Quentin A. Gouil

SMCHD1's DNA binding activity enables its stable retention on chromatin

This study shows that SMCHD1's weak DNA binding is essential for its chromatin retention and function, revealing how DNA binding affects its localization and gene repression.

Nanobodies against Plasmodium adhesins that block receptor engagement and malaria parasite invasion

This study identifies nanobodies that target Plasmodium adhesins, blocking receptor engagement and inhibiting parasite invasion of red blood cells.

SMCHD1 is a novel target for gene-activation therapy to treat Prader-Willi Syndrome

This study identifies SMCHD1 as a target for gene-activation therapy in Prader-Willi Syndrome by showing its role in repressing the PWS gene cluster and demonstrating gene activation in mouse models.

A new genome assembly of the pea cultivar Cameor provides resources for functional genomics and genetics

The paper presents an improved pea genome assembly using long-read sequencing and other techniques, resulting in a highly contiguous and complete genome resource.

DNA binding by ATPase-adjacent domains stimulates SMCHD1 ATPase activity

This study identifies a second DNA-binding site in SMCHD1 and shows that DNA binding stimulates its ATPase activity, revealing a mechanism for gene silencing.

alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing

alpseq is an open-source pipeline for processing NGS data from nanobody libraries, enabling efficient analysis and identification of enriched sequences.

Pfs48/45 nanobodies block Plasmodium falciparum transmission

This paper identifies nanobodies against Pfs48/45 that reduce malaria parasite transmission by inhibiting fertilization in Anopheles mosquitoes.

Crystal structure and nanobodies against domain 3 of the malaria parasite fusogen Plasmodium falciparum HAP2

The paper identifies nanobodies targeting domain 3 of PfHAP2 and determines its crystal structure, providing structural insights for transmission-blocking interventions against malaria.

Powerful read processing with matchbox

matchbox provides a flexible and scalable read processor for handling diverse sequencing tasks, demonstrating versatility in demultiplexing, restranding, CRISPR efficiency assessment, and haplotyping.

Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2

FLAMESv2 is a flexible R/Bioconductor package for analyzing long-read single-cell RNA-seq data, demonstrating field-leading performance in isoform analysis and cell-type identification.

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

LongBench benchmarks long-read RNA-sequencing technologies using a cross-platform dataset of cancer cell lines, showing high gene-level concordance but reduced transcript-level consistency across platforms.

Cryo-EM structure of endogenous Plasmodium falciparum Pfs230 and Pfs48/45 fertilization complex

The paper determines the cryo-EM structure of the Plasmodium falciparum Pfs230-Pfs48/45 fertilization complex and identifies domains critical for function and vaccine design.

LeGO-Teknik reveals that the neurogenesis pathway is a clone-specific hallmark of brain metastasis in breast cancer

The paper identifies neurogenesis-related gene expression as a clone-specific hallmark of brain metastasis in breast cancer using a new optical barcoding tool.

Transcriptomic alterations including p53 pathway dysregulation prime DNMT3A mutant cells for transformation

This study shows DNMT3A mutations reduce DNA methylation and disrupt p53 pathway, increasing self-renewal and cancer risk in hematopoietic cells.

D4Z4End2End: complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS and reference cohorts

This paper develops D4Z4End2End, a workflow using long-read sequencing to characterize D4Z4 macrosatellite genetics and methylation in FSHD, BAMS, and reference cohorts, revealing new variants and methylation patterns.

Towards accurate, reference-free differential expression: A comprehensive evaluation of long-read de novo transcriptome assembly

This study evaluates long-read de novo transcriptome assembly tools for differential expression analysis without a reference genome, finding RNA-Bloom2 with Corset as the most accurate and efficient.

Measuring X inactivation skew for retinal diseases with adaptive nanopore sequencing

This study uses adaptive nanopore sequencing to measure X inactivation skew in carrier females with X-linked retinal diseases, showing a strong correlation between skew and disease presentation.

An optimised protocol for quality control of gene therapy vectors using Nanopore direct RNA sequencing

This paper compares long-read sequencing technologies to identify RNA quality issues in lentiviral vectors, finding Nanopore direct RNA sequencing most effective for detecting incomplete RNA.

SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease

This study identifies a mutation in SMCHD1 that enhances gene silencing and disrupts developmental processes, revealing distinct roles of SMCHD1 in chromatin structure and gene regulation.

Restrander: rapid orientation and QC of long-read cDNA data

Restrander improves the orientation and quality control of long-read cDNA data by accurately inferring strandedness and detecting artefacts.

NAb-seq: an accurate, rapid and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells

NAb-seq provides a rapid, cost-effective, and species-independent method for sequencing full-length antibody genes from hybridoma cell lines and single B cells, outperforming Sanger sequencing in accuracy and throughput.

Maternal SMCHD1 regulates Hox gene expression andpatterning in the mouse embryo

This study shows maternal SMCHD1 prevents premature Hox gene activation in mouse embryos, leading to posterior homeotic transformations when absent.

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures

The paper benchmarks long-read RNA-sequencing tools using synthetic data to evaluate isoform detection and differential expression analysis performance.

Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation

This study shows maternal SMCHD1 is essential for imprinted Xist expression and X chromosome inactivation in mouse embryos and placenta.

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

The paper develops FLT-seq and FLAMES to characterize full-length isoforms in single cells of human and mouse, identifying thousands of unannotated isoforms and linking them to functional modules and drug resistance mutations.

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools

This study analyzes nanopore long-read RNA-seq data using short-read tools to assess differential gene and isoform expression in synthetic and mouse datasets.

NanoMethViz: an R/Bioconductor package for visualizing long-read methylation data

NanoMethViz provides an R/Bioconductor package for visualizing long-read methylation data, offering tools to explore methylation patterns at multiple resolutions.

Smchd1 is a maternal effect gene required for autosomal imprinting

This study identifies Smchd1 as a maternal effect gene that regulates imprinted expression of 16 genes by translating polycomb-mediated histone methylation marks into a heritable chromatin state.

Using long-read sequencing to detect imprinted DNA methylation

The paper uses long-read nanopore sequencing to detect imprinted DNA methylation and identifies known and novel differentially methylated regions.

Frequent paramutation-like features of natural epialleles in tomato

The paper identifies frequent paramutation-like features in natural epialleles of tomato using DNA methylation analysis of introgression lines.