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ORCIDFotis E. Psomopoulos
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2020 – today
- 2024
[j22]Vladimir Makarov
, Christophe Chabbert, Elina Koletou, Fotis E. Psomopoulos, Natalja Kurbatova, Samuel A. Ramirez, Chas Nelson, Prashant Natarajan, Bikalpa Neupane:
Good machine learning practices: Learnings from the modern pharmaceutical discovery enterprise. Comput. Biol. Medicine 177: 108632 (2024)- [i4]Styliani-Christina Fragkouli, Dhwani Solanki, Leyla Jael Castro, Fotis E. Psomopoulos, Núria Queralt-Rosinach, Davide Cirillo, Lisa C. Crossman:
Synthetic data: How could it be used for infectious disease research? CoRR abs/2407.06211 (2024) - 2023
- [j21]Konstantinos A Kyritsis, Nikolaos Pechlivanis, Fotis E. Psomopoulos:
Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL). Frontiers Bioinform. 3 (2023) - [j20]Saskia D. Hiltemann, Helena Rasche, Simon L. Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel J. Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina P. Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi A. Bacon, Fotis E. Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, The Galaxy Team, Björn A. Grüning, Bérénice Batut:
Galaxy Training: A powerful framework for teaching! PLoS Comput. Biol. 19(1) (2023) - [c13]Leyla Jael Castro, Dietrich Rebholz-Schuhmann, Nelson Quiñones, Dimitrios Bampalikis, Olga L. Giraldo, Eva Martin Del Pico, Allegra Via, Dhwani Solanki, Lukas Geist, Fotis E. Psomopoulos, Renato Alves, José María Fernández González:
A metadata schema for machine-actionable Software Management Plans. DaMaLOS 2023 - [c12]Olga L. Giraldo, Renato Alves, Dimitrios Bampalikis, José M. Fernández, Eva Martin Del Pico, Fotis E. Psomopoulos, Nelson Quiñones, Dhwani Solanki, Allegra Via, Leyla Jael Castro:
A metadata analysis for machine-actionable Software Management Plans. SWAT4HCLS 2023: 145-146 - [i3]Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Bachir Balech, Endre Barta, Katharina F. Heil, Graham M. Hughes, Lars S. Jermiin, Matús Kalas, Jerry Lanfear, Evangelos Pafilis, Aristotelis C. Papageorgiou, Fotis E. Psomopoulos, Niels Raes, Josephine Burgin, Toni Gabaldón:
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. F1000Research 12: 499 (2023) - 2022
- [j19]Laura Zaragoza-Infante, Valentin Junet, Nikos Pechlivanis, Styliani-Christina Fragkouli, Serovpe Amprachamian, Triantafyllia Koletsa, Anastasia Chatzidimitriou, Maria Papaioannou, Kostas Stamatopoulos, Andreas Agathangelidis, Fotis E. Psomopoulos:
IgIDivA: immunoglobulin intraclonal diversification analysis. Briefings Bioinform. 23(5) (2022) - [j18]Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50(W1): 345-351 (2022) - [i2]Eliu A. Huerta, Ben Blaiszik, L. Catherine Brinson, Kristofer E. Bouchard, Daniel Diaz, Caterina Doglioni, Javier M. Duarte, Murali Emani, Ian T. Foster, Geoffrey C. Fox, Philip C. Harris, Lukas Heinrich, Shantenu Jha, Daniel S. Katz, Volodymyr V. Kindratenko, Christine R. Kirkpatrick, Kati Lassila-Perini, Ravi K. Madduri, Mark S. Neubauer, Fotis E. Psomopoulos, Avik Roy, Oliver Rübel, Zhizhen Zhao, Ruike Zhu:
FAIR for AI: An interdisciplinary, international, inclusive, and diverse community building perspective. CoRR abs/2210.08973 (2022) - 2021
- [c11]Daniel S. Katz, Fotis E. Psomopoulos, Leyla Jael Castro:
Working Towards Understanding the Role of FAIR for Machine Learning. DaMaLOS 2021: 1-6 - 2020
- [j17]Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis E. Psomopoulos:
TRIP - T cell receptor/immunoglobulin profiler. BMC Bioinform. 21(1): 422 (2020) - [j16]Anna-Lena Lamprecht, Leyla J. García, Mateusz Kuzak, Carlos Martinez-Ortiz, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, Stephanie van de Sandt, Jon C. Ison, Paula Andrea Martínez, Peter McQuilton, Alfonso Valencia, Jennifer L. Harrow, Fotis E. Psomopoulos, Josep Lluis Gelpí, Neil P. Chue Hong, Carole A. Goble, Salvador Capella-Gutiérrez:
Towards FAIR principles for research software. Data Sci. 3(1): 37-59 (2020) - [j15]Maria Th. Kotouza, Fotis E. Psomopoulos, Pericles A. Mitkas:
A dockerized framework for hierarchical frequency-based document clustering on cloud computing infrastructures. J. Cloud Comput. 9: 2 (2020) - [j14]Leyla J. García, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis E. Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez Del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi:
Ten simple rules for making training materials FAIR. PLoS Comput. Biol. 16(5) (2020) - [j13]Kim T. Gurwitz, Prakash Singh Gaur, Louisa J. Bellis, Lee D. Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez Del Angel, Pedro L. Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskosek, Jessica M. Lindvall, Diana Marek, Paula Andrea Martínez, Tuur Muyldermans, Ståle Nygård, Patricia M. Palagi, Hedi Peterson, Fotis E. Psomopoulos, Vojtech Spiwok, Celia W. G. van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L. Morgan, Gabriella Rustici:
A framework to assess the quality and impact of bioinformatics training across ELIXIR. PLoS Comput. Biol. 16(7) (2020) - [c10]Leyla J. García, Michelle Barker, Neil P. Chue Hong, Fotis E. Psomopoulos, Jennifer L. Harrow, Daniel S. Katz, Mateusz Kuzak, Paula Andrea Martínez, Allegra Via:
Software as a first-class citizen in research. DaMaLOS 2020: 1-8 - [i1]Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Jen Harrow, Fotis E. Psomopoulos, Silvio C. E. Tosatto:
Recommendations for machine learning validation in biology. CoRR abs/2006.16189 (2020)
2010 – 2019
- 2019
- [j12]Mingfang Wu, Fotis E. Psomopoulos, Siri Jodha S. Khalsa, Anita de Waard:
Data Discovery Paradigms: User Requirements and Recommendations for Data Repositories. Data Sci. J. 18: 3 (2019) - [j11]Athanassios M. Kintsakis, Fotis E. Psomopoulos, Pericles A. Mitkas:
Reinforcement Learning based scheduling in a workflow management system. Eng. Appl. Artif. Intell. 81: 94-106 (2019) - [c9]Maria Th. Kotouza, Fotis E. Psomopoulos, Pericles A. Mitkas:
A Dockerized String Analysis Workflow for Big Data. ADBIS (Short Papers and Workshops) 2019: 564-569 - 2018
- [j10]Kathleen Gregory, Siri Jodha S. Khalsa, William K. Michener, Fotis E. Psomopoulos, Anita de Waard, Mingfang Wu:
Eleven quick tips for finding research data. PLoS Comput. Biol. 14(4) (2018) - [c8]Maria Th. Kotouza, Konstantinos N. Vavliakis, Fotis E. Psomopoulos, Pericles A. Mitkas:
A Hierarchical Multi-Metric Framework for Item Clustering. BDCAT 2018: 191-197 - [c7]Mateusz Kuzak, Jen Harrow, Rafael C. Jiménez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via:
Lesson Development for Open Source Software Best Practices Adoption. eScience 2018: 19-20 - [c6]Sotirios-Filippos Tsarouchis, Maria Th. Kotouza, Fotis E. Psomopoulos, Pericles A. Mitkas:
A Multi-metric Algorithm for Hierarchical Clustering of Same-Length Protein Sequences. AIAI (Workshops) 2018: 189-199 - 2017
- [j9]Fotis E. Psomopoulos, Dimitrios M. Vitsios, Shakuntala Baichoo, Christos A. Ouzounis:
BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution. Bioinform. 33(9): 1418-1420 (2017) - [j8]Emmanouil G. Tsardoulias, Athanassios M. Kintsakis, Konstantinos Panayiotou, Aristeidis G. Thallas, Sofia E. Reppou, George Karagiannis, Miren Iturburu, Stratos Arampatzis, Cezary Zielinski, Vincent Prunet, Fotis E. Psomopoulos, Andreas L. Symeonidis, Pericles A. Mitkas:
Towards an integrated robotics architecture for social inclusion - The RAPP paradigm. Cogn. Syst. Res. 43: 157-173 (2017) - [j7]Cezary Zielinski, Maciej Stefanczyk, Tomasz Kornuta, Maksym Figat, Wojciech Dudek, Wojciech Szynkiewicz, Wlodzimierz Kasprzak, Jan Figat, Marcin Szlenk, Tomasz Winiarski, Konrad Banachowicz, Teresa Zielinska, Emmanouil G. Tsardoulias, Andreas L. Symeonidis, Fotis E. Psomopoulos, Athanassios M. Kintsakis, Pericles A. Mitkas, Aristeidis G. Thallas, Sofia E. Reppou, George Karagiannis, Konstantinos Panayiotou, Vincent Prunet, Manuel Serrano, Jean-Pierre Merlet, Stratos Arampatzis, Alexandros Gkiokas, Lazaros Penteridis, Ilias Trochidis, David Daney, Miren Iturburu:
Variable structure robot control systems: The RAPP approach. Robotics Auton. Syst. 94: 226-244 (2017) - [j6]Athanassios M. Kintsakis, Fotis E. Psomopoulos, Andreas L. Symeonidis, Pericles A. Mitkas:
Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments. SoftwareX 6: 217-224 (2017) - 2016
- [j5]Sofia Reppou, Emmanouil G. Tsardoulias, Athanassios M. Kintsakis, Andreas L. Symeonidis, Pericles A. Mitkas, Fotis E. Psomopoulos, George Karagiannis, Cezary Zielinski, Vincent Prunet, Jean-Pierre Merlet, Miren Iturburu, Alexandros Gkiokas:
RAPP: A Robotic-Oriented Ecosystem for Delivering Smart User Empowering Applications for Older People. Int. J. Soc. Robotics 8(4): 539-552 (2016) - [j4]Athanassios M. Kintsakis, Fotis E. Psomopoulos, Pericles A. Mitkas:
Data-aware optimization of bioinformatics workflows in hybrid clouds. J. Big Data 3: 20 (2016) - [c5]Emmanouil Stergiadis, Athanassios M. Kintsakis, Fotis E. Psomopoulos, Pericles A. Mitkas:
A Scalable Grid Computing Framework for Extensible Phylogenetic Profile Construction. AIAI 2016: 455-462 - 2015
- [j3]Dimitrios M. Vitsios, Fotis E. Psomopoulos, Pericles A. Mitkas, Christos A. Ouzounis:
Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering. Int. J. Artif. Intell. Tools 24(1): 1540003:1-1540003:27 (2015) - [c4]Olga T. Vrousgou, Fotis E. Psomopoulos, Pericles A. Mitkas:
A Grid-Enabled Modular Framework for Efficient Sequence Analysis Workflows. EANN 2015: 47-56 - 2014
- [c3]Fotis E. Psomopoulos, Pericles A. Mitkas:
Algebraic Interpretations Towards Clustering Protein Homology Data. AIAI Workshops 2014: 136-145 - 2012
- [j2]Fotis E. Psomopoulos, Pericles A. Mitkas:
Multi-Level Clustering of Phylogenetic Profiles. Int. J. Artif. Intell. Tools 21(5) (2012) - [c2]Dimitrios M. Vitsios, Fotis E. Psomopoulos, Pericles A. Mitkas, Christos A. Ouzounis:
Multi-genome Core Pathway Identification through Gene Clustering. AIAI (2) 2012: 545-555 - 2010
- [j1]Fotis E. Psomopoulos, Pericles A. Mitkas:
Bioinformatics algorithm development for Grid environments. J. Syst. Softw. 83(7): 1249-1257 (2010) - [c1]Fotis E. Psomopoulos, Pericles A. Mitkas:
Multi Level Clustering of Phylogenetic Profiles. BIBE 2010: 308-309
Coauthor Index
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