Evangelos Pafilis

This user account status is Approved

2022

Zafeiropoulos, Haris; Paragkamian, Savvas; Ninidakis, Stelios; Pavlopoulos, Georgios A; Jensen, Lars Juhl; Pafilis, Evangelos

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types Journal Article

Microorganisms, 10 (2), pp. 293, 2022, ISSN: 2076-2607.

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2021

Baltoumas, Fotis A; Zafeiropoulou, Sofia; Karatzas, Evangelos; Paragkamian, Savvas; Thanati, Foteini; Iliopoulos, Ioannis; Eliopoulos, Aristides G; Schneider, Reinhard; Jensen, Lars Juhl; Pafilis, Evangelos; Pavlopoulos, Georgios A

OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis Journal Article

NAR Genomics and Bioinformatics, 3 (4), pp. lqab090, 2021, ISSN: 2631-9268.

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Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L; Berrios, Daniel C; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V; Damerow, Joan; Duncan, William D; Dundore-Arias, Jose Pablo; Fagnan, Kjiersten; Galazka, Jonathan M; Gibbons, Sean M; Hays, David; Hervey, Judson; Hu, Bin; Hurwitz, Bonnie L; Jaiswal, Pankaj; Joachimiak, Marcin P; Kinkel, Linda; Ladau, Joshua; Martin, Stanton L; McCue, Lee Ann; Miller, Kayd; Mouncey, Nigel; Mungall, Chris; Pafilis, Evangelos; Reddy, T B K; Richardson, Lorna; Roux, Simon; Shaffer, Justin P; Sundaramurthi, Jagadish Chandrabose; Thompson, Luke R; Timme, Ruth E; Zheng, Jie; Wood-Charlson, Elisha M; Eloe-Fadrosh, Emiley A

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities Journal Article

6 , 2021.

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Zafeiropoulos, Haris; Gioti, Anastasia; Ninidakis, Stelios; Potirakis, Antonis; Paragkamian, Savvas; Angelova, Nelina; Antoniou, Aglaia; Danis, Theodoros; Kaitetzidou, Eliza; Kasapidis, Panagiotis; Kristoffersen, Jon Bent; Papadogiannis, Vasileios; Pavloudi, Christina; Ha, Quoc Viet; Lagnel, Jacques; Pattakos, Nikos; Perantinos, Giorgos; Sidirokastritis, Dimitris; Vavilis, Panagiotis; Kotoulas, Georgios; Manousaki, Tereza; Sarropoulou, Elena; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Pafilis, Evangelos

0s and 1s in marine molecular research: a regional HPC perspective Journal Article

GigaScience, 10 (8), pp. giab053, 2021, ISSN: 2047-217X.

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2020

Zafeiropoulos, Haris; Viet, Ha Quoc; Vasileiadou, Katerina; Potirakis, Antonis; Arvanitidis, Christos; Topalis, Pantelis; Pavloudi, Christina; Pafilis, Evangelos

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes Journal Article

GigaScience, 9 (3), 2020, ISSN: 2047-217X, (_eprint: https://academic.oup.com/gigascience/article-pdf/9/3/giaa022/32894405/giaa022.pdf).

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2019

Chasapi, Anastasia; Aivaliotis, Michalis; Angelis, Lefteris; Chanalaris, Anastasios; Iliopoulos, Ioannis; Kappas, Ilias; Karapiperis, Christos; Kyrpides, Nikos C; Pafilis, Evangelos; Panteris, Eleftherios; Topalis, Pantelis; Tsiamis, George; Vizirianakis, Ioannis S; Vlassi, Metaxia; Promponas, Vasilis J; Ouzounis, Christos A

Establishment of computational biology in Greece and Cyprus: Past, present, and future Journal Article

PLOS Computational Biology, 15 (12), pp. e1007532, 2019, ISSN: 1553-7358, (BIODIV).

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2016

Faulwetter, Sarah; Pafilis, Evangelos; Fanini, Lucia; Bailly, Nicolas; Agosti, Donat; Arvanitidis, Christos; Boicenco, Laura; Capatano, Terry; Claus, Simon; Dekeyzer, Stefanie; Georgiev, Teodor; Legaki, Aglaia; Mavraki, Dimitra; Oulas, Anastasis; Papastefanou, Gabriella; Penev, Lyubomir; Sautter, Guido; Schigel, Dmitry; Senderov, Viktor; Teaca, Adrian; Tsompanou, Marilena

EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Journal Article

Research Ideas and Outcomes, 2 , pp. e9774, 2016, ISSN: 2367-7163.

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Vasileiadou, K; Pavloudi, C; Kalantzi, I; Apostolaki, E T; Chatzigeorgiou, G; Chatzinikolaou, E; Pafilis, E; Papageorgiou, N; Fanini, L; Konstas, S; Fragopoulou, N; Arvanitidis, C

Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece) Journal Article

Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers).

Abstract | Links | BibTeX

Pafilis, E; Buttigieg, P L; Ferrell, B; Pereira, E; Schnetzer, J; Arvanitidis, C; Jensen, L J

EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation Journal Article

Database, 2016 , 2016, ISSN: 17580463, (Publisher: Oxford University Press).

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Varsos, C; Patkos, T; Oulas, A; Pavloudi, C; Gougousis, A; Ijaz, U Z; Filiopoulou, I; Pattakos, N; Berghe, E V; Fernández-Guerra, A; Faulwetter, S; Chatzinikolaou, E; Pafilis, E; Bekiari, C; Doerr, M; Arvanitidis, C

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab) Journal Article

Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers).

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Wang, Q; Abdul, S S; Almeida, L; Ananiadou, S; Balderas-Martínez, Y I; Batista-Navarro, R; Campos, D; Chilton, L; Chou, H -J; Contreras, G; Cooper, L; Dai, H -J; Ferrell, B; Fluck, J; Gama-Castro, S; George, N; Gkoutos, G; Irin, A K; Jensen, L J; Jimenez, S; Jue, T R; 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, R M; Singh, O; Stefancsik, R; Su, C -H; Subramani, S; Tadepally, H D; Tsaprouni, L; Vasilevsky, N; Wang, X; Chatr-Aryamontri, A; Laulederkind, S J F; Matis-Mitchell, S; McEntyre, J; Orchard, S; Pundir, S; Rodriguez-Esteban, R; Auken, Van K; Lu, Z; Schaeffer, M; Wu, C H; Hirschman, L; Arighi, C N

Overview of the interactive task in BioCreative V Journal Article

Database, 2016 , 2016, ISSN: 17580463, (Publisher: Oxford University Press).

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Sinclair, L; Ijaz, U Z; Jensen, L J; Coolen, M J L; 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 Journal Article

PeerJ, 2016 (12), 2016, ISSN: 21678359, (Publisher: PeerJ Inc.).

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Hoopen, P T; Amid, C; Buttigieg, P L; Pafilis, E; Bravakos, P; O-Tárraga, A M C; Gibson, R; Kahlke, T; Legaki, A; Murthy, K N; Papastefanou, G; Pereira, E; Rossello, M; Toribio, A L; Cochrane, G

Value, but high costs in post-deposition data Curation Journal Article

Database, 2016 , 2016, ISSN: 17580463, (Publisher: Oxford University Press).

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Buttigieg, P L; Pafilis, E; Lewis, S E; Schildhauer, M P; Walls, R L; Mungall, C J

The environment ontology in 2016: Bridging domains with increased scope, semantic density, and interoperation Journal Article

Journal of Biomedical Semantics, 7 (1), 2016, ISSN: 20411480, (Publisher: BioMed Central Ltd.).

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2015

Pafilis, E; Frankild, S P; Schnetzer, J; Fanini, L; Faulwetter, S; Pavloudi, C; Vasileiadou, K; Leary, P; Hammock, J; Schulz, K; Parr, C S; Arvanitidis, C; Jensen, L J

ENVIRONMENTS and EOL: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life Journal Article

Bioinformatics, 31 (11), pp. 1872–1874, 2015, ISSN: 13674803, (Publisher: Oxford University Press).

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2014

Davies, N; Field, D; Amaral-Zettler, L; Clark, M S; Deck, J; Drummond, A; Faith, D P; Geller, J; Gilbert, J; Glöckner, F O; Hirsch, P R; Leong, J -A; Meyer, C; Obst, M; Planes, S; Scholin, C; Vogler, A P; Gates, R D; Toonen, R; Berteaux-Lecellier, V; Barbier, M; Barker, K; Bertilsson, S; Bicak, M; Bietz, M J; Bobe, J; Bodrossy, L; Borja, A; Coddington, J; Fuhrman, J; Gerdts, G; Gillespie, R; Goodwin, K; Hanson, P C; Hero, J -M; Hoekman, D; Jansson, J; Jeanthon, C; Kao, R; Klindworth, A; Knight, R; Kottmann, R; Koo, M S; Kotoulas, G; Lowe, A J; Marteinsson, V T; Meyer, F; Morrison, N; Myrold, D D; Pafilis, E; Parker, S; Parnell, J J; Polymenakou, P N; Ratnasingham, S; Roderick, G K; Rodriguez-Ezpeleta, N; Schonrogge, K; Simon, N; Valette-Silver, N J; Springer, Y P; Stone, G N; Stones-Havas, S; Sansone, S -A; Thibault, K M; Wecker, P; Wichels, A; Wooley, J C; Yahara, T; Zingone, A

The founding charter of the Genomic Observatories Network Journal Article

GigaScience, 3 (1), 2014, ISSN: 2047217X, (Publisher: BioMed Central Ltd.).

Abstract | Links | BibTeX

Pafilis, Evangelos; Brown, Nigel P; Horn, Heiko

Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge Incollection

Elloumi, Mourad (Ed.): Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, pp. 869–900, Wiley, 2014, (Backup Publisher: Wiley Section: Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge).

BibTeX

Papanikolaou, N; Pavlopoulos, G A; Pafilis, E; Theodosiou, T; Schneider, R; Satagopam, V P; Ouzounis, C A; Eliopoulos, A G; Promponas, V J; Iliopoulos, I

BioTextQuest+: A knowledge integration platform for literature mining and concept discovery Journal Article

Bioinformatics, 30 (22), pp. 3249–3256, 2014, ISSN: 13674803, (Publisher: Oxford University Press).

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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 Journal Article

Biodiversity Data Journal, 2 (1), 2014, ISSN: 13142828, (Publisher: Pensoft Publishers).

Abstract | Links | BibTeX

Fanini, L; Zampicinini, G; Pafilis, E

Beach parties: a case study on recreational human use of the beach and its effects on mobile arthropod fauna Journal Article

Ethology Ecology & Evolution, 26 (1), pp. 69–79, 2014, ISSN: 0394-9370, 1828-7131.

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2013

Pafilis, E; Frankild, S; I, Umer; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, C; Schnetzer, J; Vasileiadou, A; Arvanitidis, C; Quince, C; Jensen, L J

Identification of Environment Ontology terms in Text and Annotation of Biodiversity (ENVIRONMENTS-EOL) and Genomics (SEQenv) Information Inproceedings

Pafilis, E (Ed.): Biodiversity Information Standards TDWG Conference, Florence, Italy, 2013.

BibTeX

Pafilis, E; Frankild, S P; Fanini, L; Faulwetter, S; Pavloudi, C; Vasileiadou, A; Arvanitidis, C; Jensen, L J

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text Journal Article

PLoS ONE, 8 (6), 2013, ISSN: 19326203.

Abstract | Links | BibTeX

Pafilis, E; Pavlopoulos, G A; Satagopam, V P; Papanikolaou, N; Horn, H; Arvanitidis, C; Jensen, L J; Schneider, R; Iliopoulos, I

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction Inproceedings

13th IEEE International Conference on BioInformatics and BioEngineering, IEEE BIBE 2013, 2013, ISBN: 978-1-4799-3163-7.

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Hardisty, A; Roberts, D; Addink, W; Aelterman, B; Agosti, D; Amaral-Zettler, L; Ariño, AH; Arvanitidis, C; Backeljau, T; Bailly, N; Belbin, L; Berendsohn, W; Bertrand, N; Caithness, N; Campbell, D; Cochrane, G; Conruyt, N; Culham, A; Damgaard, C; Davies, N; Fady, B; Faulwetter, Sarah; Feest, A; Field, D; Garnier, E; Geser, G; Gilbert, J; Grosche, B; Grosser, D; Herbinet, B; Hobern, D; Jones, A; de Jong, Y; King, D; Knapp, S; Koivula, H; Los, W; Meyer, C; Morris, RA; Morrison, N; Morse, D; Obst, M; Pafilis, E; Page, LM; Page, R; Pape, T; Parr, C; Paton, A; Patterson, D; Paymal, E; Penev, L; Pollet, M; Pyle, R; von Raab-Straube, E; Robert, V; Robertson, T; Rovellotti, O; Saarenmaa, H; Schalk, P; Schaminee, J; Schofield, P; Sier, A; Sierra, S; Smith, V; van Spronsen, E; Thornthon-Wood, S; van Tienderen, P; van Tol, J; Tuama, É Ó; Uetz, P; Vaas, L; Lebbe, Vignes R; Vision, T; Vu, D; Wever, De A; White, R; Willis, K; Young, F

A decadal view of biodiversity informatics: challenges and priorities Journal Article

BMC Ecology, 13 , pp. 16, 2013.

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2012

Pafilis, E; Frankild, S; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, C; Vasileiadou, A; Arvanitidis, C; Jensen, L J

SPECIES: Organism Name Identification in the Scientific Literature Inproceedings

Pafilis, E (Ed.): 7th conference of the Hellenic Society for Computational Biology and Bioinformatics, Heraklion, Greece, 2012.

BibTeX

2011

Papanikolaou, Nikolas; Pafilis, Evangelos; Nikolaou, Stavros; Ouzounis, Christos A; Iliopoulos, Ioannis; Promponas, Vasilis J

BioTextQuest: a web-based biomedical text mining suite for concept discovery Journal Article

Bioinformatics, 27 (23), pp. 3327–3328, 2011, ISSN: 1460-2059, 1367-4803.

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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 Journal Article

ZooKeys, 150 , pp. 211–229, 2011, ISSN: 13132989.

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2010

O’Donoghue, Seán I; Horn, Heiko; Pafilis, Evangelos; Haag, Sven; Kuhn, Michael; Satagopam, Venkata P; Schneider, Reinhard; Jensen, Lars J

Reflect: A practical approach to web semantics Journal Article

Web Semantics: Science, Services and Agents on the World Wide Web, 8 (2-3), pp. 182–189, 2010, ISSN: 15708268.

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Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Load Hendrix; Bonnal, Raoul JP; Bruskiewich, Richard; Bryne, Jan C; Fernendez, Jose M; Funahashi, Akira; Gordon, Paul MK; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, Rene; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A; Wilkinson, Mark D; York, William; Zmasek, Christian M; Asai, Kiyoshi; Takagi, Toshihisa

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows Journal Article

Journal of Biomedical Semantics, 1 , pp. 8, 2010, ISSN: 2041-1480.

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2009

Pafilis, Evangelos; O'Donoghue, Seán I; Jensen, Lars J; Horn, Heiko; Kuhn, Michael; Brown, Nigel P; Schneider, Reinhard

Reflect: augmented browsing for the life scientist Journal Article

Nature Biotechnology, 27 (6), pp. 508–510, 2009, ISSN: 1087-0156, 1546-1696.

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Pavlopoulos, G A; Pafilis, E; Kuhn, M; Hooper, S D; Schneider, R

OnTheFly: A tool for automated document-based text annotation, data linking and network generation Journal Article

Bioinformatics, 25 , pp. 977 – 978, 2009.

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2008

Stockinger, H; Attwood, T; Chohan, S N; Côté, R; Cudré-Mauroux, P; Falquet, L; Fernandes, P; Finn, R D; Hupponen, T; Korpelainen, E; Labarga, A; Laugraud, A; Lima, T; Pafilis, E; Pagni, M; Pettifer, S; Phan, I; Rahman, N

Experience using web services for biological sequence analysis Journal Article

Briefings in Bioinformatics, 9 , pp. 493 – 505, 2008.

Abstract | Links | BibTeX

Pavlopoulos, G A; O’Donoghue, S I; Satagopam, V P; Soldatos, T G; Pafilis, E; Schneider, R

Arena3D: Visualization of biological networks in 3D Journal Article

BMC Systems Biology, 2 , 2008.

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2007

Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases Journal Article

Genetics and Molecular Research, 6 , pp. 1142 – 1150, 2007.

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