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'Omics, data integration and network analysis:
decipher the underlying mechanisms of ecosystem functioning

Hi everyone!
I am a PhD candidate in the Biology Department at University of Crete working at the IMMBC-HCMR in Greece.
This is my research profile where you can find my interests and my so-far work.

About Me

Our world, as we know it, is in 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.
That is the reason 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. It was then when I realised the great part that Bioinformatics play in every aspect of modern biology; in ecosystem functioning as well.

Then, 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 developed PEMA , a pipeline for the analysis of metabarcoding data. PEMA has been selected from LifeWatch - ERIC for the analysis of the ARMS derived data.

In the framework of the PREGO project, I am now conducting my PhD on microbial community ecology and ecosystem functioning .
I intend to merge analyses of different types of NGS data, knowledge aggregation and data integration, along with network analysis, to end up with some prommising hypotheses regarding how ecosystems work and what is what we could do to restore the balance.

My research interests focus on microbial ecology and ecosystem functioning at the microbial dimension; as each and every ecosystem type is based on the microbes hosted. Hence, bioinformatics is nothing but a means to an end ? Actually, you could 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?

In this website you may find my so-far research work as well as some issues that have caught my attention.

Alfeios river estuary.


  • Paraskevi N. Polymenakou, Paraskevi Nomikou, Haris Zafeiropoulos, Manolis Mandalakis, Thekla I. Anastasiou, Stephanos Kilias, Nikos C. Kyrpides, Georgios Kotoulas, Antoniοs Magoulas. 2021. “The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy” Energies 14, no. 5: 1414. https://doi.org/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, https://doi.org/10.1093/gigascience/giaa022


  • Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis, Savvas Paragkamian, Nelina Angelova, … Evangelos Pafilis. (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

  • Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas, Haris Zafeiropoulos. Geometric algorithms for sampling the flux space of metabolic networks. 2020. ffhal-03047049f (pre-print accepted in the 37th International Symposium on Computational Geometry) )*

in preparation

  • In silico design of blocking primers: prevention of PCR amplification of marine fungal 16S rRNA and COI genes in metabarcoding analyses. Haris Zafeiropoulos, Jon Bent Kristoffersen, Katerina Vasileiadou, Christos Arvanitidis, Pantelis Topalis, Evangelos Pafilis, Christina Pavloudi (under revision - resubmission)


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 the microbe!

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.


You may contact me directly from the platform below.