Malika Kumar Freund

Quantitative trait loci mapping of gene expression and chromatin accessibility in primary fibroblast reveals shared allelic effects between Latin American and European ancestries

The paper maps gene expression and chromatin accessibility QTLs in fibroblasts from European and Latin American ancestries, finding high concordance and shared regulatory mechanisms.

Increasing equity in science requires better ethics training: a course by trainees, for trainees

The paper describes the development of a course on genetics, ethics, and society designed by trainees to address the lack of ethics training in scientific education.

Leveraging genomic diversity for discovery in an EHR-linked biobank: the UCLA ATLAS Community Health Initiative

The paper explores the relationship between genomic ancestry and health outcomes using a biobank linked to electronic health records, finding disease stratification across ancestry clusters.

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.

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.

BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching

BATMAN integrates single-cell RNA-Seq datasets efficiently, outperforming existing methods by up to 80% in batch effect correction while preserving cell relationships.

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.

Probabilistic fine-mapping of transcriptome-wide association studies

This paper introduces a probabilistic framework to fine-map transcriptome-wide association study signals, prioritizing causal genes while accounting for linkage disequilibrium and pleiotropy.

Leveraging polygenic functional enrichment to improve GWAS power

This paper introduces a method to enhance GWAS power by incorporating functional annotations, resulting in increased detection of genome-wide significant loci.

Phenotype-specific enrichment of Mendelian disorder genes near GWAS regions across 62 complex traits

The paper quantifies the overlap between GWAS genes for 62 complex traits and Mendelian disorder genes, finding significant enrichment and elevated effect sizes for phenotypically-matched genes.