Pafilis E, Brown NP, Horn H. Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge. In: Elloumi M, editor. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data. Wiley; Submitted.
Pafilis E, Frankhild SP, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, et al. The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text. PLOS One. In Press.
Hardisty A, Roberts D, Addink W, Aelterman B, Agosti D, Amaral-Zettler L, et al. A decadal view of biodiversity informatics: challenges and priorities. BMC Ecology. 2013;13:16.
Papanikolaou N, Pafilis E, Nikolaou S, Ouzounis CA, Iliopoulos I, Promponas VJ. BioTextQuest: a web-based biomedical text mining suite for concept discovery. Bioinformatics. 2011;27(23):3327-8.
Arvanitidis C, Faulwetter S, Chatzigeorgiou G, Penev L, Bankí O, Dailianis T, et al. Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT. Zookeys. 2011;150:211-29.
O’Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, et al. Reflect: A practical approach to web semantics. Web Semantics: Science, Services and Agents on the World Wide Web. 2010;8(2-3):182-9.
Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, et al. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics. 2010;1(1):8.
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics. 2009;25(7):977-8.
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, et al. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 2009;27(6):508-10.
Pafilis E. Web-based data integration and text mining techniques to accelerate biomedical research (PhD). Heidelberg: EMBL (European Molecular Biology Laboratory) – University of Heidelberg (joint PhD); 2009.