| The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation PL Buttigieg, E Pafilis, SE Lewis, MP Schildhauer, RL Walls, CJ Mungall Journal of biomedical semantics 7, 1-12, 2016 | 230 | 2016 |
| The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text E Pafilis, SP Frankild, L Fanini, S Faulwetter, C Pavloudi, A Vasileiadou, ... PloS one 8 (6), e65390, 2013 | 217 | 2013 |
| Arena3D: visualization of biological networks in 3D GA Pavlopoulos, SI O'Donoghue, VP Satagopam, TG Soldatos, E Pafilis, ... BMC systems biology 2, 1-7, 2008 | 139 | 2008 |
| Reflect: augmented browsing for the life scientist E Pafilis, SI O'Donoghue, LJ Jensen, H Horn, M Kuhn, NP Brown, ... Nature biotechnology 27 (6), 508-510, 2009 | 118 | 2009 |
| Polytraits: A database on biological traits of marine polychaetes MS Faulwetter, MV Markantonatou, MC Pavloudi, N Papageorgiou, ... Biodiversity data journal, 2014 | 105 | 2014 |
| The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows T Katayama, K Arakawa, M Nakao, K Ono, KF Aoki-Kinoshita, ... Journal of biomedical semantics 1, 1-19, 2010 | 55 | 2010 |
| PEMA: a flexible pipeline for environmental DNA metabarcoding analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes H Zafeiropoulos, HQ Viet, K Vasileiadou, A Potirakis, C Arvanitidis, ... GigaScience 9 (3), giaa022, 2020 | 54* | 2020 |
| The founding charter of the Genomic Observatories Network N Davies, D Field, L Amaral-Zettler, MS Clark, J Deck, A Drummond, ... GigaScience 3 (1), 2047-217X-3-2, 2014 | 53 | 2014 |
| Microbiome metadata standards: report of the National Microbiome Data Collaborative’s workshop and follow-on activities P Vangay, J Burgin, A Johnston, KL Beck, DC Berrios, K Blumberg, ... Msystems 6 (1), 10.1128/msystems. 01194-20, 2021 | 45 | 2021 |
| EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation E Pafilis, PL Buttigieg, B Ferrell, E Pereira, J Schnetzer, C Arvanitidis, ... Database 2016, baw005, 2016 | 44 | 2016 |
| Overview of the interactive task in BioCreative V Q Wang, S S. Abdul, L Almeida, S Ananiadou, YI Balderas-Martínez, ... Database 2016, baw119, 2016 | 39 | 2016 |
| Experience using web services for biological sequence analysis H Stockinger, T Attwood, SN Chohan, R Côté, P Cudré-Mauroux, ... Briefings in bioinformatics 9 (6), 493-505, 2008 | 36 | 2008 |
| Seqenv: linking sequences to environments through text mining L Sinclair, UZ Ijaz, LJ Jensen, MJL Coolen, C Gubry-Rangin, ... PeerJ 4, e2690, 2016 | 32 | 2016 |
| BioTextQuest + : a knowledge integration platform for literature mining and concept discovery N Papanikolaou, GA Pavlopoulos, E Pafilis, T Theodosiou, R Schneider, ... Bioinformatics 30 (22), 3249-3256, 2014 | 32 | 2014 |
| Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT C Arvanitidis, S Faulwetter, G Chatzigeorgiou, L Penev, O Bánki, ... ZooKeys, 211, 2011 | 30 | 2011 |
| ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life E Pafilis, SP Frankild, J Schnetzer, L Fanini, S Faulwetter, C Pavloudi, ... Bioinformatics 31 (11), 1872-1874, 2015 | 27 | 2015 |
| Beach parties: a case study on recreational human use of the beach and its effects on mobile arthropod fauna L Fanini, G Zampicinini, E Pafilis Ethology Ecology & Evolution 26 (1), 69-79, 2014 | 25 | 2014 |
| 0s and 1s in marine molecular research: A regional HPC perspective H Zafeiropoulos, A Gioti, S Ninidakis, A Potirakis, S Paragkamian, ... GigaScience 10 (8), giab053, 2021 | 23 | 2021 |
| Reflect: A practical approach to web semantics SI O’Donoghue, H Horn, E Pafilis, S Haag, M Kuhn, VP Satagopam, ... Web Semantics: Science, Services and Agents on the World Wide Web 8 (2-3 …, 2010 | 23 | 2010 |
| A dictionary-and rule-based system for identification of bacteria and habitats in text HV Cook, E Pafilis, LJ Jensen Proceedings of the 4th BioNLP shared task workshop, 50-55, 2016 | 22 | 2016 |
