Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. - Baltoumas, Fotis A.; Karatzas, Evangelos; Páez-Espino, David; Venetsianou, Nefeli K.; Aplakidou, Eleni; Oulas, Anastasis; Finn, Robert D.; Ovchinnikov, Sergey; Pafilis, Evangelos; Kyrpides, Nikos; Pavlopoulos, Georgios A. (Frontiers Bioinform., 2023)

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. - Waterhouse, Robert M.; Adam-Blondon, Anne-Françoise; Balech, Bachir; Barta, Endre; Heil, Katharina F.; Hughes, Graham M.; Jermiin, Lars S.; Kalas, Matús; Lanfear, Jerry; Pafilis, Evangelos; Papageorgiou, Aristotelis C.; Psomopoulos, Fotis E.; et al. (F1000Research, 2023)

Establishment of computational biology in Greece and Cyprus: Past, present, and future. - Chasapi, Anastasia; Aivaliotis, Michalis; Angelis, Lefteris; Chanalaris, Anastasios; Iliopoulos, Ioannis; Kappas, Ilias; Karapiperis, Christos; Kyrpides, Nikos; Pafilis, Evangelos; Panteris, Eleftherios; Topalis, Pantelis; Tsiamis, George; et al. (PLoS Comput. Biol., 2019)

Value, but high costs in post-deposition data curation. - Hoopen, Petra ten; Amid, Clara; Buttigieg, Pier Luigi; Pafilis, Evangelos; Bravakos, Panos; Cerdeño-Tárraga, Ana; Gibson, Richard; Kahlke, Tim; Legaki, Aglaia; Murthy, Kada Narayana; Papastefanou, Gabriella; Pereira, Emiliano; et al. (Database J. Biol. Databases Curation, 2016)

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. - Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl (Database J. Biol. Databases Curation, 2016)

Overview of the interactive task in BioCreative V. - Wang, Qinghua; Syed-Abdul, Shabbir; Almeida, Lara; Ananiadou, Sophia; Balderas-Martínez, Yalbi I.; Batista-Navarro, Riza; Campos, David; Chilton, Lucy; Chou, Hui-Jou; Contreras, Gabriela; Cooper, Laurel; Dai, Hong-Jie; et al. (Database J. Biol. Databases Curation, 2016)

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. - Buttigieg, Pier Luigi; Pafilis, Evangelos; Lewis, Suzanna E.; Schildhauer, Mark P.; Walls, Ramona L.; Mungall, Christopher J. (J. Biomed. Semant., 2016)

A dictionary- and rule-based system for identification of bacteria and habitats in text. - Cook, Helen; Pafilis, Evangelos; Jensen, Lars Juhl (2016)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Papanikolaou, Nikolas; Pavlopoulos, Georgios A.; Pafilis, Evangelos; Theodosiou, Theodosios; Schneider, Reinhard; Satagopam, Venkata P.; Ouzounis, Christos A.; Eliopoulos, Aristides G.; Promponas, Vasilis J.; Iliopoulos, Ioannis (Bioinform., 2015)

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. - Pafilis, Evangelos; Pletscher-Frankild, Sune; Schnetzer, Julia; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, Christina; Vasileiadou, Katerina; Leary, Patrick; Hammock, Jennifer; Schulz, Katja; Parr, Cynthia Sims; Arvanitidis, Christos; et al. (Bioinform., 2015)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Papanikolaou, Nikolas; Pavlopoulos, Georgios A.; Pafilis, Evangelos; Theodosiou, Theodosios; Schneider, Reinhard; Satagopam, Venkata P.; Ouzounis, Christos A.; Eliopoulos, Aristides G.; Promponas, Vasilis J.; Iliopoulos, Ioannis (Bioinform., 2014)

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction. - Pafilis, Evangelos; Pavlopoulos, Georgios A.; Satagopam, Venkata P.; Papanikolaou, Nikolas; Horn, Heiko; Arvanitidis, Christos; Jensen, Lars Juhl; Schneider, Reinhard; Iliopoulos, Ioannis (2013)

BioTextQuest: a web-based biomedical text mining suite for concept discovery. - Papanikolaou, Nikolas; Pafilis, Evangelos; Nikolaou, Stavros; Ouzounis, Christos A.; Iliopoulos, Ioannis; Promponas, Vasilis J. (Bioinform., 2011)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F.; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord H.; et al. (J. Biomed. Semant., 2010)

Reflect: A practical approach to web semantics. - O'Donoghue, Seán I.; Horn, Heiko; Pafilis, Evangelos; Haag, Sven; Kuhn, Michael; Satagopam, Venkata P.; Schneider, Reinhard; Jensen, Lars Juhl (J. Web Semant., 2010)

Web-based named entity recognition and data integration to accelerate molecular biology research. - Pafilis, Evangelos (2009)

OnTheFly: a tool for automated document-based text annotation, data linking and network generation. - Pavlopoulos, Georgios A.; Pafilis, Evangelos; Kuhn, Michael; Hooper, Sean D.; Schneider, Reinhard (Bioinform., 2009)

Experience using web services for biological sequence analysis. - Stockinger, Heinz; Attwood, Teresa K.; Chohan, Shahid Nadeem; Côté, Richard G.; Cudré-Mauroux, Philippe; Falquet, Laurent; Fernandes, Pedro L.; Finn, Robert D.; Hupponen, Taavi; Korpelainen, Eija; Labarga, Alberto; Laugraud, Aurélie; et al. (Briefings Bioinform., 2008)

Arena3D: visualization of biological networks in 3D. - Pavlopoulos, Georgios A.; O'Donoghue, Seán I.; Satagopam, Venkata P.; Soldatos, Theodoros G.; Pafilis, Evangelos; Schneider, Reinhard (BMC Syst. Biol., 2008)

Index-Driven XML Data Integration to Support Functional Genomics. - Hunt, Ela; Pafilis, Evangelos; Tulloch, Inga; Wilson, John (2004)