Degree, Department, University, Town (optional), Country
2009
Bioinformatics PhD, EMBL - Ruprecht Karl University of Heidelberg, Heidelberg, Germany, Magna cum Laude
2003
Bioinformatics MRes, University of Glasgow, Glasgow, United Kingdom, Distinction
2002
Biology BS, University of Crete, Herakleion Crete, Greece
Work Experience
Year (start)
Position – Organization, Town (optional), Country
2018
Bioinformatics and Biodiversity Informatics Researcher C at IMBBC, HCMR, Crete, Greece
2011
Postdoctoral Researcher in Bioinformatics and Biodiversity Informatics at IMBBC, HCMR, Crete, Greece
2009
Post-doctoral Researcher in Bioinformatics, School of Medicine, University of Crete, Greece
Personal skills
Mother tongue(s)
Greek
Other language(s)
Language
Basic/Intermediate/Proficient
English
Proficient
German
Intermediate
Computer skills
Advanced
Other skills
Photography
Educational activities
Teaching experience
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
Supervision
PhD
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
MSc
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)
Practicals
• 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
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
Bioinformatics
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
