Savvas Paragkamian

Irakleio, Crete, Greece · s.paragkamian@gmail.com · +30 6934008102

GitHub · ORCID 0000-0002-8508-2521 · LinkedIn

Education

PhD — Deciphering the relation of microbiome interactome with ecosystem function and biogeochemical processes
December 2019 – December 2024
University of Crete, Department of Biology · IMBBC
Advisory Committee: Prof. P. F. Sarris, Dr E. Pafilis, Prof. I. Antoniou
DOI: 10.12681/eadd/57558

MSc — Complex Systems and Networks · Grade 9.58 (Excellent)
2015 – 2017
Thesis: Exploring the centrality-lethality rule in signed protein networks.
Aristotle University, Thessaloniki · Supervisors: Prof. I. Antoniou, Prof. S. Sgardelis

BSc — Biology · Grade 7.30 (Very Good)
2010 – 2015
Thesis: Menzerath-Altmann’s law in human gene families at the gene-exon level and their evolutionary history.
University of Crete, Irakleio · Supervisor: Prof. C. Nikolaou

Fellowships & Awards

PhD Scholarship — 3rd call for Doctorate Scholarships (no. 5726), Hellenic Foundation for Research and Innovation.

Dawn Field Award 2024 — for Outstanding Contributions to Genomic Standards, Genomic Standards Consortium. Awarded for contributions to the genomics and island microbiome research communities.

Teaching and Supervision

2026 — Undergraduate thesis co-supervision: Ms Pelagia Kapouralou on characterisation of seven new bacterial strains of Janthinobacterium from Gourgouthakas cave.

2025 — Master thesis co-supervision: Ms Nektaria Kokolaki on beneficial microbes of plants against drought and high salinity abiotic stress.

Nov–Dec 2025 — TETTRIS: Soil Data Science, Standards and Integration. Online course, Horizon. 10 hours.

May 2025 — Network Science Workshop, BC204 Course, Bioinformatics MSc, University of Crete. 6 hours.

December 2024 — Field-Work Methods in Speleology: Different data and standards. Aristotle University of Thessaloniki, Centre for Education and Lifelong Learning. 2 hours.

Jan–Feb 2020 — GEO-IN: Geotourism in insular geoparks. Workshop for the general public and entrepreneurs, Interreg V-A Greece–Cyprus. 15 hours.

2018, 2025, 2026 — Network Science Workshop, Bioinformatics MSc, University of Crete. 15 hours.

Skills

Languages — Greek (mother tongue), English (C2), French (A2)

Programming — Proficient: R, AWK · Intermediate: Python, Bash · Basic: Julia, Perl

Computational — Metagenomic microbiome workflows, complex network analysis, microbial genomics, agentic information retrieval and text mining, data engineering, biodiversity data standards, species hotspot assessment, geospatial analysis (GIS), statistical and mathematical modelling.

Databases & Ontologies — GBIF, OBIS, IUCN, MICROBEATLAS, WoRMS, NCBI Taxonomy, GTDB, SILVA, ENA, MGnify, GenBank, Ensembl, PubMed, OpenAlex, Copernicus, NASA MODIS, JGI IMG/M, KEGG, STRING, EnvO, Gene Ontology.

Workflow — Unix, Vim, Git, Tmux, Conda, Claude Code, Ollama, LaTeX, r-spatial, R Targets, Tidyverse, QGIS, HPC (Slurm), Podman, Docker.

Field Sampling — Expertise in extreme environments: high cliffs and deep caves. Logistics for expeditions with 30+ participants. Soil, cave (microbes and arthropods), raptor bird sampling. 50+ raptor bird captures from cliff nests (Bonelli’s eagle, Golden eagle, Gypaetus barbatus) using rope access.

Soft skills — Project administration, team building, thesis supervision, science communication, technical support for online and hybrid events.

Outdoor — Certified canyoning instructor (moniteur) by the French Federation of Speleology. Caving explorer and instructor. Master Rescue Scuba Open Water Diver (SSI). Speedboat operator (Hellenic Coast Guard). Certified UAV operator (A1-A2-A3). Assistant to photographer Heinz Troll 2018–2025.

Research Experience

Biosolutions (Oct 2024 – Nov 2025) — Sustainable solutions for climate change in inducing crop tolerance. Prasino Tameio. Host: University of Crete. PI: Prof P. F. Sarris.

Invertebrates Monitoring (Oct 2024 – Oct 2025) — Conservation status of protected species and habitats, Art 17 Directive 92/43/EEC. Host: N.E.C.C.A. PI: Dr Konstantinos Triantis.

EMODnet Biology III/IV (Oct 2021 – Mar 2022) — Text mining on marine taxa and traits. Host: IMBBC. PI: Ms D. Mavraki.

PREGO (Jan 2020 – Dec 2021) — Development of PREGO, a literature and data integration platform associating organisms, environments, and processes. HFRI. Host: IMBBC. PI: Dr E. Pafilis.

CMBR (Jan 2020 – Sep 2021) — Centre for the study and sustainable exploitation of Marine Biological Resources. NSRF 2014–2020. Host: IMBBC. PI: Dr A. Magoulas.

Conservation of the Cave Fauna of Greece (Jul 2017 – May 2019) — Development of the CFG Database. MAVA Foundation, WWF Greece. Host: INSPEE-HISR. PI: K. Paragamian.

EU Rural Development – LEADER — Co-organised 3 projects to document, improve rigging, and engage local communities around the canyons of Crete. Host: INSPEE-HISR. PI: K. Paragamian & S. Paragkamian.

Funding

TETTRIX — Transforming European Taxonomy through Training, Research and Innovations. EU Horizon. PI: Dr I. Stathi, NHMC.

KYBELE — Knowledge Yield from Biodiversity Literature through LLM Extraction. ELIXIR. PI: Mr Stelios Ninidakis, HCMR.

CCMRI — Climate Change Metagenomic Record Index. GSRI–HFRI. PI: Dr Evangelos Pafilis, HCMR.

Expeditions

Soil microbiome — Co-organised the Island Sampling Day Crete 2022 with 29 participants. HCMR.

Cave microbiome — Sampling from the deepest cave of Greece, Gourgouthakas Cave (−1,100 m). University of Crete.

TREC — Traversing European Coastlines expedition, EMBL superstop at Athens, July 2024.

Arthropods — Sampling from caves (100+ cave samplings). INSPEE-HISR.

Raptor birds — Captures from cliff nests across the Aegean and Crete. Bonelli’s eagle, Golden eagle, Gypaetus barbatus. Host: Natural History Museum of Crete.

Platforms & Tools

Crete Soil Information System — Open portal with soil data of Crete from literature, samplings, and maps.

CFG Database — First complete national open database on cave biodiversity. INSPEE-HISR.

CCMRI Database — Climate Change Metagenomic Record Index, dynamic researcher-notification and sample classification system.

PREGO — Linking microbes, environments, and processes through data integration and text mining.

Presentations

Joint International MIKROBIOKOSMOS and CEESME Conference (Thessaloniki, 09/2025) — A Thousand Meters Deep: Vertical Profiling of the Subterranean Microbiome of Gourgouthakas Cave.

2nd Young Soil Researchers Forum (EUSO Stakeholders Forum 2024, Oct 2024) — From Micro to Macro: Crete island biodiversity and its soil microbial interactome.

Soil Health: Current Status and Future Needs 2024 (Chania, Oct 2024) — From microbes to ecosystems: towards a Crete island soil system.

TREC Symposium 2024 (Heidelberg, Sep 2024) — Traversing European Coastlines superstop at Athens. With Evangelos Pafilis.

Qlife Winter School (Paris, Mar 2024) — Travel Grant for the Poster: Defining Crete’s Macroecology based on its soil Microbial Interactome.

10th International Conference of MIKROBIOKOSMOS (Larisa, 12/2023) — From Micro to Macro, Defining Crete’s Macroecology based on its soil Microbial Interactome.

EMBO Satellite Workshop on Ecology Informatics (Irakleio, 05/2023) — Integrating data and methods: what can we learn about the soil ecosystems of Crete.

9th International Conference of MIKROBIOKOSMOS (Athens, 12/2021) — PREGO: mining literature and -omics (meta)data to associate microorganisms, biological processes, and environment types.

Other: 5 presentations and 10 posters in international conferences and workshops.

Press

Safety goes out the window in the search for thrills and photo ops — Kathimerini, 01/2026

Aerial rescue falling short — Kathimerini, 12/2025

Microbes in the Underground — Ypokosmos Caving Journal, 10/2025

Radio interview about the soil microbes of Crete — Hxonews, 07/2025

Soil microbes of Crete interview — Cretalive, 08/2025

Scientific Awards: Savvas Paragkamian receives the Dawn Field Award — Vima Science, 08/2025

Microbe sampling in Gourgouthakas cave — Cretalive, 08/2022

Publications

co-first authorship denoted by *

See the full list on the Publications page.