Evangelos Karatzas

@vagkaratzas

Hi! I am a postdoctoral bioinformatics researcher at EMBL-EBI and Nextflow Ambassador, building pipelines and web tools that help biologists make sense of complex genomic and metagenomic data.

About me

I come from a computer science background, where I finished my bachelor's in informatics at the Athens University of Economics and Business in 2012. I then completed a master's in bioinformatics at the National and Kapodistrian University of Athens, followed by a PhD in the same institute, focused on computational drug repurposing and genetic network analyses for Idiopathic Pulmonary Fibrosis, a rare and fatal respiratory disease. During 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 in the Pavlopoulos Lab, to develop bioinformatics web tools to assist biologists in the areas 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, where I developed bioinformatics pipelines using Nextflow/nf-core to create and annotate metagenomics-derived protein families.

Scientific Research

My publications mainly revolve around bioinformatics visualization tools, genomics and metagenomics pipelines, and computational drug repurposing. Here are my three personal favourites!

My favourite publication so far is the nf-core/proteinfamilies paper. This is the main project I have been working on during my postdoc at the EBI. nf-core/proteinfamilies is a scalable Nextflow pipeline for the generation and update of protein families from large sets of amino acid sequences.
Publication: nf-core/proteinfamilies: a scalable pipeline for the generation of protein families
PMID: 41563008
GitHub: nf-core/proteinfamilies

Another personal favourite is the Arena3D^web tool. This was my main assignment during my time at Alexander Fleming. Arena3D^web is an online application for visualizing interactive, 3D, multi-layered networks.
Publication: Arena3D^web: interactive 3D visualization of multilayered networks
PMID: 33885790
GitHub: PavlopoulosLab/Arena3Dweb

Finally, I would like to highlight our extensive review on biological networks, which we used as material in our related 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