Laurent Frantz

This study examines phenotypic variation in native chickens across Java and Wallacea, finding diffuse structure linked to human-mediated connectivity and decentralized selection.

Twenty-three new Yersinia pestis genomes from Scandinavia, the Netherlands, Iceland and Armenia extend the Second Plague Pandemic phylogeny, with the first Icelandic plague genome and eastward-spreading pestis secunda strains.

This study identifies candidate genes for trypanotolerance in African cattle by integrating genomic and transcriptomic data from hybrid populations.

This study evaluates the reliability of local ancestry inference methods for imputed ancient genomes across various demographic and sampling scenarios.

This study shows that brain size reduction in dogs began in the Late Neolithic, 5,000 years ago, with a 46% decrease compared to prehistoric wolves.

The paper presents CattleGTEx, a resource characterizing regulatory effects in cattle, resolving GWAS signals and providing insights into adaptive evolution and selection.

The paper analyzes 1,001 wolf genomes to reveal distinct evolutionary lineages and genetic health issues across Europe, highlighting the need for region-specific conservation strategies.

The paper uses genomic and morphometric analyses to show that pigs in Wallacea and Oceania have diverse ancestries linked to Austronesian dispersal 4,000-3,000 years ago.

This study imputes ancient dog and wolf genomes to analyze inbreeding history over 10,000 years, finding lower inbreeding in ancient populations and associations between low ROH regions and olfaction/immune genes.

This study shows that small island populations of anoa and babirusa have higher genetic quality despite lower diversity, suggesting they should be prioritized for conservation over mainland translocations.

The paper constructs a cattle cell-type-specific regulatory variant atlas by integrating bulk and single-cell RNA-seq data, identifying eQTL and linking them to GWAS loci for breeding insights.

The ChickenGTEx project provides a multi-tissue reference of regulatory variants in chicken, analyzing their functional impacts and utility in genetics, genomics, and evolutionary studies.

This study uses ancient and modern cat genomes to show domestic cats reached Europe within the last 2,000 years from North Africa, not with Neolithic farmers, and identifies an earlier wildcat introduction to Sardinia.

The paper identifies leopard cats as the earliest felines in Chinese human settlements, predating domestic cats by over 2,500 years, and traces the arrival of domestic cats via the Silk Road.

The paper uses local ancestry inference tools to analyze admixture in African and European cattle populations, identifying functional consequences of ancestry on disease resistance and physiological traits.

This study uses whole-genome sequencing and SNP arrays to analyze Criollo cattle from Colombia and Venezuela, revealing African and Asian admixture and selection signatures linked to adaptive traits.

The paper presents PigGTEx, a resource linking genetic variants to transcriptomic phenotypes in pigs, showing pigs' similarity to humans in gene regulation and complex traits.

The paper analyzes the genomes of Sicilian wolves to reveal their complex history of isolation and admixture with ancient dogs, showing admixture with European dog breeds and signs of inbreeding.

HAYSTAC provides a Bayesian framework for accurate and efficient species identification in metagenomic data, outperforming existing tools in reducing false positives and handling degraded DNA.

ifCNV detects copy number variations using isolation forests and a scoring method, validated on diverse datasets with high accuracy.

The paper predicts the viability of archaic human hybrids using mitochondrial DNA divergence patterns to assess fertility differences between species pairs.