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mgr Michał Karlicki

Scientific interests

  • Ecology of water ecosystems, including phototrophic microorganisms
  • Interspecies interactions (protista – protista and protista – prokaryota)
  • Bioinformatics, meta–omics, machine learning

Research projects

  • Analysing the biodiversity of eukaryotic microorganisms on the saline- freshwater border utilising the amplicon sequence of region V9 of the 18S rRNA gene. Grant DSM 2019, Faculty of Biology UW


  • July – October 2017: Singapore Centre Of Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
  • June – September 2014: Center for Research and Development of Industrial Fermentations, La Plata, Argentina

Societies memberships and functions

  • International Society of Protistologists (ISOP)
  • Polish Microbiologists Society (Polskie Towarzystwo Mikrobiologów)

Prizes and distinctions

  • Holz-Conner Travel Grant (conference attendance; International Society of Protistologists, ISOP) (2019)
  • Distinction in the 9th Competition for the best Master Thesis in Bioinformatics awarded by the Polish Bioinformatics Society (2019)


Oral presentations

  • Karlicki M., Rymuza J., Antonowicz S., Karnkowska A. Machine learning-based approach for classification of metagenomic data. 4th EMBO Workshop on Computational and Structural Biology and Chemistry. Waplewo, Poland; 2020.
  • Karlicki M., Karnkowska A. Metagenomics insight into eukaryotic picoplankton community of the Baltic Sea. 49th Jirovec’s Protozoological Days. Kostelec nad Cernymi Lesy, Czech Republic; 2019.
  • Karnkowska A., Maciszewski K., Karlicki M., Bennett M.S., Triemer R.E. Why do we need more algal plastid genomes? Phycological Society of America and the International Society of Protistologists Conference. Vancouver, Canada; 2018.
  • Karlicki M., Karnkowska A. MetaPlastHunter: An efficient pipeline for classifying chloroplast reads from metagenomic data. VII Intercollegiate Biotechnology Symposium “Symbioza”. Warsaw, Poland; 2018.
  • Karlicki Michał, Karnkowska Anna. Searching for Plastid Genomes in the Metagenomic Data; 48th Jirovec’s Protozoological Days. Kuncice pod Ondrejkiem, Czech Republic; 2018.


  • Karlicki M., Karnkowska A. Temporal dynamics of prokaryotic and microbial eukaryotic community in the freshwater lake revealed by 16S and 18S rDNA metabarcoding. FEMS Conference on Microbiology 2020 (online, 2020).
  • Karlicki M., Lukešová S., Hadariová L., Szabová J., Hampl V., Karnkowska A. Looking for a needle in a haystack searching for plastids in the environmental DNA. VIII European Congress of Protistology – ISOP joint meeting. Rome, Italy; 2019.



Karlicki, Michał; Antonowicz, Stanisław; Karnkowska, Anna

Tiara: deep learning-based classification system for eukaryotic sequences Journal Article

In: Bioinformatics, vol. 38, no. 2, pp. 344–350, 2022.

Abstract | Links | BibTeX


Lukešová, Soňa; Karlicki, Michał; Hadariová, Lucia Tomečková; Szabová, Jana; Karnkowska, Anna; Hampl, Vladimír

Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments Journal Article

In: Environmental Microbiology Reports, vol. 12, no. 1, pp. 78-91, 2020.

Abstract | Links | BibTeX