Gabriel Renaud

Ancient Reconstructed Proteins: A Framework for Resurrecting Protein Structures from Million-Year-Old Metagenomes

This paper presents a computational framework to reconstruct ancient protein structures from degraded metagenomic data, successfully recovering methane metabolism proteins from 2-million-year-old Greenlandic samples.

CHARON: Estimating the drift time and the number of individuals in environmental DNA with diploid individuals

CHARON estimates the number of individuals and drift time in eDNA samples using statistical methods, validated with simulations and synthetic data.

SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings

SAFARI improves ancient DNA alignment by using RYmer indices to handle chemical damage patterns, resulting in more accurate alignments and better damage rate estimation.

AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles

AdDeam estimates and clusters DNA damage profiles from ancient DNA fragments to identify contaminants and outliers efficiently.

Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages

The paper uses ancient DNA and strontium isotope analyses to show a deep east-west divergence in steppe ancestry in Southern Europe, supporting specific linguistic divergence models for Indo-European languages.

soibean: High-resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs

soibean improves species-level classification of ancient environmental DNA using mitochondrial pangenome graphs, revealing new insights from archaeological datasets.

Number of ancestors and length of identity-by-descent tracks over time

This study simulates genetic ancestry in small populations, showing that genetic ancestors grow more slowly than genealogical ancestors and that ROHs are common due to genetic drift.

CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets

CarpeDeam improves de novo assembly of ancient metagenomic datasets by incorporating damage-aware models, recovering longer sequences and proteins better than existing tools.

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

The paper benchmarks adapter trimming and read merging tools for ancient DNA sequencing, finding significant differences in quality score calculation but not in population genetics analysis.

The Limits of Haplotype-Based Approaches: Exploring the Applicability of the Li and Stephens Haplotype-Copying Model to Ancient Samples

This paper evaluates the Li and Stephens haplotype-copying model's performance on ancient DNA by using forward-simulated data and a constant-sized population model, finding it robust for haplotypes up to 900,000 years old.

HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph

HaploCart classifies human mtDNA haplogroups using a pangenomic reference graph and Bayesian inference, outperforming existing tools with more accurate and unbiased confidence scores.

euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.

euka improves taxonomic identification and abundance estimation in ancient eDNA by using pangenomic graphs and maximum-likelihood methods, outperforming existing tools.

Discovering fragment length signatures of circulating tumor DNA using Non-negative Matrix Factorization

This paper uses non-negative matrix factorization to analyze cfDNA fragment length distributions, showing it can infer tumor load, detect cancer, and identify open chromatin-associated signatures.

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

The paper identifies ancient Clostridium tetani genomes and TeNT variants from archaeological remains, revealing new species and a pathogenic toxin variant.

Benchmarking freely available human leukocyte antigen typing algorithms across varying genes, coverages and typing resolutions

This study benchmarks five HLA typing tools across different genes, coverages, and resolutions, finding HLA*LA has highest accuracy for some loci while Optitype performs best for others.

Population genomics of the Viking world

This study analyzes ancient genomes from the Viking Age to understand genetic structure and migration patterns, finding significant foreign gene flow and population differentiation.

The genetic origins of Saint Helena’s liberated Africans

The paper uses ancient DNA analysis of 20 individuals from St Helena to determine the genetic origins of liberated Africans, finding they came from West Central Africa and were culturally diverse.

A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data

This paper introduces a likelihood method to estimate present-day human contamination in ancient DNA samples using low-depth haploid chromosome data, showing improved accuracy compared to existing methods.

The population history of northeastern Siberia since the Pleistocene

This paper analyzes ancient genomes from northeastern Siberia to reveal complex population migrations and admixture events over the past 40,000 years.

glactools: a command-line toolset for the management of genotype likelihoods and allele counts

glactools manages genotype likelihoods and allele counts with command-line utilities for population genomics data.

Joint estimation of contamination, error and demography for nuclear DNA from ancient humans

This paper presents a method to estimate contamination, error, and demographic parameters in ancient human DNA, showing accurate recovery of these parameters even at high contamination rates.

Ancient human genomes suggest three ancestral populations for present-day Europeans

The paper analyzes ancient genomes to show present-day Europeans derive from three populations: WHG, ANE, and EEF, with EEF having Basal Eurasian ancestry.