Maido Remm

This paper develops a k-mer-based method to design PCR primers for rapid, low-cost sequence typing of L. monocytogenes with 100% sensitivity and specificity.

GeneToCN estimates gene copy numbers from NGS reads using gene-specific k-mer frequencies, showing strong correlation with experimental data across multiple genes and sequencing technologies.

The paper develops a Golden Gate Assembly platform (RtGGA) for Rhodotorula toruloides to enhance metabolic pathway engineering, resulting in a 41% increase in carotenoid production.

KATK is a tool for variant calling from raw sequencing reads, achieving low false negative and discovery rates while avoiding bias against rare variants.

AluMine identifies polymorphic Alu element insertions in personal genomes using alignment-free methods, achieving high genotype concordance.

The paper analyzes transcriptomic and genomic data from Conus consors to identify protein sequences and conopeptides.

PhenotypeSeeker predicts bacterial phenotypes from genomic sequences with high accuracy using k-mer-based models, achieving fast inference on assembled genomes.

FastGT calls common SNVs from raw sequencing reads using k-mer frequency analysis, achieving high concordance with reference genotypes.

StrainSeeker identifies bacterial strains from unassembled sequencing reads using guide trees, successfully detecting Escherichia coli strains in mixed samples within 5 minutes.