Shuangjia Lu

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Pangenome-based human genome analysis improves trait association and genomic prediction

This paper develops a pangenome-based method to improve trait association and genomic prediction by capturing complex genetic variation missed by traditional approaches.

Boosting GPT Models for Genomics Analysis: Generating Trusted Genetic Variant Annotations and Interpretations through RAG and fine-tuning

This paper enhances GPT models for genomics by integrating variant annotations via RAG and fine-tuning, improving variant interpretation accuracy and efficiency.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

Association of Structural Variation with Cardiometabolic Traits in Finns

This study identifies 31 genome-wide significant associations between structural variations and cardiometabolic traits in Finns, including two novel loci with strong phenotypic effects.