Fotis E. Psomopoulos

According to our database, Fotis E. Psomopoulos authored at least 38 papers between 2010 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Synthetic data: How could it be used for infectious disease research?

Styliani-Christina Fragkouli, Dhwani Solanki, Leyla Jael Castro, Fotis E. Psomopoulos, Núria Queralt-Rosinach, Davide Cirillo, Lisa C. Crossman

CoRR, 2024

Good machine learning practices: Learnings from the modern pharmaceutical discovery enterprise.

Vladimir Makarov, Christophe Chabbert, Elina Koletou, Fotis E. Psomopoulos, Natalja Kurbatova, Samuel A. Ramirez, Chas Nelson, Prashant Natarajan, Bikalpa Neupane

Comput. Biol. Medicine, 2024

2023

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).

Konstantinos A Kyritsis, Nikolaos Pechlivanis, Fotis E. Psomopoulos

Frontiers Bioinform., May, 2023

Galaxy Training: A powerful framework for teaching!

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

PLoS Comput. Biol., January, 2023

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.

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

F1000Research, 2023

A metadata analysis for machine-actionable Software Management Plans.

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

Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

A metadata schema for machine-actionable Software Management Plans.

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

Proceedings of the 3rd Workshop on Metadata and Research (objects) Management for Linked Open Science, 2023

2022

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.

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

Nucleic Acids Res., 2022

FAIR for AI: An interdisciplinary, international, inclusive, and diverse community building perspective.

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

CoRR, 2022

IgIDivA: immunoglobulin intraclonal diversification analysis.

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

Briefings Bioinform., 2022

2021

Working Towards Understanding the Role of FAIR for Machine Learning.

Daniel S. Katz, Fotis E. Psomopoulos, Leyla Jael Castro

Proceedings of the DaMaLOS, 2021

2020

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

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

PLoS Comput. Biol., 2020

Ten simple rules for making training materials FAIR.

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

PLoS Comput. Biol., 2020

A dockerized framework for hierarchical frequency-based document clustering on cloud computing infrastructures.

Maria Th. Kotouza, Fotis E. Psomopoulos, Pericles A. Mitkas

J. Cloud Comput., 2020

Towards FAIR principles for research software.

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

Data Sci., 2020

Recommendations for machine learning validation in biology.

Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Jen Harrow, Fotis E. Psomopoulos, Silvio C. E. Tosatto

CoRR, 2020

TRIP - T cell receptor/immunoglobulin profiler.

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

BMC Bioinform., 2020

Software as a first-class citizen in research.

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

Proceedings of the DaMaLOS, 2020

2019

Reinforcement Learning based scheduling in a workflow management system.

Athanassios M. Kintsakis, Fotis E. Psomopoulos, Pericles A. Mitkas

Eng. Appl. Artif. Intell., 2019

Data Discovery Paradigms: User Requirements and Recommendations for Data Repositories.

Mingfang Wu, Fotis E. Psomopoulos, Siri Jodha S. Khalsa, Anita de Waard

Data Sci. J., 2019

A Dockerized String Analysis Workflow for Big Data.

Maria Th. Kotouza, Fotis E. Psomopoulos, Pericles A. Mitkas

Proceedings of the New Trends in Databases and Information Systems, 2019

2018

Eleven quick tips for finding research data.

Kathleen Gregory, Siri Jodha S. Khalsa, William K. Michener, Fotis E. Psomopoulos, Anita de Waard, Mingfang Wu

PLoS Comput. Biol., 2018

A Multi-metric Algorithm for Hierarchical Clustering of Same-Length Protein Sequences.

Sotirios-Filippos Tsarouchis, Maria Th. Kotouza, Fotis E. Psomopoulos, Pericles A. Mitkas

Proceedings of the Artificial Intelligence Applications and Innovations, 2018

Lesson Development for Open Source Software Best Practices Adoption.

Mateusz Kuzak, Jen Harrow, Rafael C. Jiménez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via

Proceedings of the 14th IEEE International Conference on e-Science, 2018

A Hierarchical Multi-Metric Framework for Item Clustering.

Maria Th. Kotouza, Konstantinos N. Vavliakis, Fotis E. Psomopoulos, Pericles A. Mitkas

Proceedings of the 5th IEEE/ACM International Conference on Big Data Computing Applications and Technologies, 2018

2017

Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments.

Athanassios M. Kintsakis, Fotis E. Psomopoulos, Andreas L. Symeonidis, Pericles A. Mitkas

SoftwareX, 2017

Variable structure robot control systems: The RAPP approach.

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

Robotics Auton. Syst., 2017

Towards an integrated robotics architecture for social inclusion - The RAPP paradigm.

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

Cogn. Syst. Res., 2017

BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution.

Fotis E. Psomopoulos, Dimitrios M. Vitsios, Shakuntala Baichoo, Christos A. Ouzounis

Bioinform., 2017

2016

Data-aware optimization of bioinformatics workflows in hybrid clouds.

Athanassios M. Kintsakis, Fotis E. Psomopoulos, Pericles A. Mitkas

J. Big Data, 2016

RAPP: A Robotic-Oriented Ecosystem for Delivering Smart User Empowering Applications for Older People.

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

Int. J. Soc. Robotics, 2016

A Scalable Grid Computing Framework for Extensible Phylogenetic Profile Construction.

Emmanouil Stergiadis, Athanassios M. Kintsakis, Fotis E. Psomopoulos, Pericles A. Mitkas

Proceedings of the Artificial Intelligence Applications and Innovations, 2016

2015

Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering.

Dimitrios M. Vitsios, Fotis E. Psomopoulos, Pericles A. Mitkas, Christos A. Ouzounis

Int. J. Artif. Intell. Tools, 2015

A Grid-Enabled Modular Framework for Efficient Sequence Analysis Workflows.

Olga T. Vrousgou, Fotis E. Psomopoulos, Pericles A. Mitkas

Proceedings of the Engineering Applications of Neural Networks, 2015

2014

Algebraic Interpretations Towards Clustering Protein Homology Data.

Fotis E. Psomopoulos, Pericles A. Mitkas

Proceedings of the Artificial Intelligence Applications and Innovations, 2014

2012

Multi-Level Clustering of Phylogenetic Profiles.

Fotis E. Psomopoulos, Pericles A. Mitkas

Int. J. Artif. Intell. Tools, 2012

Multi-genome Core Pathway Identification through Gene Clustering.

Dimitrios M. Vitsios, Fotis E. Psomopoulos, Pericles A. Mitkas, Christos A. Ouzounis

Proceedings of the Artificial Intelligence Applications and Innovations, 2012

2010

Bioinformatics algorithm development for Grid environments.

Fotis E. Psomopoulos, Pericles A. Mitkas

J. Syst. Softw., 2010