Classifying Candida species using Mixed Integer Optimization based optimal classification trees

Global medical use of azole antifungals and echinocandins has led to an enormous increase in resistant <i>Candida</i> species, that are most commonly associated with fungal infections. A possible mechanism causing resistance are single or simultaneous point mutations in the genes responsible for encoding antifungal target enzymes. The aim of...

A Bayesian approach to haplotype-aware de novo genome assembly for polyploid organisms

Capturing all genetic variation within a polyploid organism is a challenge. Most current de novo assemblers have no notion of the concept “ploidy”. Consequently, when assembling the genome of diploid or higher ploidy organisms, the assembler mixes reads coming from either chromosome copy and builds a single DNA sequence representing an arbitrary...