Olivier D. Fedrigo

The paper generates high-quality genome assemblies for two manta and devil ray species and identifies structural variations linked to pelagic adaptation.

The paper identifies convergent gene losses and expression changes associated with blood-feeding loss in non-blood-feeding mosquitoes.

The paper presents a chromosome-level genome assembly for the European leaf-toed gecko, providing a high-quality reference for studying genome evolution and sex chromosome dynamics.

The paper investigates hatching failure in Alala, the Hawaiian crow, after a near-extinction event, identifying recessive lethal haplotypes as the main cause.

This study uses paleogenomes of dire wolves to resolve their evolutionary relationships and identify genes under diversifying selection.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

The paper assesses climate adaptation in Canada lynx populations at their southern trailing edge using genomic data, identifying adaptive loci and highlighting conservation risks.

This study establishes a long-term culture system for rock dove primordial germ cells, enabling germline manipulation and conservation applications.

The paper identifies genomic and transcriptomic changes associated with chromosomal instability and seasonal brain size plasticity in the Eurasian common shrew.

The paper presents the first chromosome-level genome assembly of the Brazilian merganser, revealing genomic features and population history insights.

The paper analyzes genomic diversity loss in whooping cranes despite population recovery, finding 70% genetic diversity loss and increased inbreeding.

The paper examines sex chromosomes in 14 elasmobranch species, identifying conserved X chromosomes and a shared candidate gene for sex determination.

The paper presents a chromosome-scale reference genome for the Andean cavefish Trichomycterus rosablanca to study evolutionary mechanisms in cave environments.

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

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.

The paper analyzes single-cell long-read mRNA isoform regulation across mouse brain regions, cell types, and development, finding pervasive isoform variability and cell-type specific splicing patterns.

The paper uses genome assembly and population genomics to show Altai falcons are a distinct species with unique genetic traits.

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

The paper presents a pangenome for the barn swallow and identifies genes under selection linked to synanthropy and domestication traits.

This paper presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper evaluates new vertebrate genome assemblies from the VGP against previous references, finding significant improvements in completeness and accuracy.

Gfastats, a C++ tool, computes genome assembly statistics in linear time, converts between FASTA, FASTQ and GFA files, and edits assemblies through a bidirected graph.

The paper identifies convergent gene expression patterns between songbird and human vocal motor circuits, highlighting shared molecular specializations in specific brain regions.

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

The paper benchmarks DNA preservation methods for long-read and long-range sequencing across vertebrates, finding that optimal methods vary by taxa, tissue, and application.

The paper introduces SnISOr-Seq, a method for single-nuclei isoform RNA sequencing, and finds distinct combination patterns of transcript elements in human brain cell types.