomization or Transcriptome Analysis

This paper introduces hJAM, a hierarchical model that improves causal inference in Mendelian randomization and transcriptome-wide association studies by incorporating prior information and accounting for SNP correlations.

Integrative analyses identify susceptibility genes underlying COVID-19 hospitalization

Genome-wide association study and integrative analyses identify 27 genes in inflammation and coagulation pathways linked to COVID-19 hospitalization risk and symptomology.

Localizing components of shared transethnic genetic architecture of complex traits from GWAS summary data

The paper estimates population-specific and shared causal SNPs from GWAS summary data across East Asian and European populations and finds shared SNPs are enriched in functional categories.

Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture

This paper introduces a method to accurately estimate SNP-heritability from large biobank data without assuming genetic architecture, showing existing methods can be off by up to 30%.

Integrative analysis of Dupuytren’s disease identifies novel risk locus and reveals a shared genetic etiology with BMI

This study identifies 43 tissue-specific gene associations with Dupuytrens disease risk and finds significant genetic correlations with BMI, type II diabetes, and lipid traits.