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Hello friend!

I am (now :-) ) a post doctoral researcher focusing on microbial communities ecology using bioinformatics approaches. Here is my so-far work and experieneces as well as in some thoughts of mine.

About Me

Our world, as we know it, is in a constant crisis. Two are the most pressing problems of our time; the relationships among the different classes of our modern community and the relationships between our community and the nature. Comprehending ecosystems' ecology can help us address a wide range of issues in a viriety of aspects, both scientific and societal. And this is why I chose to focus my research curiosity on elucidating ecosystem function.

In 2016, I completed my BSc in Biology at the National and Kapodistrian University of Athens.
After that, I joined the Bioinformatics MSc program in the University of Crete (2016-2018). During my master thesis, I became a member of lab42open at IMBBC-HCMR. Since then, I have been working on PEMA, a pipeline for the analysis of metabarcoding data. After that, I conducted my PhD on microbial community ecology through the lens of NGS technologies, data integration and metabolic networks in the framework of the PREGO project, .

In 2020, I also started to contribute to the GeomScale research and development project bringing together computational geometry with metabolic modelling.
After defending my PhD in 2022, I joined lab of microbial systems biology at the Rega institute at KU Leuven and the 3D' omics project.
My research interests focus on microbial interactions, ecology and evolution. Hence, bioinformatics is nothing but a means to an end? One might say so. But it is quite similar for the way to lead you to places you have never thought in the first place. Is it not?

Alfeios river estuary.


  • Daniel Rios Garza, Didier Gonze, Haris Zafeiropoulos, Bin Liu and Karoline Faust. “Metabolic models of human gut microbiota: Advances and challenges.” Cell Systems (2023). DOI

  • Pavloudi, Christina, and Haris Zafeiropoulos. “Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community.” FEMS Microbiology Ecology (2022), DOI.

  • Haris Zafeiropoulos, Savvas Paragkamian, Stelios Ninidakis, Georgios A. Pavlopoulos, Lars Juhl Jensen, and Evangelos Pafilis. “PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types.” Microorganisms 10, no. 2 (2022): 293, DOI: 10.3390/microorganisms10020293

  • Haris Zafeiropoulos, Laura Gargan, Sanni Hintikka, Christina Pavloudi, and Jens Carlsson. “The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data.” Metabarcoding and Metagenomics 5 (2021): e69657, DOI: 10.3897/mbmg.5.69657

  • Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis et al. “0s and 1s in marine molecular research: a regional HPC perspective”, GigaScience, Volume 10, Issue 8, August 2021, giab053, DOI: 10.1093/gigascience/giab053

  • Paraskevi N. Polymenakou, Paraskevi Nomikou, Haris Zafeiropoulos et al. “The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy” Energies 14, no. 5: 1414. March 2021, DOI: 10.3390/en14051414

  • Haris Zafeiropoulos, Ha Quoc Viet, Katerina Vasileiadou, Antonis Potirakis, Christos Arvanitidis, Pantelis Topalis, Christina Pavloudi, Evangelos Pafilis, “PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes”, GigaScience, Volume 9, Issue 3, March 2020, giaa022, Doi: 10.1093/gigascience/giaa022



  • Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis et al. (2021, April 5). “The IMBBC HPC facility: history, configuration, usage statistics and related activities” (Version 1.0.0). Zenodo. http://doi.org/10.5281/zenodo.4646133


PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes

Main page on pema.hcmr.gr. PEMA is reposited in Docker Hub as well as in Singularity Hub.

Pipeline for Environmental Metabarcoding Analysis (PEMA) is a HPC-centered, containerized assembly of key metabarcoding analysis tools. PEMA combines state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune thoroughly each study thanks to roll-back checkpoints and on-demand partial pipeline execution features

Mining microbiomes!

Process, environment, organism (PREGO) is a systems-biology approach to elucidate ecosystem function at the microbial dimension. To understand how ecosystems function it is fundamental to understand what processes occur in which environments (where), and which organisms carry them out (who). Its main motivation is to provide a one-stop-shop for researchers interested in searching and visually exploring such what - where - who associations.

a C++ library for high-dimensional sampling and volume approximation for modelling metabolic networks.

VolEsti is a C++ library for volume approximation and sampling of convex bodies (e.g. polytopes) with an R and limited python interface. VolEsti is part of the GeomScale project.
Along with the GeomScale group, we are building a complete toolobx for the analysis of metabolic network. Our aim is to address the challenges of high dimensional networks (e.g the human Recon 3D) as well as those rising from networks of networks, just like in the case of metabolic networks of microbial communities.

Dark mAtteR iNvestigator: diving into the dark matter of your COI sequences

The Dark mAtteR iNvestigator tool (DARN) uses a COI reference tree of life we built, to assign your sequences to the 3 domains of life. Its purpose is not to provide you with certain taxonomic assignment but to give an overview of the species present.

Teaching material

Talks - tutorials

  • Geometric and statistical methods in systems biology the case of metabolic networks @ PyData2020 url

  • Microbiome Data Analyses Workshop - Online (MDAWO) GitHub repo

  • Seminar HPC - DNA metabarcoding @ IMMBC url

  • PEMA tutorial @ Mikrobiokosmos 2019 slides


You can find me at the social you see at the down-left of your screen, in the "Menu" column.

You can also contact me directly from the platform below.