Publications

Research articles

2026

Loukas A, Kalaentzis K, Venetsianou NK, Damianou C, Paragkamian S, Lagani V, Jensen LJ, Pafilis E. 2026. CCMRI: a classification and curated database of climate change-related microbiome studies. Sci Rep 16, 20829 (2026); https://doi.org/10.1038/s41598-026-51914-z Abstract Full Text WWW

Venetsianou NK, Paragkamian S, Kalaentzis K, Loukas A, Damianou C, Lagani V, Jensen LJ, Pafilis E. 2026. LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity. Microb Ecol. 89, 104 (2026) doi: 10.1007/s00248-026-02730-5. Abstract Full Text WWW

2025

Holm JB, Paragkamian S, Humphreys M, Chatterjee A, Yarwood S, Gaimaro J, et al. 2025. First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity. Environmental Microbiome. 2025; doi: 10.1186/s40793-025-00752-z. Abstract Full Text WWW

Finn RD, Balech B, Burgin J et al. 2025. Establishing the ELIXIR Microbiome Community [version 2; peer review: 2 approved, 1 approved with reservations]. F1000Research 2025, 13(ELIXIR):50 (https://doi.org/10.12688/f1000research.144515.2) Abstract Full Text WWW

2024

Waterhouse RM, Adam-Blondon AF, Balech B et al. 2024. The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity [version 2; peer review: 3 approved]. F1000Research 2024, 12(ELIXIR):499 (https://doi.org/10.12688/f1000research.133724.2) Abstract Full Text WWW

Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. 2024. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J. 2024 May 3;23:2011-2033. doi: 10.1016/j.csbj.2024.04.060. Abstract Full Text

2023

Zafeiropoulos H, Beracochea M, Ninidakis S, Exter K, Potirakis A, De Moro G, et al. 2023. metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data. GigaScience. 2023; doi: 10.1093/gigascience/giad078. Abstract Full Text WWW

Luoma J, Nastou K, Ohta T, Toivonen H, Pafilis E, Jensen LJ, Pyysalo S. 2023. S1000: a better taxonomic name corpus for biomedical information extraction. Bioinformatics. 2023 Jun 1;39(6):btad369. doi: 10.1093/bioinformatics/btad369. Abstract Full Text WWW

Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S, Doncheva NT, Jensen LJ, Pavlopoulos GA. 2023. Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. NAR Genom Bioinform. 2023 May 30;5(2):lqad053. doi: 10.1093/nargab/lqad053. Abstract Full Text WWW

Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. 2023. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. Front Bioinform. 2023 Mar 3;3:1157956. doi: 10.3389/fbinf.2023.1157956. Abstract Full Text

2022

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. 2022. PREGO: a literature and data-mining resource to associate microorganisms, biological processes, and environment types. Microorganisms 10.2 (2022). Abstract Full Text WWW

2021

Lucia Fanini, Omar Defeo, Michael Elliott, Savvas Paragkamian, Maurizio Pinna, Vanessa-Sarah Salvo. 2021. 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, 2021. 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, 2021. 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 KL, et al. 2021. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities. mSystems. 2021 Feb 23;6(1):e01194-20. doi: 10.1128/mSystems.01194-20. Erratum in: mSystems. 2021 May 4;6(3):e00273-21. doi: 10.1128/mSystems.00273-21. Abstract Full Text WWW

2020

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

2019

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

2016

Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ. 2016 The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. Journal of Biomedical Semantics., 7,57
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.
Abstract Full text

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.
Abstract Full text

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.
Abstract Full text WWW

Vasileiadou K, Pavloudi C, Kalantzi I, Apostolaki ET, Chatzigeorgiou G, Chatzinikolaou E, Pafilis E, Papageorgiou N, Fanini L, Konstas S, Fragopoulou N, Arvanitidis C. 2026. Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece). Biodivers Data J. 2016 Nov 1;(4):e8233. doi: 10.3897/BDJ.4.e8233. Abstract Full text

ten Hoopen P, Amid C, Buttigieg PL, et al. 2016. Value, but high costs in post-deposition data curation. Database (Oxford). 2016 Feb 9;2016:bav126. doi: 10.1093/database/bav126. 26861660 Abstract Full text

2015

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.
Abstract Full text WWW

2014

Davies N, Field D, Amaral-Zettler L, et al. 2014. The founding charter of the Genomic Observatories Network. Gigascience. 2014 Mar 7;3(1):2. doi: 10.1186/2047-217X-3-2. Abstract Full text

Papanikolaou N, Pavlopoulos GA, Pafilis E, et al. 2014. BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery. Bioinformatics. 2014 Nov 15;30(22):3249-56. doi: 10.1093/bioinformatics/btu524. Epub 2014 Aug 6. Erratum in: Bioinformatics. 2015 Mar 15;31(6):979. doi: 10.1093/bioinformatics/btv029. Abstract Full text WWW

Faulwetter S, Markantonatou V, Pavloudi C, et al. 2014. Polytraits: A database on biological traits of marine polychaetes. Biodivers Data J. 2014 Jan 17;(2):e1024. doi: 10.3897/BDJ.2.e1024. Abstract Full text

Fanini, L., Zampicinini, G., & Pafilis, E. 2014. Beach parties: a case study on recreational human use of the beach and its effects on mobile arthropod fauna. Ethology Ecology & Evolution, 26(1), 69–79. https://doi.org/10.1080/03949370.2013.821674 Abstract Full text

2013

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.
Abstract Full text WWW

Schriml, L., Mizrachi, I., Sterk, P. et al. 2013. The 15th Genomic Standards Consortium meeting. Stand in Genomic Sci 8, 124–164 (2013). https://doi.org/10.4056/sigs.3457 Abstract Full text

2011

Arvanitidis C, Faulwetter S, Chatzigeorgiou G, et al. 2011. Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT. ZooKeys 150: 211-229. https://doi.org/10.3897/zookeys.150.2149 Abstract Full text

2010

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.
Full text

Katayama T, Arakawa K, Nakao M, et al. 2010. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium. J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8. Abstract Full text

2009

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. Abstract Full text WWW

2008

Stockinger H, Attwood T, Chohan SN, et al. 2008. Experience using web services for biological sequence analysis. Brief Bioinform. 2008 Nov;9(6):493-505. doi: 10.1093/bib/bbn029. Abstract Full text

Preprints

2022

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

2021

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

2019

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

2018

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

2017

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.
Full text WWW

2016

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.
Full text

2015

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