Thomas M Bataillon

This paper introduces BBQ, a tool that improves rare somatic variant calling by modeling sample-specific error rates using overlapping reads, reducing false positives compared to existing tools.

The paper curates a genome-scale nucleotide diversity panel of non-human primates using ploidy-aware variant calling and multiple-genome alignment.

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Ancestree infers ancestral alleles using genealogies, supporting various inputs and providing posterior probabilities, with improved accuracy over fixed-tree methods.

This study uses ESM2 to identify beneficial genetic variants in a Sorghum bicolor diversity panel by analyzing PRC scores and their association with agronomic traits.

The paper introduces a method to estimate gene conversion tract length and rate from PacBio HiFi data, showing low visibility of NCO events in human sperm due to low SNV density.

This study quantifies natural variation in root exudate composition across 105 Arabidopsis thaliana accessions in the Iberian Peninsula, identifying genetic and environmental factors influencing exudate traits.

This study uses long-read sequencing to analyze gene conversion and crossover events in human, chimpanzee, and gorilla testes and sperm, revealing species-specific patterns and GC bias in gene conversion.

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

polyDFEv2.0 tests if fitness effect distributions are consistent across genomic regions and species using SFS data and likelihood ratio tests.