Dr. Patrick Schacksen

I joined EDGE in 2025 to support the Christian Doppler Laboratory for Biodegradation of Water-Soluble Polymers as a bioinformatician and to study the functional characterisation and gene expression dynamics of microbiomes in wastewater and freshwater systems.

My previous research focused on advancing long-read sequencing technologies through the development and application of reproducible and standardised bioinformatic pipelines for microbial studies, enabling robust annotation of long-read sequences. This includes developing the framework and pipeline for processing Oxford Nanopore long-read metabarcoding data into a manageable OTUtable. 

Generally, I process data from both laboratory experiments and environmental samples using high-performance computing to investigate microbial community composition and functional potential, including the genetic basis for metabolic transformations, through combined metabarcoding and metagenomic analysis. 

• Practical application of (long-read) sequencing technologies for characterising microbial population structure and function.
• Development and implementation of reproducible bioinformatic pipelines for the processing and analysis of sequencing data.
• Functional annotation and interpretation of metagenome-assembled genomes (MAGs) to elucidate genetic repertoire, ecological roles, and functional potential.
• Integrative multi-omics analyses to uncover microbial community dynamics and metabolic interactions.