Publications

Research articles

Paragkamian, S., Sarafidou, G., Mavraki, D., Pavloudi, C., Beja, J., Eliezer, M., Lipizer, M., Boicenco, L., Vandepitte, L., Perez-Perez, R., Zafeiropoulos, H., Arvanitidis, C., Pafilis, E., Gerovasileiou, V., 2022. Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow. Frontiers in Marine Science, 9. Abstract Full Text WWW

Zafeiropoulos, H.; Paragkamian, S.; Ninidakis, S.; Pavlopoulos, GA.; Jensen, LJ.; Pafilis, E. PREGO: a literature and data-mining resource to associate microorganisms, biological processes, and environment types. Microorganisms 10.2 (2022). Abstract Full Text WWW

Lucia Fanini, Omar Defeo, Michael Elliott, Savvas Paragkamian, Maurizio Pinna, Vanessa-Sarah Salvo, Coupling beach ecology and macroplastics litter studies: Current trends and the way ahead, Marine Pollution Bulletin , Volume 173, Part A, 2021, 112951, ISSN 0025-326X, Abstract Full Text WWW

Fotis A Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Savvas Paragkamian, Foteini Thanati, Ioannis Iliopoulos, Aristides G Eliopoulos, Reinhard Schneider, Lars Juhl Jensen, Evangelos Pafilis, Georgios A Pavlopoulos, OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis, NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab090. Abstract Full Text WWW

Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis, Savvas Paragkamian, Nelina Angelova, Aglaia Antoniou, Theodoros Danis, Eliza Kaitetzidou, Panagiotis Kasapidis, Jon Bent Kristoffersen, Vasileios Papadogiannis, Christina Pavloudi, Quoc Viet Ha, Jacques Lagnel, Nikos Pattakos, Giorgos Perantinos, Dimitris Sidirokastritis, Panagiotis Vavilis, Georgios Kotoulas, Tereza Manousaki, Elena Sarropoulou, Costas S Tsigenopoulos, Christos Arvanitidis, Antonios Magoulas, Evangelos Pafilis, 0s and 1s in marine molecular research: a regional HPC perspective, GigaScience, Volume 10, Issue 8, August 2021, giab053. Abstract Full Text WWW

Vangay, P.; Burgin, J.; Johnston, A.; Beck, K.L.; Berrios, D.C.; Blumberg, K.; Canon, S.; Chain, P.; Chandonia, J.-M.; Christianson, D.; Pafilis, E.; et al. *Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities. *mSystems 2021, 6, e01194-20. Abstract Full Text WWW

Zafeiropoulos H, Viet HQ, Vasileiadou K, Potirakis A, Arvanitidis C, Topalis P, Pavloudi C, Pafilis E 2020. PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. GigaScience 2020 9:3:giaa022. Abstract Full text WWW

Chasapi A, Aivaliotis M, Angelis L, Chanalaris A, Iliopoulos I, Kappas I, Karapiperis C, Kyrpides NC, Pafilis E, Panteris E, Topalis P, Tsiamis G, Vizirianakis IS, Vlassi M, Promponas VJ, Ouzounis CA 2019 Establishment of computational biology in Greece and Cyprus: Past, present, and future. PLoS Comput Biol., 15(12):e1007532. Abstract Full text

Varsos C, Patkos T, Oulas A, Pavloudi C, Gougousis A, Ijaz U, Filiopoulou I, Pattakos N, Vanden Berghe E, Fernández-Guerra A, Faulwetter S, Chatzinikolaou E, Pafilis E, Bekiari C, Doerr M, Arvanitidis C 2016. Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab). Biodiversity Data Journal 4: e8357. Abstract Full text WWW

Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C and Pafilis E 2016. Seqenv: linking sequences to environments through text mining. PeerJ, 4:e2690.
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Wang Q, Abdul SS, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L and Arighi CN (2016). Overview of the interactive task in BioCreative V. Database, 2016:baw119.
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Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C and Jensen LJ (2016). EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database, 2016:baw005.
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Pafilis E, Pletscher-Frankild S, Schnetzer J, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou V, Leary P, Hammock J, Schulz K, Parr CS, Arvanitidis C and Jensen LJ (2015). ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics, 31:1872-1874.
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Pafilis E, Pletscher-Frankild S, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Arvanitidis C and Jensen LJ (2013). The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text. PLOS ONE, 8:e65390.
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O’Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R and Jensen LJ (2010). Reflect: a practical approach to web semantics. Journal of Web Semantics, 8:182-189.
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Pafilis E, O’Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP and Schneider R (2009). Reflect: augmented browsing for the life scientist. Nature Biotechnology, 27:508-510.
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Preprints

Luoma, J., Nastou, K.C., Ohta, T., Toivonen, H., Pafilis, E., Jensen, L.J., Pyysalo, S., 2023. S1000: A better taxonomic name corpus for biomedical information extraction. bioRxiv preprint 2023.02.20.528934 Abstract Full Text WWW

Kokoli, M., Karatzas, E., Baltoumas, F.A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, N.T., Jensen, L.J., Pavlopoulos, G., 2022. Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. bioRxiv preprint 2022.10.01.510435 Abstract Full Text WWW

Aravanopoulos, F.A., Arvanitidis, C., Bista, I., Dailianis, T., Galanis, A., Ioannidis, P., Kapli, P., Klapa, M.I., Kolovos, P., Kotoulas, G., Magoulas, A.N., Manousaki, T., Pafilis, E., Papageorgiou, A.C., Papakostas, S., Paragkamian, S., Pavlidis, P., Pavloudi, C., Poulakakis, N., Psomopoulos, F., Reczko, M., Sagonas, K., Stamatakis, A., Theofanopoulou, C., Triantafyllidis, A., Tsigenopoulos, C.S., Vasileiadou, K., Zafeiropoulos, H., 2022. Building the Molecular Biodiversity Greece Community. Zenodo preprint 7078816 Abstract Full Text

Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Savvas Paragkamian, Foteini Thanati, Ioannis Iliopoulos, Aristides G. Eliopoulos, Reinhard Schneider, Lars Juhl Jensen, Evangelos Pafilis, Georgios A. Pavlopoulos. 2021 OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis bioRxiv preprint 2021.05.14.444150. Abstract Full Text WWW

Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis, Savvas Paragkamian, Nelina Angelova, Aglaia Antoniou, Theodoros Danis, Eliza Kaitetzidou, Panagiotis Kasapidis, Jon Bent Kristoffersen, Vasileios Papadogiannis, Christina Pavloudi, Quoc Viet Ha, Jacques Lagnel, Nikos Pattakos, Giorgos Perantinos, Dimitris Sidirokastritis, Panagiotis Vavilis, Georgios Kotoulas, Tereza Manousaki, Elena Sarropoulou, Costas S Tsigenopoulos, Christos Arvanitidis, Antonios Magoulas and Evangelos Pafilis. 2021. The IMBBC HPC facility: history, configuration, usage statistics and related activities (1.0.0). Zenodo preprint 4665308. Abstract Full Text WWW

Zafeiropoulos H, Viet HQ, Vasileiadou K, Potirakis A, Arvanitidis C, Topalis P, Pavloudi C, Pafilis E, 2019. PEMA: from the raw .fastq files of 16S rRNA and COI marker genes to the (M)OTU-table, a thorough metabarcoding analysis. bioRxiv preprint 709113. Abstract Full text WWW

Arvanitidis CD, Warwick RM, Somerfield PJ, Pavloudi C, Pafilis E, Oulas A, Chatzigeorgiou G, et al. 2018. Research Infrastructures offer capacity to address scientific questions never attempted before: Are all taxa equal? PeerJ Preprints 6:e26819v2 Abstract Full text

Conference proceedings

Pafilis E, Bērziņš R and Jensen LJ (2017). EXTRACT 2.0: text-mining-assisted interactive annotation of biomedical named entities and ontology terms. Proceedings of Bio-Ontologies 2017.
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Cook H, Pafilis E and Jensen LJ (2016). A dictionary- and rule-based system for identification of bacteria and habitats in text. Proceedings of the 4th BioNLP Shared Task Workshop, 50-55.
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Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C and Jensen LJ (2015). EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Proceedings of BioCreative V, 384-395.
WWW

Wang Q, Abdul SS, Almeida L, Ananiadou S, Balderas-Martnez YI, Batista-Navarro R, Campos D, Chilton L, Chou H-J, Contreras G, Cooper L, Dai H-J, Fluck J, Gama S, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue T, Keseler I, Madan S, Matos S, McQuilton P, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Salgado D, Singh O, Stefancsik R, Su C-H, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-aryamontri A, Laulederkind S, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Hirschman L and Arighi C (2015). Overview of the Interactive Task in BioCreative V. Proceedings of BioCreative V, 364-383.

Book chapters

Pafilis, E, Horn H, Brown NP. (2014) Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Wiley:ISBN:978-1-1181-3273-9