Guillaume Bourque

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.

Long-read sequencing reveals telomere inheritance patterns from human trios

The paper uses long-read sequencing to analyze telomere inheritance patterns in human trios, finding parent-of-origin effects and heritable influences on telomere length.

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.

TEExplorer: A Web Portal to Investigate TE-Epigenome Associations Across Human Cell Types

TEExplorer provides a web tool to explore TE-histone mark associations across human cell types using the EpiATLAS dataset and allows user data integration.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations

The paper analyzes the relationship between transposable elements (TEs) and histone marks across cell types, finding cell-type specific enrichments and associations with biological processes.

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.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA

The paper introduces e2MPRA, a method that simultaneously measures regulatory activity and epigenomic features of CREs using lentivirus-based MPRA and targeted Cut&Tag or ATAC-seq.

Integrated Metabolic Complex Genetic Interaction Network of Chromosome 4p Loss in Basal Breast Cancer

This study maps the metabolic complex genetic interaction network of chromosome 4p loss in basal breast cancer to identify targetable vulnerabilities.

Altered sperm DNA methylation in overweight men associates with transposable element regulation of paternal origins of risk in children

The paper identifies altered sperm DNA methylation in overweight men linked to transposable element regulation and potential impacts on offspring neurodevelopmental risks.

PARPAL: PARalog Protein Redistribution using Abundance and Localization in Yeast Database

PARPAL is a web database that analyzes protein redistribution in yeast after paralog deletion using high-content screening and deep learning, providing insights into gene retention and evolution.

Finding an optimal sequencing strategy to detect short and long genetic variants in a human genome

This paper benchmarks sequencing technologies and variant callers for detecting SNPs, indels, and SVs, finding that SRS is optimal for small variants while LRS excels in SV detection and complex regions.

Genome-wide Association Study of Long COVID

This study performs a genome-wide association study for Long COVID, identifying a significant association with the FOXP4 locus and highlighting the role of pulmonary dysfunction and COVID-19 severity.

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.

Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation

The paper examines sex-biased transcription of genes, lncRNAs, and TEs in four mouse organs, finding organ-specific patterns and clustering of sex-biased TEs near sex-biased genes and lncRNAs.

STRkit: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation

STRkit is a software tool for accurate STR genotyping using long reads and single-nucleotide variants, achieving high F1 scores and Mendelian inheritance rates.

Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells

This paper investigates whether rescuing DNMT1 activity can reverse its loss in mouse embryonic stem cells, finding only partial reversal with lasting effects on epigenetic landscapes and cellular function.

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.

Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring

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.

EpiVar Browser: advanced exploration of epigenomics data under controlled access

The paper introduces EpiVar Browser, a tool for exploring epigenomics data under controlled access, enabling genotype-chromatin phenotype analysis without releasing identifiable information.

WEGS: a cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome

WEGS combines low-depth whole genome and high-depth whole exome sequencing to reduce costs while maintaining variant detection accuracy in genetic studies.

Cryptic endogenous retrovirus subfamilies in the primate lineage

The paper refines the annotation of endogenous retrovirus LTRs in primates by identifying new subfamilies and their regulatory roles through phylogenetic analysis and functional validation.

ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development

This study identifies ZMYM2 as essential for DNA methylation and silencing of germline genes and active transposons in embryonic development, revealing its role in maintaining genomic stability.

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.

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.

Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis

The paper identifies immune evasion mechanisms in SARS-CoV-2 by mapping epitopes and analyzing viral genome sequences to understand evolutionary pressures and immune responses.

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.