Xihao Li

Relation of Self-Reported Race and Genetic Ancestry to Hypertension Prevalence Among Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos

The paper examines the relationship between self-reported race, genetic ancestry, and hypertension prevalence among Hispanics/Latinos using the HCHS/SOL dataset.

Integrating Genomic and Proteomic Data Improves Complex Trait Prediction in Diverse Populations

This study integrates polygenic risk scores and proteomic risk scores to improve prediction of complex traits across diverse populations.

MetaSTAARlite: An all-in-one tool for biobank-scale whole-genome sequencing meta-analysis

MetaSTAARlite is a tool for rare variant meta-analysis using summary statistics from biobank-scale whole-genome sequencing data, showing linear scaling and concordance with pooled analysis.

Rare coding and noncoding variants map 1,342 diseases and biomarkers in 490,549 whole genomes

The paper maps rare coding and noncoding variants to 1,342 diseases and biomarkers using whole genome sequencing data from 490,549 UK Biobank participants.

Large Impact of Genetic Data Processing Steps on Stability and Reproducibility of Set-Based Analyses in Genome-Wide Association Studies

This paper shows how data processing steps in GWAS affect reproducibility and stability of set-based analyses, and provides tools to address these issues.

A novel two-sample Mendelian randomization framework integrating common and rare variants: application to assess the effect of HDL-C on preeclampsia risk

This paper introduces MR-CARV, a two-sample Mendelian randomization framework integrating common and rare variants to assess the causal effect of HDL-C on preeclampsia risk, showing improved statistical power and precision.

CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies

CoxMDS identifies causal mediators in DNA methylation studies with survival outcomes, maintaining FDR control and higher power than existing methods.

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

cellSTAAR integrates single-cell ATAC-seq with whole-genome sequencing to enhance power and interpretation of rare variant association tests in non-coding regions.

A Scalable Framework for Identifying Allelic Series from Summary Statistics

The paper introduces COAST-SS, a method to identify allelic series using summary statistics, showing it is effective and robust to LD matrix misspecification.

Streamlining Large-Scale Genomic Data Management: Insights from the UK Biobank Whole-Genome Sequencing Data

The paper introduces vcf2agds, a toolkit converting WGS data to aGDS format, enabling efficient analysis of UK Biobank data and identifying 480 genome-wide significant associations for total cholesterol.

Old vs. New Local Ancestry Inference in HCHS/SOL: A Comparative Study

This study compares old and new local ancestry inference methods in Hispanic/Latino populations using HCHS/SOL data, finding high similarity but some regional discrepancies.

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

The paper introduces MultiSTAAR, a statistical framework for multi-trait rare variant analysis in WGS studies, identifying new lipid trait associations in diverse populations.

A comprehensive comparison on clustering methods for multi-slide spatially resolved transcriptomics data analysis

This study compares clustering methods for multi-slide spatial transcriptomics data using simulated and real datasets, evaluating preprocessing techniques' impact on performance.

Population scale whole genome sequencing provides novel insights into cardiometabolic health

This study uses population-scale whole genome sequencing to identify novel rare protein-coding variants associated with cardiometabolic traits, revealing new biological mechanisms and gene functions.

Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study

The paper identifies 83 rare lncRNA variant sets associated with blood lipid levels using WGS data from the TOPMed program and validates some in UK Biobank data.

Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium

The paper analyzes inflammation biomarkers using whole-genome sequencing from the TOPMed consortium, identifying both single-variant and rare variant associations with inflammatory traits.

A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies

The paper introduces a framework for detecting noncoding rare variant associations using whole-genome sequencing data, applying it to lipid traits in the TOPMed program.

FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome

FAVOR provides an online resource and tool for functional annotation of variants from whole genome sequencing studies to aid in disease gene prioritization.

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

The paper performs whole genome sequence analysis of plasma lipid levels in 66,329 individuals, identifying new lipid-associated alleles, including rare non-coding variants.

STAAR Workflow: A cloud-based workflow for scalable and reproducible rare variant analysis

The paper introduces a cloud-based workflow for rare variant analysis in whole genome sequencing studies, enabling scalable and reproducible analysis with functional annotations.

Recovery of trait heritability from whole genome sequence data

The paper estimates heritability for height and BMI using whole-genome sequence data and finds that rare variants contribute significantly to the missing heritability.

A multi-dimensional integrative scoring framework for predicting functional variants in the human genome

The paper introduces MACIE, a framework for predicting functional variants by integrating diverse annotations, and applies it to fine-mapping using GWAS data.

Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity

The paper maps the spatiotemporal development of bipolar interneuron subtypes in the mammalian retina, revealing a hierarchical model of subtype genesis through ordered birthdates and oscillatory waves.

A versatile toolkit for molecular QTL mapping and meta-analysis at scale

APEX is a toolkit for molecular QTL mapping and meta-analysis that improves scalability and accuracy for large datasets and summary statistics.

Dynamic Scan Procedure for Detecting Rare-Variant Association Regions in Whole Genome Sequencing Studies

The paper introduces SCANG, a dynamic scan statistic method for detecting rare-variant association regions in WGS data without pre-specifying window sizes, showing improved performance over existing methods.