Evangelos Karatzas
Hi! I am a postdoctoral bioinformatics researcher working on various projects within and outside academia.
About me
I come from a computer science background, where I finished my bachelor on informatics at the Athens University of Economics and Business in 2012. I then did my master's in bioinformatics at the National and Kapodistrian University of Athens, followed by a PhD in the same institute, regarding computational drug repurposing and genetic network analyses for Idiopathic Pulmonary Fibrosis, a rare and fatal respiratory disease. For a part of my PhD, I relocated to Nicosia, Cyprus for a couple of months, where I worked at the Cyprus Institute of Neurology and Genetics.
In 2020, I was hired as a postdoctoral researcher at BSRC Alexander Fleming to develop bioinformatics web tools that will assist biologists in the directions of data visualization, text-mining and genomics/metagenomics analyses.
In 2023, I was hired as a research fellow at EMBL-EBI via the ARISE H2020 program, to work with the MGnify team on the MGnifams project. Here I constructed bioinformatics pipelines via the Nextflow (nf-core) workflow management software to create and annotate metagenomics derived protein families.
Scientific Research
My publications mainly revolve around bioinformatics vizualization tools, genomics/metagenomics analyses pipelines and computational drug repurposing. Here are my three personal favourites!
My favourite publication so far is the Arena3Dweb tool. This was my main assignment during my time at Alexander Fleming. Arena3Dweb is an online application for visualizing interactive, 3D, multi-layered networks.
Publication: Arena3Dweb: interactive 3D visualization of multilayered networks
PMID: 33885790
Another web application we developed with my team at Alexander Fleming is Darling. Based on text-mining disease-related resources, Darling creates biological entity networks based on their literature co-occurrence. What is even cooler, is that these networks can be readily sent to Arena3Dweb for 3D and VR visualization. Wow! Right?
Publication: Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining
PMID: 35454109
Then, I would like to highlight our extensive review on biological networks which we also use as material in our relative lectures. From graph theory, to different network types, structures, models, properties, data formats and visualization tools, this review covers everything for both aspiring as well as established researchers in the field.
Publication: A Guide to Conquer the Biological Network Era Using Graph Theory
PMID: 32083072
Technical Expertise
My first coding language was Java, which we mainly used during my bachelor studies for data structures and algorithms. In my opinion, it is one of the more suitable first languages to teach students, in order to grasp key concepts such as data types, especially when variables are passed from one function to the other. In my later years in the university, I picked a course regarding web development where I started learning JavaScript. The ease of debugging HTML, CSS and JavaScript through the browser and watching the changes on the fly, is what got me hooked into web development. We were also taught about relational schemas, databases and serving data from the back- to the front-end. We were using a combination of PHP, MySQL and JavaScript at that time. Then, we briefly got into C and C++ as well as developed some basic Android applications. When I got into bioinformatics, I was introduced to Pearl, R and Python.
Now, I am mainly constructing bioinformatics pipelines in Nextflow (nf-core), coding bioinformatics web tools in R(Shiny)/JavaScript as well as other web applications and sites in Python/Django or Next.js/React. I set my APIs in Node.js via the Express framework.
