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Evangelos Pafilis - Publications

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Website:
http://epafilis.info/
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28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S, Doncheva NT, Jensen LJ, Pavlopoulos GA. Arena3D: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. Nar Genomics and Bioinformatics. 5: lqad053. PMID 37260509 DOI: 10.1093/nargab/lqad053  0.64
2023 Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. Frontiers in Bioinformatics. 3: 1157956. PMID 36959975 DOI: 10.3389/fbinf.2023.1157956  0.587
2022 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. PMID 35208748 DOI: 10.3390/microorganisms10020293  0.63
2021 Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I, Eliopoulos AG, Schneider R, Jensen LJ, Pafilis E, Pavlopoulos GA. OnTheFly: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. Nar Genomics and Bioinformatics. 3: lqab090. PMID 34632381 DOI: 10.1093/nargab/lqab090  0.689
2020 Zafeiropoulos H, Viet HQ, Vasileiadou K, Potirakis A, Arvanitidis C, Topalis P, Pavloudi C, Pafilis E. PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. Gigascience. 9. PMID 32161947 DOI: 10.1093/Gigascience/Giaa022  0.34
2016 Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJ, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E. Seqenv: linking sequences to environments through text mining. Peerj. 4: e2690. PMID 28028456 DOI: 10.7717/Peerj.2690  0.409
2016 Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. Journal of Biomedical Semantics. 7: 57. PMID 27664130 DOI: 10.1186/S13326-016-0097-6  0.376
2016 Wang Q, S Abdul S, 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, ... ... Pafilis E, et al. Overview of the interactive task in BioCreative V. Database : the Journal of Biological Databases and Curation. 2016. PMID 27589961 DOI: 10.1093/Database/Baw119  0.32
2016 Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C, Jensen LJ. EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database : the Journal of Biological Databases and Curation. 2016. PMID 26896844 DOI: 10.1093/Database/Baw005  0.408
2016 Ten Hoopen P, Amid C, Luigi Buttigieg P, Pafilis E, Bravakos P, Cerdeño-Tárraga AM, Gibson R, Kahlke T, Legaki A, Narayana Murthy K, Papastefanou G, Pereira E, Rossello M, Luisa Toribio A, Cochrane G. Value, but high costs in post-deposition data curation. Database : the Journal of Biological Databases and Curation. 2016. PMID 26861660 DOI: 10.1093/Database/Bav126  0.355
2016 Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, et al. EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Research Ideas and Outcomes. 2: e9774. DOI: 10.3897/Rio.2.E9774  0.329
2015 Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 31: 979. PMID 25673338 DOI: 10.7490/F1000Research.1096805.1  0.657
2015 Pafilis E, Frankild SP, Schnetzer J, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou K, Leary P, Hammock J, Schulz K, Parr CS, Arvanitidis C, Jensen LJ. ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics (Oxford, England). 31: 1872-4. PMID 25619994 DOI: 10.1093/Bioinformatics/Btv045  0.408
2014 Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 30: 3249-56. PMID 25100685 DOI: 10.1093/Bioinformatics/Btu524  0.711
2014 Faulwetter S, Markantonatou V, Pavloudi C, Papageorgiou N, Keklikoglou K, Chatzinikolaou E, Pafilis E, Chatzigeorgiou G, Vasileiadou K, Dailianis T, Fanini L, Koulouri P, Arvanitidis C. Polytraits: A database on biological traits of marine polychaetes. Biodiversity Data Journal. e1024. PMID 24855436 DOI: 10.3897/Bdj.2.E1024  0.39
2014 Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch PR, Leong JA, Meyer C, Obst M, Planes S, ... ... Pafilis E, et al. The founding charter of the Genomic Observatories Network. Gigascience. 3: 2. PMID 24606731 DOI: 10.1186/2047-217X-3-2  0.316
2013 Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Arvanitidis C, Jensen LJ. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. Plos One. 8: e65390. PMID 23823062 DOI: 10.1371/Journal.Pone.0065390  0.387
2013 Pavlopoulos GA, Pafilis E, Satagopam VP, Horn H, Arvanitidis C, Jensen L, Iliopoulos I, Schneider R. OnTheFly 2.0 beta: automated annotation of scientific documents F1000research. 4. DOI: 10.7490/F1000Research.1093964.1  0.612
2013 Pafilis E, Pavlopoulos GA, Satagopam VP, Papanikolaou N, Horn H, Arvanitidis C, Jensen LJ, Schneider R, Iliopoulos I. OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction 13th Ieee International Conference On Bioinformatics and Bioengineering, Ieee Bibe 2013. DOI: 10.1109/BIBE.2013.6701679  0.65
2011 Arvanitidis C, Faulwetter S, Chatzigeorgiou G, Penev L, Bánki O, Dailianis T, Pafilis E, Kouratoras M, Chatzinikolaou E, Fanini L, Vasileiadou A, Pavloudi C, Vavilis P, Koulouri P, Dounas C. Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT. Zookeys. 211-29. PMID 22207815 DOI: 10.3897/Zookeys.150.2149  0.328
2011 Papanikolaou N, Pafilis E, Nikolaou S, Ouzounis CA, Iliopoulos I, Promponas VJ. BioTextQuest: a web-based biomedical text mining suite for concept discovery. Bioinformatics (Oxford, England). 27: 3327-8. PMID 21994227 DOI: 10.1093/Bioinformatics/Btr564  0.432
2010 Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, ... ... Pafilis E, et al. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. Journal of Biomedical Semantics. 1: 8. PMID 20727200 DOI: 10.1186/2041-1480-1-8  0.364
2010 O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ. Reflect: A practical approach to web semantics Journal of Web Semantics. 8: 182-189. DOI: 10.1016/J.Websem.2010.03.003  0.558
2009 Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 27: 508-10. PMID 19513049 DOI: 10.1038/Nbt0609-508  0.54
2009 Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics (Oxford, England). 25: 977-8. PMID 19223449 DOI: 10.1093/Bioinformatics/Btp081  0.71
2008 Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Arena3D: visualization of biological networks in 3D. Bmc Systems Biology. 2: 104. PMID 19040715 DOI: 10.1186/1752-0509-2-104  0.665
2008 Stockinger H, Attwood T, Chohan SN, Côté R, Cudré-Mauroux P, Falquet L, Fernandes P, Finn RD, Hupponen T, Korpelainen E, Labarga A, Laugraud A, Lima T, Pafilis E, Pagni M, et al. Experience using web services for biological sequence analysis. Briefings in Bioinformatics. 9: 493-505. PMID 18621748 DOI: 10.1093/Bib/Bbn029  0.379
2007 Barbosa-Silva A, Pafilis E, Ortega JM, Schneider R. Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases. Genetics and Molecular Research : Gmr. 6: 1142-50. PMID 18273808  0.545
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