Jean Monlong

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.

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

This paper uses long-read sequencing to comprehensively identify pathogenic variants in the CYP21A2 locus for Congenital Adrenal Hyperplasia, including phasing and module counts, improving diagnostic accuracy.

This study evaluates the diagnostic yield of long-read nanopore sequencing in rare disease detection, finding it covers more genes and detects additional variants compared to short-read sequencing.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

The paper introduces tools to efficiently index and query annotations in pangenome graphs using GAF format, demonstrating applications on human pangenome data.

The paper introduces a personalized pangenome approach to improve short-read mapping and variant calling by reducing reference bias and errors.

The paper introduces methods for haplotype-resolved de novo assembly using Shasta and GFAse, showing improved assembly quality with newer Oxford Nanopore reads.

The paper investigates the evolution of chromosome 4p loss in basal breast cancer, identifying C4orf19 as a novel gene that suppresses proliferation and is part of a kinase module.

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.

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

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

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.

The paper introduces Giraffe, a pangenome mapper that improves genotyping of SNVs, indels, and SVs in 5,202 human genomes using the vg toolkit.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.

The paper demonstrates that variation graphs using the vg toolkit improve structural variant genotyping compared to traditional methods and VCF-based catalogs.

The paper uses single-cell RNA-seq to show glioblastoma recapitulates normal brain development, identifying a conserved trilineage hierarchy with glial progenitor-like cells as the origin of cancer heterogeneity and therapeutic targets.

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

The paper identifies recurrent copy number variants in low-mappability regions using PopSV, finding they are 5 times more common in germline than somatic CNVs.

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

This study uses whole-genome sequencing and a new algorithm to comprehensively characterize copy number variants in epilepsy patients and controls, finding enrichment of rare exonic and non-coding variants.

The paper analyzes RNA-seq data from multiple mouse tissues to identify genes with conserved expression patterns across species and cell types, revealing evolutionary constraints in gene expression.