Wilfried Haerty

This study maps genome-wide chromatin accessibility in A. calliptera embryos across three stages, revealing dynamic changes in regulatory elements and transcription factor activity during early development.

This study maps the telencephalon transcriptome of cleaner wrasse to identify conserved neural cell populations and gene networks involved in social behavior.

This study shows that removing the germline in zebrafish reprograms somatic DNA repair and stress responses, favoring high-fidelity mechanisms and altering gene expression patterns across multiple organs.

The paper analyzes deleterious mutations in cheetah populations, finding higher inbreeding and sperm-related mutation enrichment in certain populations.

The paper describes an automated robotic pipeline for high-throughput plasmid DNA purification and uses it to build a lentiviral DNA plasmid library for lineage tracing.

The paper shows that nitrogen responses in plant roots are cell-type specific and evolve across species, with NLP7 proteins modulating these responses in Arabidopsis and tomato.

This study uses spatial transcriptomics to analyze gene expression gradients in wheat inflorescences, revealing dynamic spatio-temporal organization along the apical-basal axis.

This study links chromatin accessibility divergence to phenotypic diversity in cichlid fishes by analyzing ATAC-seq and transcriptomes across multiple tissues and species.

The paper investigates a human-specific VNTR in CACNA1C and shows it modulates neuronal calcium responses and transcription programs.

This study characterizes the demographic decline and recovery of the British European polecat population using whole-genome analyses, revealing a genetic bottleneck and admixture events.

This study sequenced the genome of Bombus haematurus, a range-expanding bumblebee, and found genomic signatures of recent population expansion and selection in developmental and signaling genes.

This study compares long-read single-cell sequencing platforms, identifying common limitations and demonstrating their utility for isoform-resolved analyses.

The paper presents a high-quality genome assembly for the GIANT Nile tilapia strain, enabling the reconstruction of X and Y haplotypes and identifying sex determination loci on LG23.

The paper identifies pseudogenization events in cheetah fertility-associated genes linked to sterility, using comparative genomic analysis of eight felid genomes.

The paper presents a reference genome assembly for the Violet Carpenter Bee, including gene annotation and mitochondrial genome, as part of the European Reference Genome Atlas.

The paper shows that m6A modification of U6 snRNA by METT-10 is essential for accurate and efficient cis- and trans-splicing in C. elegans pre-mRNAs.

The paper generates a molecular map of the avian trunk and tailbud using single-cell and spatial transcriptomics, identifying cell lineages and spatially restricted genes.

This study annotates the wheat pan-transcriptome de novo and identifies gene diversity and expression patterns across multiple wheat cultivars and tissues.

The paper identifies regulatory variants associated with aquaculture traits in tilapia using ATAC-seq and genetic data.

The paper presents a chromosome-level genome assembly for the GIFT tilapia strain, identifying introgressed regions from O. mossambicus associated with growth and immunity traits.

The paper investigates miRNA and TF binding site evolution in cichlids, linking regulatory site turnover to GRN rewiring and adaptive traits.

The paper uses long-read sequencing to identify novel isoforms and splicing regulators during neuronal differentiation in human neuroblastoma cells.

This study uses nanopore direct RNA sequencing to accurately detect differential gene and isoform expression between human cell populations during differentiation.

The paper identifies distinct regulatory mechanisms and functions of ULK1 and ULK2, showing they are less redundant than previously thought.

The paper evaluates de novo genome assembly methods for a low-quality non-model mammal sample, finding that more data types do not always improve assembly quality.

This study combines short- and long-read scRNA-seq to analyze gene and isoform expression changes in hematopoietic stem and progenitor cells during differentiation and ageing.

The paper uses transcriptomics and network analysis to study regulatory networks in Paneth and goblet cell enriched gut organoids, identifying key regulators and their links to inflammatory bowel disease.

The paper uses long-read sequencing to uncover the complex splicing profile of the CACNA1C gene in human brain, identifying numerous novel exons and transcripts with potential functional implications.

The paper develops Galaxy-based tools for scRNA-seq quality control and analysis, making the process more accessible through simple scripts and a user-friendly interface.

The paper identifies and functionally characterizes long non-coding RNAs in C. elegans using transcriptome analysis and CRISPR/Cas9 mutagenesis.