Book Chapter

• Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge.

  Evangelos Pafilis, Heiko Horn, Nigel P. Brown (submitted) To appear within 2012 in Wiley's Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data

Articles

• Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT.

  Arvanitidis, C, Faulwetter S, Chatzigeorgiou G, Penev L, Bankí O, Dailianis T, Pafilis E, Kouratoras M, Chatzinikolaou E, Fanini L et al.  (2011). Zookeys, 2011, 150:211-219. doi: 10.3897/zookeys.150.2149 [PubMed] [HTML] [PDF]

• BioTextQuest: a web-based biomedical text mining suite for concept discovery.

  Papanikolaou, N, Pafilis E, Nikolaou S, Ouzounis CA, Iliopoulos I, Promponas VJ.  (2011).  Bioinformatics, 2011, 27(23):3327-3328. doi: 10.1093/bioinformatics/btr564 [PubMed] [HTML] [PDF]

• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

  Toshiaki Katayama et al., The DBCLS BioHackathon Consortium. (2010) Journal of Biomedical Semantics, 2010, 1:8 doi:10.1186/2041-1480-1-8 [PubMed] [HTML] [PDF]

• Reflect: a practical approach to web semantics.

  Sean I. O'Donoghue, Heiko Horn, Evangelos Pafilis, Sven Haag, Michael Kuhn, Venkata P. Satagopam, Reinhard Schneider, Lars J. Jensen. (2010) Journal of Web Semantics, 2010, ISSN 1570-8268 (doi: 10.1016/j.websem.2010.03.003) [HTML]

• Reflect: Augmented Browsing for the Life Scientist.

  Evangelos Pafilis, Sean I. O'Donoghue, Lars Jensen, Heiko Horn, Michael Kuhn, Nigel Brown, Reinhard Schneider. (2009) Nature Biotechnology, 2009, 27, 508-510 (doi:10.1038/nbt0609-508) [PubMed] [HTML] [PDF]

• OnTheFly: A Tool for automated document-based text annotation, data linking and network generation.

  Georgios A. Pavlopoulos, Evangelos Pafilis, Michael Kuhn, Sean D Hooper, Reinhard Schneider. (2009) Bioinformatics 2009, Apr 1;25(7):977-8 (doi:10.1093/bioinformatics/btp081) [PubMed] [HTML] [PDF]

• Arena3D: Visualization of Biological Networks in 3D.

  Georgios A. Pavlopoulos, Sean I. O'Donoghue, Venkata P. Satagopam, Theodoros Soldatos, Evangelos Pafilis, Reinhard Schneider. (2008) BMC Systems Biology, 2008, 2:104 (doi:10.1186/1752-0509-2-104) [PubMed] [HTML] [PDF]

• Experience using web services for biological sequence analysis.

  Stockinger H, Attwood T, Chohan SN, Cote R, Cudre-Mauroux P, Falquet L, Fernandes P, Finn RD, Hupponen T, Korpelainen E, Labarga A, Laugraud A, Lima T, Pafilis E, Pagni M, Pettifer S, Phan I, Rahman N. (2008) Briefings in Bioinformatics, 2008, 9(6):493-505 (doi:10.1093/bib/bbn029) [PubMed] [HTML] [PDF]

• Development of SRS.php, a SOAP-based library for data acquisition from integrated biological databases.

  Barbosa-Silva, A., Ortega, J. M., Pafilis, E., Schneider, R. (2007) Genetics And Molecular Research, 2007, 6(4):1142-1150 [PubMed] [HTML] [PDF]

• Index-Driven XML Data Integration to Support Functional Genomics.

  Ela Hunt, Evangelos Pafilis, Inga Tulloch and John Wilson. (2004). Proceeding of the International Workshop on Data Integration in Life Sciences, DILS'04, Lecture Notes in Computer Science 2994. pp95-109 [HTML] [PDF]

Posters

• OnTheFly 2.0: A Service to automatically annotate files and extract biological information.

  HSCBB 2011, Patras, Greece, Pafilis et al. [PDF]

• wwwTextQuest: A Biomedical Text Mining Suite for Concept Discovery.

  HSCBB 2010, Alexandroupoli, Greece, Papanikolaou, Pafilis et al. [PDF]

• Reflect: improving how biological research is communicated.

  ISMB 2010, Boston, USA, O'Donoghue et al. [PDF]

• Visualization and Data Integration Techniques in Systems Biology.

  HSCBB 2009, Athens, Greece, Pavlopoulos et al. [PDF]

• Unified access to bioinformatic resources: SRS, Biomart and EB-Eye.

  ECCB 2008, Italy, Labarga et al. [PDF]

• Reflect and OnTheFly, automated annotation of web sites and documents.

  HSCBB 2008, Thessaloniki, Greece, Pafilis et al. [PDF] (in Greek)

• Reflect: automated markup of biological terms in web pages.

  EEBE 2008, Thessaloniki, Greece, Pafilis et al. [PDF] (in Greek)

• Cross-discipline knowledge and data integration.

  ISMB 2007, Wien, Austria, Pafilis et al. [PDF]

• Cross-discipline knowledge integration.

  ECCB 2006, Eilat Israel, Pafilis et al. [PDF]

• XTeCT, Using XML Technology to enhance the search for treatment targets.

  ISMB 2004, Glasgow, UK, Pafilis et al. [PDF]