You wouldn’t expect it, but here where we are living (Brandenburg, Germany), 6th grade is a major milestone in a child’s life. Their performance in the first semester determines whether they’ll continue with a Gymnasium education, putting them on a university-bound path, or move toward a more skill-focused education. It’s quite early for such a life-shaping decision, in my opinion, but that’s how the system works.

Fingers crossed for my son!

Quite often in my research life, and somewhat by itself, my brain identifies activities that could be optimized by software solutions, especially when coupled with powerful graphical user interfaces. As a programmer, I’m more of a data analyst, so I cannot bring these visions to life on my own. Luckily for me, my life partner is a formidable programmer with the necessary skills to create powerful software with beautiful graphical interfaces. Together, we have decided to embark on our next entrepreneurial adventure and have founded SciVance Technologies UG (Germany). Guess who the CEO is?

A while ago, I decided to switch the programming language I use for bioinformatics data analysis pipelines and algorithms from R to Julia. After reading a few books on Julia and navigating the initial learning pains, I began developing my own bioinformatics packages. DoVIP (Do Virus Prediction Pipeline) is not the first package I’ve written in Julia, but it’s the first to make it onto GitHub. It combines data from five individual virus predictors to enable accurate identification of viral contigs in environmental samples.

Here, in the Department of Environmental Microbiology, led by Prof. Alexander Probst, I have found a new research home. I will continue to work with prokaryotic viruses, diving deeper into the exploration of environmental samples using metagenomics and Fluorescence in situ Hybridization. At the same time, my investigations into phage-bacteria interactions using isolates will continue with Ismael, my PhD student who followed me here from Oldenburg.

In the second year of the COVID-19 pandemic, my family and I moved to our new house near Berlin. The demands of the job market … The move was difficult, and each of us left friends behind. Hopefully, the weather, along with the green, quiet streets, running trails, and friendly neighbors, will make up for it.

Finally, the VirClust paper is published! I initially developed VirClust to help cluster all marine phage isolates that my students, collaborators, and I isolated from the North Sea. For instance, we used VirClust to classify diverse dsDNA phages infecting flavobacteria and ssDNA Microviridae infecting marine and terrestrial alphaproteobacteria. Later, I decided to share it with the world. VirClust first clusters all viral proteins based on their BLASTp or HMM-profile similarities. Then, it hierarchically clusters the viral genomes based on the presence or absence of these protein clusters. VirClust is available as a web service, or as Singularity container, or source code.

The paper describing VIRIDC, a bioinformatics tool that calculates intergenomic identities of viruses, is out! This tool is available as a webservice, Singularity package, or source code.

Together with Jimena Barrero-Canosa and colleagues, we have developed a new protocol for single-copy gene detection in prokaryotic cells. The protocol uses multiple polynucleotides directly labeled with fluorochromes as a single probe to bind to both extrachromosomal and chromosomal genes.

And this is how I started isolating bacteriophages of marine Rhodobacteraceae.

We can now use Fluorescence In Situ Hybridization to visualize and quantify virus infection in prokaryotic cells! We named this method phageFISH and had a lot of fun observing phage-infected Pseudoalteromonas cells.

This is the day the sun light has touched my son!

My first PhD work to get published! I developed geneFISH, a method for detecting single-copy genes in bacterial and archaeal cells in environmental samples, coupled with simultaneous cell identification using rRNA-targeted probes.

DNA Baser – our first product. It performs automatic and batch assembly of contigs, starting from Sanger sequencing chromatograms! It includes bad end trimming and error correction.