Evangelos Pafilis is a Post-doctoral researcher at the Biodiversity Lab in the Institute of Marine Biology and Genetics at the Hellenic Center of Marine Research in Crete, Greece.
He is working on MARBIGEN, a European Comission FP7 project, aiming at supporting marine biodiversity and genomics research in the Eastern Mediterranean (Click here to view Evangelos's MARBIGEN profile).
In the context of this project he is:
- gaining more experience in biodiversity informatics
- working closely with experimental biologists in the field so as to understand their specific requirements. This includes tasks ranging from specimen sampling to genetic analyses
- experimenting with novel web tools
- employing his experience in data management, data integration, document annotation, clustering, and network analysis/visualisation to support his associates
Prior to MARBIGEN Evangelos was a Post-doctoral researcher at the Computational Biology Group at the University of Crete.
He was working on a text mining system of biological databases aiming to support knowledge discovery by concept association. For this purpose he was involved in developing web-based applications that employ document clustering, ontology generation and graph-based visualisations.
The main motive was to replace incomprehensible long lists and tables of results with intuitive term-based interactive graphs representing group of records, describing different biological phenomena.
In January 2009, Evangelos completed his PhD studies at the Data Integration and Knowledge Management group at the European Molecular Biology Laboratory (EMBL) (PhD awarded jointly with the University of Heidelberg).
For his PhD project Evangelos employed technologies, such as web services and browser extensions, and combined them with existing data integration and text mining solutions.
The end result was the automated dissemination of biological knowledge pertinent to the biological entities and the small molecules mentioned in a web page and/or a user document.
His target user-groups range from plain-users to developers. Evangelos is involved in developing simple-to-use tools, such as Reflect and OnTheFly, for the former and programmatic interfaces for the latter.
Before moving to Heidelberg, Evangelos received his MRes in Bioinformatics from the University of Glasgow and completed a placement as a research assistant at XTeCT, a project that introduced him to the field of data integration in life sciences.
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PhD Thesis: Web-based data integration and text mining techniques to accelerate biomedical research. EMBL - University of Heidelberg, 2009, magna cum laude [PDF]
Master's Project: Visualisation Mechanisms Supporting Genotype Analysis. University of Glasgow, 2003, Distinction [DOC]
Topics of Interest: augmented browsing, named entity recognition, text mining, web services, browser extensions, data integration, biological databases, data visualisation, automated experimental result annotation, scientific publishing, summary sheets, document annotation, singe nucleotide polymorphisms, proteomics, collaborative and interactive database curation
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