Hyun Min Kang

Molecule-resolved inference reveals the spatial organization of transcriptional programs

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

Histopathology and spatial transcriptomics jointly map myofiber-specific pathological programs in mTORC1-driven myopathy

This study combines histopathology and spatial transcriptomics to show that mTORC1 hyperactivation causes fiber-type-specific pathological changes in skeletal muscle.

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Seq-Scope-X improves spatial transcriptomics resolution by expanding tissues, revealing detailed nuclear and cytoplasmic transcriptome differences in liver cells and enabling proteomic analysis in other tissues.

Practical utility of sequence-to-omics models for improving the reproducibility of genetic fine-mapping

This study evaluates sequence-to-omics models to improve reproducibility in genetic fine-mapping across eQTL datasets, showing reduced replication failure rates and enhanced SNP prioritization.

Variant Classification Using Proteomics-Informed Large Language Models Increases Power of Rare Variant Association Studies and Enhances Target Discovery

The paper improves rare variant association studies by using proteomics-informed large language models, identifying more gene-trait associations than existing methods.

A Benchmark of Modern Statistical Phasing Methods

This paper benchmarks three statistical phasing methods using synthetic diploids, finding consistent error patterns across methods and populations.

Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

This paper describes a protocol to repurpose Illumina sequencing flow cells for high-resolution spatial transcriptomics, enabling detailed spatial gene expression analysis with improved resolution and cost efficiency.

Joint testing of rare variant burden scores using non-negative least squares

The paper introduces SBAT, a method for joint testing of rare variant burden scores, showing it is well calibrated and outperforms existing tests in some scenarios.

FICTURE: Scalable segmentation-free analysis of submicron resolution spatial transcriptomics

FICTURE provides a scalable segmentation-free method for analyzing high-resolution spatial transcriptomics data, revealing detailed tissue architecture in complex regions.

The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations

The paper develops a method to quantify somatic mutation burden in whole-genome sequencing data without paired-tissue samples and identifies genetic and phenotypic correlates of clonal hematopoiesis without known driver mutations.

Accurate cross-platform GWAS analysis via two-stage imputation

This paper introduces TSIM, a two-stage imputation method for GWAS that harmonizes heterogeneous genotyping data, controlling errors and replicating known associations without false positives.

Genetic regulation of the human plasma proteome in 54,306 UK Biobank participants

The paper maps genetic associations with plasma proteins in 54,306 UK Biobank participants, identifying 10,248 new protein quantitative trait loci (pQTLs) and expanding the genetic architecture of the plasma proteome.

Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune response

The paper introduces clue, a reference-free framework for multiplexed single-cell sequencing to identify genetic modifiers of immune responses using SNP-based clustering and eQTL mapping.

A deep catalog of protein-coding variation in 985,830 individuals

This paper presents the largest catalog of human protein-coding variation from 985,830 individuals, identifying rare variants and their functional implications for precision medicine.

Structural variation across 138,134 samples in the TOPMed consortium

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

Rare coding variants in CHRNB2 reduce the likelihood of smoking

The paper identifies rare coding variants in CHRNB2 associated with reduced smoking likelihood and links them to downstream smoking-related phenotypes.

Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia

Exomes of 24,248 schizophrenia cases and 97,322 controls implicate ultra-rare damaging variants in 10 genes, including GRIN2A and GRIA3, with odds ratios of 3 to 50.

Genome-wide analysis in 756,646 individuals provides first genetic evidence that ACE2 expression influences COVID-19 risk and yields genetic risk scores predictive of severe disease

The paper identifies a rare variant that lowers ACE2 expression and reduces COVID-19 risk, and develops a genetic risk score predicting severe disease.

Meta-imputation of transcriptome from genotypes across multiple datasets using summary-level data.

This paper introduces SWAM, a meta-imputation method that combines multiple transcriptome imputation models to improve gene expression prediction from genotypes using summary-level data.

Exome sequencing of 628,388 individuals identifies common and rare variant associations with clonal hematopoiesis phenotypes

This study uses exome sequencing of 628,388 individuals to identify genetic variants associated with clonal hematopoiesis and its health outcomes.

Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes

This study identifies 35 genes associated with circulating lipid levels using rare coding variants from 170,000 exomes across multiple ancestries.

Utility of family history in disease prediction in the era of polygenic scores

The paper evaluates family history and polygenic scores as predictors for coronary artery disease and type 2 diabetes using the Trondelag Health Study and UK Biobank.

Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes

The paper evaluates penetrance and variable expressivity of monogenic metabolic conditions using exome data from 77,184 individuals, finding that monogenic variants have larger effect sizes than polygenic scores but low penetrance.

Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries

This paper introduces RUTH, a new HWE test that accounts for population structure and genotype uncertainty, showing it reduces false positives compared to traditional methods.

Genetic architectures of proximal and distal colorectal cancer are partly distinct

This study identifies 13 new genetic loci specific to proximal or distal colorectal cancer subtypes, revealing partly distinct genetic architectures for these tumor locations.

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

FASTQuick: Rapid and comprehensive quality assessment of raw sequence reads

FASTQuick provides fast and comprehensive quality metrics for raw sequence reads without full genome alignment, enabling efficient quality assessment in large-scale genomic studies.

FIVEx: an interactive multi-tissue eQTL browser

FIVEx is an interactive eQTL browser that helps interpret tissue-specific genetic variants using GTEx data.

Integrating Comprehensive Functional Annotations to Boost Power and Accuracy in Gene-Based Association Analysis

This study introduces a framework to integrate functional annotations with GWAS data to improve gene-based association analysis power and accuracy.

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

The paper identifies two types of eRNA QTLs associated with enhancer function and reveals a bipartite enhancer architecture through population-scale eRNA analysis.