Franz Baumdicker

The paper shows sampling bias in prokaryotic genome collections distorts diversity estimates and proposes a method to detect and reduce this bias.

This study investigates how convolutional neural networks in population genetics implicitly compute summary statistics and reveals their ability to efficiently approximate long-range linkage disequilibrium.

This paper introduces neural posterior estimation for population genetics, showing it provides accurate and efficient posterior distributions compared to existing methods.

The paper analyzes CRISPR systems in prokaryotes, finding that multiple CRISPR arrays co-occur with Cas loci, vary in structure, and may function independently or collaboratively.

The paper analyzes CRISPR array repeat mutations across prokaryotic genomes, revealing subtype-specific patterns and a link between repeat mutations and spacer dynamics.

CRISPR-evOr predicts CRISPR array orientation by analyzing evolutionary patterns, improving accuracy for arrays other tools cannot confidently resolve.

This study evaluates how CRISPR-Cas plasmids can sensitize bacteria with plasmid-encoded antibiotic resistance to conventional antibiotics, finding that DNA cleaving is effective for low copy numbers and gene silencing for high copy numbers.

tangleGen infers ancestral relationships using a hierarchical soft clustering approach, improving interpretability and explainability of genetic ancestry.

The paper shows that maximum likelihood estimates in the admixture model are non-unique and provides an algorithm to compute the set of equally likely estimates.

SpacerPlacer reconstructs ancestral CRISPR array evolution, revealing frequent spacer deletions and a decrease in deletion frequency towards both ends of arrays.

Goldfinder infers gene co-occurrence and co-avoidance in bacterial pangenomes by considering phylogenetic relationships, reducing spurious associations compared to existing tools.

The paper expands the stdpopsim species catalog and improves genome simulations by adding non-crossover recombination and species-specific annotations, making simulations more realistic for non-model organisms.

The paper introduces msprime 1.0, a high-performance simulation tool for ancestry and mutation in population genetics, showing it is faster and more memory efficient than existing alternatives.

This paper improves BGA inference methods to account for recent admixture, showing improved accuracy and a likelihood ratio test for detecting recent admixture in genotype data.

The paper develops a supervised feature selection method to identify Ancestry Informative Markers (AIMs) for Biogeographical Ancestry inference, showing improved performance over traditional methods.