Atsushi Takeda

Improving the Resolution and Informativity of the Majority-Rule Consensus Tree Using Fine-Grained Dissimilarity Measures

The paper introduces methods to improve consensus tree resolution using fine-grained dissimilarity measures, showing better performance on datasets with low to moderate phylogenetic signal.

BWR-finder: BWT-based de novo interspersed repeat detection for gigantic genomes

BWR-finder detects interspersed repeats in large genomes using a BWT-based algorithm, outperforming existing tools in speed and memory usage.

REPrise: de novo interspersed repeat detection using inexact seeding

REPrise improves de novo interspersed repeat detection by incorporating inexact seeding and other techniques, outperforming RepeatScout in sensitivity for mutated repeats.

Mobile elements in human population-specific genome and phenotype divergence

The paper develops a tool to genotype mobile element variants (MEVs) using short-read data and identifies population-specific MEs linked to disease and gene regulation.