Casey Bergman

The paper presents a high-quality reference genome for Hymenolepis diminuta using PacBio HiFi long-read sequencing, achieving high contiguity and completeness.

The paper introduces an improved pipeline for evaluating transposable element detectors in yeast, revealing best-in-class methods and novel biological insights.

The paper develops a method to analyze transposable elements in polyploid genomes using long-read sequencing, revealing somatic transposition events and TE family proliferation.

The paper sequenced 25 Drosophila S2 cell sub-lines to show ongoing transposition and use TE insertions for phylogenetic reconstruction in cell culture.

This paper develops a TE-based authentication protocol for Drosophila cell lines to improve reproducibility by distinguishing between different cell lines and sub-lines.

This paper uses transposable element profiles to identify and authenticate Drosophila cell lines and reveal loss of heterozygosity.

The paper presents a haplotype-resolved genome assembly for the red palm weevil, identifying 23,413 protein-coding loci and improving gene discovery compared to previous assemblies.

The paper examines how meiotic recombination in Drosophila virilis is affected by transposable element activation during hybrid dysgenesis, finding it robust but with mitotic recombination effects.

The paper generates phased diploid genome assemblies for three Candida albicans strains isolated from oak trees using PacBio sequencing.

The paper shows that trapping a somatic endogenous retrovirus into a germline piRNA cluster silences it in germ cells, protecting the germline from further invasion.

The paper analyzes P element insertions in Drosophila melanogaster populations to understand variation in gonadal dysgenesis phenotypes and shows that insertion numbers do not strongly correlate with phenotype severity.

McClintock is a pipeline that integrates multiple TE detection methods to evaluate their performance on simulated and real yeast genomes, showing that combining methods improves detection of non-reference TEs.