Evangelos Pafilis

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Full CV
Personal InformationEvangelos Pafilis
Principal Researcher
Bioinformatics Biodiversity Inform/cs Data Science

HCMR Thalassocosmos 71500 Gournes, Crete, Greece

+30 2810337748


Field & DegreeBioinformatics, PhD
SectionBiodiversity & Genetics
LocationMain Building
Personal Web Pagehttp://lab42open.hcmr.gr/people/evangelospafilis/
ORCID iD0000-0001-5079-0125
Scientific impact
Publication recordNo of ProjectsThesis supervision
H-index (scopus): 13PhD: 2
Articles: 31Princ. Invest.: 2MSc: 4
Citations-total: 605Project member: 24BSc: 1
Citations-nonself: 577Funding: 322,000
Education & training
Year (completed) Degree, Department, University, Town (optional), Country
2009Bioinformatics PhD, EMBL - Ruprecht Karl University of Heidelberg, Heidelberg, Germany, Magna cum Laude
2003Bioinformatics MRes, University of Glasgow, Glasgow, United Kingdom, Distinction
2002Biology BS, University of Crete, Herakleion Crete, Greece
Work Experience
Year (start) Position – Organization, Town (optional), Country
2018Bioinformatics and Biodiversity Informatics Researcher C at IMBBC, HCMR, Crete, Greece
2011Postdoctoral Researcher in Bioinformatics and Biodiversity Informatics at IMBBC, HCMR, Crete, Greece
2009Post-doctoral Researcher in Bioinformatics, School of Medicine, University of Crete, Greece
Personal skills
Mother tongue(s)Greek
Other language(s)
Language Basic/Intermediate/Proficient
Computer skills Advanced
Other skills Photography
Educational activities
Teaching experience
  1. Postgraduate Seminars

    • "Web Techniques in Bioinformatics"; MSc Bioinformatics, School of Medicine, University of Crete, Greece (Third Semester lecture)

    • “The STRING and STITCH protein-protein and protein-chemical interaction resources” MSc Bioinformatics; MSc Biomedical Engineering, University of Crete, Greece (as part of "Big Databases in Bioinformatics", lead by Dr. Pantelis Topalis, IMBB, FORTH, Crete, Greece)

    • 2016 – 2018, “Introduction to Programming and the Unix Operating System for Biologists”, MSc Bioinformatics, School of Medicine, University of Crete, Greece

    • 2011, “Automated annotation of scientific data and documents” University of Cyprus, Nicosia, Cyprus; MSc Molecular Biology, University of Crete, Greece

    • 2011, “Document clustering of Medline abstracts for concept discovery in molecular biology”, University of Cyprus, March, Nicosia, Cyprus; MSc Molecular Biology, University of Crete, Greece

    • 2009, “Reflect and OnTheFly: Automatic annotation of biological entities in web pages and scientific documents”, MSc in Bioinformatics, University of Athens, Greece

      Mixed Scientific Audience (from undergraduates to top-level researchers)

    • 2017, “Microbiome Data Interpretation”, Novo Nordisk Foundation, University of Copenhagen, Copenhagen, Denmark

    • 2014, “Text Mining and Environmental Metadata Suggestion” at the "ENA/EMG Sample Record Annotation Workshop (Jamboree)", European Bioinformatics Institute, Hinxton, UK

    • 2014, “Metadata and Standardization, OSD - a Powerful Example”, MicroB3 Summer School, From sampling to analyzing microbial diversity & function, HCMR, Crete, Greece

    • 2012, “A Short Introduction to Unix for Bioinformatics” as part of “Principles of Coalescent Theory and Applications”, HCMR, Crete, Greece

    • 2011, “Introduction to Programming Using Python”, HCMR, Crete, Greece

    • 2008, “Exploring Protein Modular Architecture course”, EMBL, Heidelberg, Germany

  • 2019 – ongoing, “Microbial community metabolism and its associations to ecosystem functioning and biogeochemical processeses”, Paragamian S, School of Biology, University of Crete, Greece

  • 2018 – ongoing, “Assessment of ecosystem function based on knowledge aggregation and data integration techniques, Next Generation Sequencing data and ecological network analyses for the interpretation of microbial ecology results”, Zafeiropoulos H, School of Biology, University of Crete, Greece

  • 2017 – 2018, “DNA-based analysis of the Heraklion gulf eukaryotic macro-organism communities: algorithm design and meta-barcoding bionformatics analysis pipeline implementation”, Zafeiropoulos, H., MSc Bioinformatics Thesis, School of Medicine, University of Crete, Greece

  • 2008, “Improved existing text mining pipeline ("Reflect")”, Horn, H., European Molecular Biology Laboratory (co-supervision)


• 2016, “Metagenomics research and the metadata annotation of the Crete Island Sampling Day 2016 samples”, Vretzakis, I., Aristotle University Thessaloniki (hosted by IMBBC)

Scientific reviewing

Journals: Database, PLOS One

Membership of scientific societies

Hellenic Bioinformatics

Genomic Standard Consortium

Awards & distinctions
  • 2009, 1st place Award, the Reflect team in: The Elsevier Grand

    Challenge: Knowledge Enhancement in the Life Sciences ($35000)

  • 2018, 1st Hellenic Foundation for Research and Innovation (HFRI

    «ΕΛΙΔΕΚ») Postdoctoral Researchers, “PREGO” project (155.000 €)

  • 2018, Travel Award to Japan - Database Center for Life Sciences, Tokyo (also in 2015, 2008)

  • 2016, Top ranking, A dictionary- and rule-based system for identification of bacteria and habitats in text by Cook H, Pafilis E, Jensen LJ. in BioNLP-ST 2016 BB3 “cat+ner” Task

  • 2015, Top ranking, EXTRACT tool, BioCreative V challenge, Interactive Annotation Task

  • Encyclopedia of Life - Rubenstein 2013 Fellowship for the ENVIRONMENTS-

    EOL project

  • 2012, Bio Triangle Project Fellowship to attend the EU-US Training in Marine


  • 2011, EMBO Short Term Fellowship (356-2011) to visit the Novo Nordisk Foundation Center for

    Protein Research in Copenhagen, Denmark

  • 2009, The Reflect system has been piloted at the Elsevier's Cell journal

  • 2009, PhD in Bioinformatics, Manga cum Laude

  • 2004-2009, EMBL PhD Program Fellowship

  • 2003, MRes in Bioinformatics with distinction

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