Cristian Groza

Integrated genotyping, annotation and epigenetic characterization of transposable elements with GraffiTE

GraffiTE v1.1 is a Nextflow pipeline that genotypes structural variants, annotates polymorphic mobile elements, and maps epigenetic data to transposable elements using pangenome graphs, revealing hypomethylated elements and age-related demethylation.

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

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.

Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Proteogenomic analysis of 5,411 plasma proteins in sickle cell disease patients

The paper identifies 560 plasma protein quantitative trait loci (pQTL) in sickle cell disease patients and links them to HbF production through Mendelian randomization.

Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA

This paper expands methylome analysis and detects quantitative trait loci by long-read sequencing of personal DNA, revealing tens of thousands of methylation QTLs associated with structural variants.

A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Genome-graphs

GraffiTE analyzes transposable element insertion polymorphisms using genome-graphs, achieving high precision and recall across multiple species and sequencing technologies.

Pangenome graphs improve the analysis of rare genetic diseases

The paper uses pangenome graphs to improve detection of rare structural variants in a rare disease cohort, identifying novel diagnostic variants.

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.

Genome graphs detect human polymorphisms in active epigenomic states during influenza infection

The paper uses genome graphs to detect polymorphic mobile elements in active epigenomic states during influenza infection, revealing novel peaks and modifying quantitative trait loci estimates.

Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection

The paper shows ancestry-related differences in transcriptional response to influenza are driven by epigenetic variation and genetic control of enhancer activity.

Personalized and graph genomes reveal missing signal in epigenomic data

The paper shows that using personalized and graph genomes improves epigenomic analysis by recovering new peaks associated with genetic variants.