Lisa Vader Email and Phone Number

As a bioinformatician, I work on the development of the antiSMASH platform for genome mining. During my PhD project, I want to improve the prediction of fungal biosynthetic gene clusters (BGCs) encoding natural products, e.g. polyketides, nonribosomal peptides and terpenes. These BGC predictions are relevant for the discovery of new fungal natural products, such as antibiotics, drugs, pesticides and food additives. Another important application is the detection of BGCs encoding mycotoxins in fungal workhorses of the food industry.This project is part of the MAGic-MOLFUN doctoral network, a great international network of PhD students and researchers within the field of natural products research.

Helping BSc students with Python programming

Metagenomic analysis of soil DNA from ancient domestic waste sites (middens) in Nuuk, Greenland. I compared different methods for metagenomic assembly based on Nanopore and Illumina reads. I identified plant and animal species that were likely part of the diet of Norse settlers, and their relative abundances in the soil.

During this project, I investigated the way plasmids shape antimicrobial resistance and virulence in the pathogen E. coli ST131. I developed the intial version of plasmidEC, a program that predicts whether contigs originate from plasmids or the chromosome by ensembling multiple classification algorithms.

During my Bachelor internship I researched the biological functions of terpene metabolites in bacteria, especially in relation to stress. I used phase-contrast microscopy to investigate the osmotic stress response of Streptomyces strains in which terpene production was (partly) disrupted. I also analysed the occurence of the MEP (methylerythritol 4-phosphate) and MVA (mevalonate) pathways in relation to bacterial phylogeny. Finally, I wrote a review article about the current knowledge on the role of terpenes in the stress response of bacteria.