Publications

Below is a set of (selected) PREGO-related publications. A extended listing of the team publications can be found here

Research articles

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

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

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

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

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.
Abstract Full text WWW

Preprints

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

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

Theses

Zafeiropoulos, H., 2022. Microbial communities through the lens of high throughput sequencing, data integration and metabolic networks analysis (PhD Thesis). University of Crete, Greece, Herakleion, Crete, Greece. Abstract DOI

Theologi, O., 2021. Chemical text and association rule mining to facilitate the study of metabolic processes in hyperthermophilic microorganisms. MSc Thesis 89. National and Kapodistrian University of Athens, Greece. Abstract Full Text WWW

Conference proceedings

Savvas Paragkamian, Haris Zafeiropoulos, Stylianos Ninidakis, Georgios A. Pavlopoulos, Lars Juhl Jensen, Evangelos Pafilis. PREGO (Process, Environment, Organism), mining literature and -omics (meta)data to associate microorganisms, biological processes, and environment types. 9th Conference of MIKROBIOKOSMOS. 16 to 18 December 2021, Athens, Greece. Oral presentation

Haris Zafeiropoulos, Savvas Paragkamian, Christina Pavloudi, George Tsamis, Stylianos Ninidakis, Ioulia Santi, Georgios A. Pavlopoulos, Lars Juhl Jensen, Evangelos Pafilis. PREGO (Process, Environment, Organism), mining literature and -omics (meta)data to associate microorganisms, biological processes, and environment types. World Microbe Forum 2021. 20 - 24 June. iPoster.

Zafeiropoulos H, Gargan L, Pavloudi C, Pafilis E, Carlsson J (2021) Bacteria are everywhere, even in your COI data: Τhe art of getting to know the unknown unknowns and shine light on the dark matter! 1st DNAQUA International Conference (March 9-11, 2021). ARPHA Conference Abstracts 4: e64966. https://doi.org/10.3897/aca.4.e64966

Zafeiropoulos H, Pavloudi C, Pafilis E (2021) PEMA v2: addressing metabarcoding bioinformatics analysis challenges. 1st DNAQUA International Conference (March 9-11, 2021). ARPHA Conference Abstracts 4: e64902. https://doi.org/10.3897/aca.4.e64902

Haris Zafeiropoulos, Savvas Paragkamian, Christina Pavloudi, George Tsamis, Stylianos Ninidakis, Ioulia Santi, Georgios A. Pavlopoulos, Lars Juhl Jensen, Evangelos Pafilis. Mining literature and -omics (meta)data to associate microorganisms, biological processes, and environment types. FEMS Online Conference on Microbiology 2020. 28 – 31 October 2020. Video Recordings.

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

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