Bibliography

This page contains my publications prior to the start of the Biodata Analysis Group, i.e. until 2018. For up to date information, please refer to the publications page there.

Book Book Chapter Journals Conferences and Announcements Other

Book

  1. Bezjak, S., Clyburne-Sherin, A., Conzett, P., Fernandes, P. L., Görögh, E., Helbig, K., Kramer, B., Labastida, I., Niemeyer, K., Psomopoulos, F. E., Ross-Hellauer, T., Schneider, R., Tennant, J., & Verbakel, E. (2018). The Open Science Training Handbook. https://doi.org/10.5281/zenodo.1212495

Book Chapter

  1. Psomopoulos, F. E., & Mitkas, P. A. (2009). Data Mining in Proteomics using Grid Computing. In M. Cannataro (Ed.), Handbook of Research on Computational Grid Technologies for LifeSciences, Biomedicine and Healthcare (pp. 245–267). IGI Global. https://doi.org/10.4018/978-1-60566-374-6

Journals

2018

  1. Gavriilaki, E., Touloumenidou, T., Sakellari, I., Batsis, I., Mallouri, D., Psomopoulos, F., Kotouza, M., Koutra, M., Yannaki, E., Papalexandri, A., Stamouli, M., Holbro, A., Baltadakis, I., Liga, M., Spyridonidis, A., Tsirigotis, P., Charchalakis, N., Passweg, J. R., Stamatopoulos, K., & Anagnostopoulos, A. (2018). Pre-Transplant Genetic Susceptibility in Adult Allogeneic Hematopoietic Cell Transplant Recipients: Incidence and Clinical Relevance in Transplant-Associated Thrombotic Microangiopathy. Blood, 132(Suppl 1), 3401–3401. https://doi.org/10.1182/blood-2018-99-112041
  2. Vardi, A., Vlachonikola, E., Ioannou, N., Psomopoulos, F., Kotta, K., Papazoglou, D., Kotouza, M., Koravou, E., Galigalidou, C., Gemenetzi, K., Pasentsis, K., Iskas, M., Stavroyianni, N., Anagnostopoulos, A., Ramsay, A. G., Stamatopoulos, K., & Hadzidimitriou, A. (2018). Longitudinal High-Throughput T Cell Repertoire Profiling of Chronic Lymphocytic Leukemia Patients Under Different Types of Treatment: Implications for Combination Strategies. Blood, 132(Suppl 1), 4400–4400. https://doi.org/10.1182/blood-2018-99-118006
  3. Papakonstantinou, N., Ntoufa, S., Tsagiopoulou, M., Moysiadis, T., Bhoi, S., Malousi, A., Psomopoulos, F., Mansouri, L., Laidou, S., Papazoglou, D., Gounari, M., Pasentsis, K., Plevova, K., Kuci-Emruli, V., Duran-Ferrer, M., Davis, Z., Ek, S., Rossi, D., Gaidano, G., … Stamatopoulos, K. (2018). Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia. International Journal of Cancer, 0(ja). https://doi.org/10.1002/ijc.31999
  4. Parlapani, F. F., Michailidou, S., Anagnostopoulos, D. A., Sakellariou, A. K., Pasentsis, K., Psomopoulos, F., Argiriou, A., Haroutounian, S. A., & Boziaris, I. S. (2018). Microbial spoilage investigation of thawed common cuttlefish (Sepia officinalis) stored at 2 °C using next generation sequencing and volatilome analysis. Food Microbiology, 76, 518–525. https://doi.org/10.1016/j.fm.2018.08.004
  5. Gregory, K., Khalsa, S. J., Michener, W. K., Psomopoulos, F. E., de Waard, A., & Wu, M. (2018). Eleven quick tips for finding research data. PLOS Computational Biology, 14(4), 1–7. https://doi.org/10.1371/journal.pcbi.1006038

2017

  1. Kintsakis, A. M., Psomopoulos, F. E., Symeonidis, A. L., & Mitkas, P. A. (2017). Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments. SoftwareX, 6(Supplement C), 217–224. https://doi.org/10.1016/j.softx.2017.07.007
  2. Kalivas, A., Ganopoulos, I., Psomopoulos, F., Grigoriadis, I., Xanthopoulou, A., Hatzigiannakis, E., Osathanunkul, M., Tsaftaris, A., & Madesis, P. (2017). Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce. Genomics Data, 14(Supplement C), 14–17. https://doi.org/10.1016/j.gdata.2017.07.013
  3. Xanthopoulou, A., Ganopoulos, I., Psomopoulos, F., Manioudaki, M., Moysiadis, T., Kapazoglou, A., Osathanunkul, M., Michailidou, S., Kalivas, A., Tsaftaris, A., Nianiou-Obeidat, I., & Madesis, P. (2017). De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers. Gene, 622(Supplement C), 50–66. https://doi.org/10.1016/j.gene.2017.04.035
  4. Zieliński, C., Stefańczyk, M., Kornuta, T., Figat, M., Dudek, W., Szynkiewicz, W., Kasprzak, W., Figat, J., Szlenk, M., Winiarski, T., Banachowicz, K., Zielińska, T., Tsardoulias, E. G., Symeonidis, A. L., Psomopoulos, F. E., Kintsakis, A. M., Mitkas, P. A., Thallas, A., Reppou, S. E., … Iturburu, M. (2017). Variable structure robot control systems: The RAPP approach. Robotics and Autonomous Systems, 94(Supplement C), 226–244. https://doi.org/10.1016/j.robot.2017.05.002
  5. Psomopoulos, F. E., Vitsios, D. M., Baichoo, S., & Ouzounis, C. A. (2017). BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution. Bioinformatics, 33(9), 1418–1420. https://doi.org/10.1093/bioinformatics/btw813
  6. Tsardoulias, E. G., Kintsakis, A. M., Panayiotou, K., Thallas, A. G., Reppou, S. E., Karagiannis, G. T., Iturburu, M., Arampatzis, S., Zielinski, C., Prunet, V., Psomopoulos, F. E., Symeonidis, A. L., & Mitkas, P. A. (2017). Towards an integrated robotics architecture for social inclusion – The RAPP paradigm. Journal of Cognitive Systems Research, 43, 157–173. https://doi.org/10.1016/j.cogsys.2016.08.004

2016

  1. Kintsakis, A. M., Psomopoulos, F. E., & Mitkas, P. A. (2016). Data-aware optimization of bioinformatics workflows in hybrid clouds. Journal of Big Data, 3(1), 20. https://doi.org/10.1186/s40537-016-0055-2
  2. Zambounis, A., Psomopoulos, F. E., Ganopoulos, I., Avramidou, E., Aravanopoulos, F. A., Tsaftaris, A., & Madesis, P. (2016). In silico analysis of the LRR receptor-like serine threonine kinases subfamily in Morus notabilis. Plant Omics Journal, 9(5), 319–326. https://doi.org/10.21475/poj.09.05.16.pne126
  3. Reppou, S. E., Tsardoulias, E. G., Kintsakis, A. M., Symeonidis, A. L., Mitkas, P. A., Psomopoulos, F. E., Karagiannis, G. T., Zielinski, C., Prunet, V., Merlet, J.-P., Iturburu, M., & Gkiokas, A. (2016). RAPP: A Robotic-Oriented Ecosystem for Delivering Smart User Empowering Applications for Older People. International Journal of Social Robotics, 1–14. https://doi.org/10.1007/s12369-016-0361-z
  4. Chatzidimopoulos, M., Psomopoulos, F., Malandrakis, E. E., Ganopoulos, I., Madesis, P., Vellios, E. K., & Drogoudi, P. (2016). Comparative Genomics of Botrytis cinerea Strains with Differential Multi-Drug Resistance. Frontiers in Plant Science, 7(April), 1–3. https://doi.org/10.3389/fpls.2016.00554
  5. Xanthopoulou, A., Psomopoulos, F., Ganopoulos, I., Manioudaki, M., Tsaftaris, A., Nianiou-Obeidat, I., & Madesis, P. (2016). De novo transcriptome assembly of two contrasting pumpkin cultivars. Genomics Data, 7, 200–201. https://doi.org/10.1016/j.gdata.2016.01.006

2015

  1. Duarte, A. M. S., Psomopoulos, F. E., Blanchet, C., Bonvin, A. M. J. J., Corpas, M., Franc, A., Jimenez, R. C., de Lucas, J. M., Nyrönen, T., Sipos, G., & Suhr, S. B. (2015). Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis. Frontiers in Genetics, 6(June), 197. https://doi.org/10.3389/fgene.2015.00197
  2. Vitsios, D. M., Psomopoulos, F. E., Mitkas, P. a., & Ouzounis, C. a. (2015). Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering. International Journal on Artificial Intelligence Tools, 24(01), 1540003. https://doi.org/10.1142/S0218213015400035

2013

  1. Psomopoulos, F. E., Mitkas, P. A., & Ouzounis, C. A. (2013). Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PloS One, 8(1), e52854. https://doi.org/10.1371/journal.pone.0052854

2012

  1. Psomopoulos, F. E., Siarkou, V. I., Papanikolaou, N., Iliopoulos, I., Tsaftaris, A. S., Promponas, V. J., & Ouzounis, C. A. (2012). The chlamydiales pangenome revisited: structural stability and functional coherence. Genes, 3(2), 291–319. https://doi.org/10.3390/genes3020291
  2. Psomopoulos, F. E., & Mitkas, P. A. (2012). Multi-Level Clustering of Phylogenetic Profiles. International Journal on Artificial Intelligence Tools (Special Issue on Bioinformatics and Bioengineering), 21(5), 1240023. https://doi.org/10.1142/S0218213012400234

2010

  1. Psomopoulos, F. E., & Mitkas, P. A. (2010). Bioinformatics algorithm development for Grid environments. Journal of Systems and Software, 83(7), 1249–1257. https://doi.org/10.1016/j.jss.2010.01.051

2009

  1. Psomopoulos, F. E., Mitkas, P. A., Krinas, C. S., & Demetropoulos, I. N. (2009). A grid-enabled algorithm yields figure-eight molecular knot. Molecular Simulation, 35(9), 725–736. https://doi.org/10.1080/08927020902833103

Conferences and Announcements

2018

  1. Kotouza, M. T., Vavliakis, K. N., Psomopoulos, F. E., & Mitkas, P. A. (2018). A hierarchical multi-metric framework for item clustering. 5th IEEE/ACM International Conference on Big Data Computing Applications and Technologies, BDCAT 2018, Zurich, Switzerland, December 17-20, 2018, 191–197. https://doi.org/10.1109/BDCAT.2018.00031
  2. Kuzak, M., Harrow, J., Jimenez, R. C., Martinez, P., Psomopoulos, F. E., Svobodová Vařeková, R., & Via, A. (2018). Lesson development for Open Source Software best practices adoption. Working Towards Sustainable Software for Science Practice and Experiences. https://doi.org/10.5281/zenodo.1420462
  3. Tsarouchis, S.-F., Kotouza, M. T., Psomopoulos, F. E., & Mitkas, P. A. (2018). A Multi-metric Algorithm for Hierarchical Clustering of Same-Length Protein Sequences. 7th Mining Humanistic Data Workshop (MHDW2018) in Conjunction with the 14th International Conference on Artificial Intelligence Applications and Innovations (AIAI 2018), 189–199. https://doi.org/10.1007/978-3-319-92016-0_18

2017

  1. Mpatziakas, A., Psomopoulos, F. E., Moysiadis, T., & Sgardelis, S. (2017). Computing pangenome statistics in R, [v1; not peer reviewed]. F1000research 2017 (5th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB,) / 16th European Conference on Computational Biology (ECCB)), 6(ISCB Comm J)(1529), 1. https://doi.org/10.7490/f1000research.1114765.1
  2. Culina, A., Kuzak, M., & Psomopoulos, F. E. (2017). Training Life Scientists in Open Reproducible Research; a Data Science scenario. Digital Infrastructures for Research 2017, 1–2. https://doi.org/10.6084/m9.figshare.5644279.v1
  3. Gemenetzi, K., Stalika, E., Vardi, A., Psomopoulos, F. E., Minga, E., Anagnostopoulos, A., Stamatopoulos, K., Hadzidimitriou, A., & Sutton, L. A. (2017). HIGH THROUGHPUT IMMUNOPROFILING OF CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS ASSIGNED TO STEREOTYPED SUBSET# 4: NOVEL INSIGHTS INTO THE DEPTH, DIVERSITY AND TEMPORAL DYNAMICS OF CLONAL EVOLUTION. HAEMATOLOGICA, 102, 67–67.
  4. Agathangelidis, A., Galigalidou, C., Scarfo, L., Rovida, A., Gounari, M., Psomopoulos, F., Ranghetti, P., Gemenetzi, K., Davi, F., Stamatopoulos, K., Hadzidimitriou, A., & Ghia, P. (2017). CLL-Specific B Cell Receptor Immunoglobulin Stereotypes Are Very Infrequent in Low Count Monoclonal B Cell Lymphocytosis: Implications for Disease Ontogeny. Blood, 130(Suppl 1), 1710–1710. http://www.bloodjournal.org/content/130/Suppl_1/1710
  5. Agathangelidis, A., Galigalidou, C., Scarfo, L., Rovida, A., Moysiadis, T., Vlachonikola, E., Psomopoulos, F., Ranghetti, P., Vardi, A., Stamatopoulos, K., Hadzidimitriou, A., & Ghia, P. (2017). High Throughput Immunoprofiling of Low Count B Lymphocytosis Reveals a Distinct T Cell Receptor Repertoire from Chronic Lymphocytic Leukemia. Blood, 130(Suppl 1), 4296–4296. http://www.bloodjournal.org/content/130/Suppl_1/4296

2016

  1. Mokos, P., Psomopoulos, F. E., Ainali, C., Argiriou, A., Charalampidou, A., Hadzopoulou-Cladaras, M., & Dafou, D. (2016). Network analysis and regularized regression modeling identifies key regulatory molecular events underlying hepatocellular carcinoma dedifferentiation. 67th Annual Conference of the Hellenic Society for Biochemistry and Molecular Biology (HSBMB), 1–4.
  2. Mokos, P., Psomopoulos, F. E., Ainali, C., Argiriou, A., Charalampidou, A., Hadzopoulou-Cladaras, M., & Dafou, D. (2016). Integrated network analysis and regularized regression modeling reveal regulatory miRNA-mRNA networks associated with hepatocellular carcinoma dedifferentiation. 8th Conference of the Hellenic Crystallographic Association (HeCrA) / 11th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HeCrA-HSCBB16), 1–2.
  3. Xanthopoulou, A., Psomopoulos, F., Ganopoulos, I., Kalyvas, A., Tsaftaris, A., Madesis, P., & Nianiou-Obeidat, I. (2016). De novo sequencing and comparative analysis of the transcriptome of two Cucurbita pepo cultivars (in Greek). 16th Conference of the Hellenic Plant Breeding Society, 1–2.
  4. Via, A., Fernandes, P., Korpelainen, E., Duarte, A. M. S., & Psomopoulos, F. E. (2016). E-Infrastructures for the Bioinformatics long tail of science: a user perspective. Digital Infrastructures for Research 2016, 1–2.
  5. Psomopoulos, F. E. (2016). Managing the Data Ecosystem in Life Sciences through Bioinformatics. 8th RDA Plenary, 1–1.
  6. Stergiadis, E., Kintsakis, A. M., Psomopoulos, F. E., & Mitkas, P. A. (2016). A scalable Grid Computing framework for extensible phylogenetic profile construction. 5th Mining Humanistic Data Workshop (MHDW2016) in Conjunction with the 12th International Conference on Artificial Intelligence Applications and Innovations (AIAI 2016), 1–8.
  7. Psomopoulos, F. E., Kintsakis, A. M., & Mitkas, P. A. (2016). A pan-genome approach and application to species with photosynthetic capabilities, [v1; not peer reviewed]. F1000Research 2016, 5(ECCB 2016(2132), 1. https://doi.org/10.7490/f1000research.1112964.1
  8. Psomopoulos, F. E., Korpelainen, E., Mattila, K., & Scardaci, D. (2016). Bioinformatics resources on EGI Federated Cloud, [v1; not peer reviewed]. F1000Research 2016, 5(ECCB 2016(2131), 1. https://doi.org/10.7490/f1000research.1112963.1

2015

  1. Kintsakis, A., Vrousgou, O., Vardi, A., Karypidou, M., Stalika, E., Korabou, E., P Zerva, P., Anagnostopoulos, A., Chatzidimitriou, A., Stamatopoulos, K., & Psomopoulos, F. E. (2015). Large-scale detection of sequencing errors using immunogenetic data of β chain T cell receptors (in Greek). 26th Panhellenic Haematology Congress, 1–2.
  2. Ntoufa, S., Papakonstantinou, N., Tsagiopoulou, M., Moisiadis, T., Malousi, A., Papazoglou, D., Pasentsis, K., Psomopoulos, F., Stalika, E., Laidou, M., Maglaveras, N., Anagnostopoulos, A., & Stamatopoulos, K. (2015). Distinct methylation patterns in subgroups of patients with Chronic Lymphocytic Leukemia reveal TP63 as a new player in clinical aggressiveness ("Arkagathos Gouttas" Prize award). 26th Panhellenic Haematology Congress, 1–2.
  3. Mokos, P., Psomopoulos, F. E., Ainali, C., Charalampidou, A., Hadzopoulou-Cladaras, M., & Dafou, D. (2015). Large integrative analysis for the identification of novel molecular targets in hepatocellular carcinoma. 66th Congress of the Hellenic Society of Biochemistry and Molecular Biology, 1–4.
  4. Duarte, A., Psomopoulos, F. E., Sipos, G., Ferreira, N., & Scardaci, D. (2015). EGI Support for Genome Analysis and Protein Folding - A Virtual Team for Life Sciences. International Symposium on Grids and Clouds ( ISGC ) 2015, 2.
  5. Psomopoulos, F. E., Vrousgou, O. T., & Mitkas, P. A. (2015). Large-scale modular comparative genomics: the Grid approach [v1; not peer reviewed]. F1000Research 2015, 4(ISCB Com(377), 1. https://doi.org/10.7490/f1000research.1110127.1
  6. Vrousgou, O. T., Psomopoulos, F. E., & Mitkas, P. A. (2015). A grid-enabled modular framework for efficient sequence analysis workflows. 16th International Conference on Engineering Applications of Neural Networks, 10.

2014

  1. Psomopoulos, F. E., & Mitkas, P. A. (2014). Algebraic Interpretations Towards Clustering Protein Homology Data. Artificial Intelligence Applications and Innovations, IFIP Advances in Information and Communication Technology Volume 437. https://doi.org/10.1007/978-3-662-44722-2_15
  2. Psomopoulos, F. E., & Ouzounis, C. A. (2014). Computation and visualization of ancestral pathway reconstruction and inference. ECCB 2014, 8, 52854.
  3. Psomopoulos, F., Tsardoulias, E., Giokas, A., Zielinski, C., Prunet, V., Trochidis, I., Daney, D., Serrano, M., Courtes, L., Arampatzis, S., & Mitkas, P. A. (2014). RAPP System Architecture. Workshop on Assistance and Service Robotics in a Human Environment (ASROB), in Conjunction with the IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS’14), 8.

2012

  1. Psomopoulos, F. E., Argiriou, A., Tsaftaris, A. S., & Ouzounis, C. A. (2012). A Pangenome Analysis of the Glucosinolate Pathway in Plants. 7th Conference of the Hellenic Society for Computational Biology & Bioinformatics - HSCBB ’12, 63.
  2. Psomopoulos, F. E., & Ouzounis, C. A. (2012). Ancestral Reconstruction of Metabolic Pathway Content at the Paleome Level. 7th Conference of the Hellenic Society for Computational Biology & Bioinformatics - HSCBB ’12, 90.
  3. Vitsios, D., Psomopoulos, F. E., Mitkas, P. A., & Ouzounis, C. A. (2012). Detection of closely correlated genes across genomes using pathway data. 5th National Student Conference of Electrical and Computer Engineering, 111–117.
  4. Vitsios, D., Psomopoulos, F. E., & Ouzounis, C. A. (2012). Null Entries for BioPAX Pathways, Visualization and Pathway Phylogenetic Profiling Based on Paxtools. 7th Conference of the Hellenic Society for Computational Biology & Bioinformatics - HSCBB ’12, 92.

2011

  1. Vitsios, D., Psomopoulos, F. E., Mitkas, P. A., & Ouzounis, C. A. (2011). Detecting species evolution through metabolic pathways. 6th Conference of the Hellenic Society For Computational Biology and Bioinformatics - HSCBB ’11, 16.

2010

  1. Chatzidimitriou, K. C., Psomopoulos, F. E., & Mitkas, P. A. (2010). Grid-enabled parameter initialization for high performance machine learning tasks. 5th EGEE User Forum, 113–114.
  2. Psomopoulos, F. E., & Mitkas, P. A. (2010). Multi Level Clustering of Phylogenetic Profiles. 10th IEEE International Conference on Bioinformatics and Bioingineering, 308–309. https://doi.org/10.1109/BIBE.2010.67
  3. Psomopoulos, F. E., Mitkas, P. A., & Ouzounis, C. A. (2010). Clustering of discrete and fuzzy phylogenetic profiles. 5th Conference of the Hellenic Society For Computational Biology and Bioinformatics - HSCBB ’10, 58.
  4. Tzima, F. A., Psomopoulos, F. E., & Mitkas, P. A. (2010). An investigation of the effect of clustering-based initialization on Learning Classifiers Systems’ effectiveness: leveraging the Grid infrastructure. 5th EGEE User Forum, 111–112.

2009

  1. Karagiannis, K. M., Psomopoulos, F. E., & Mitkas, P. A. (2009). Multi Level Clustering of Phylogenetic Profiles. 4th Conference of the Hellenic Society For Computational Biology and Bioinformatics - HSCBB ’09, 1.
  2. Psomopoulos, F. E., & Mitkas, P. A. (2009). BADGE: Bioinformatics Algorithm Development for Grid Environments. 13th Panhellenic Conference on Informatics, 93–107.
  3. Mitkas, P. A., Delopoulos, A., Vavliakis, K., Maramis, C., Falelakis, M., Psomopoulos, F. E., Koutkias, V., Lekka, I., Tantsis, A., Mikos, A., Maglaveras, N., & Agorastos, T. (2009). Combining multiple sources towards cervical cancer prognosis – the ASSIST platform (in Greek). 8th Scientific Forum on "New Trends in Prognosis and Treatment of Cervical Cancer", 109–118.

2008

  1. Agorastos, T., Mitkas, P. A., Falelakis, M., Psomopoulos, F. E., Delopoulos, A. N., Symeonidis, A. L., Diplaris, S., Maramis, C., Batzios, A., Lekka, I., Koutkias, V., Mikos, T., Tatsis, A., & Maglaveras, N. (2008). Large Scale Association Studies Using Unified Data for Cervical Cancer and beyond: The ASSIST Project. World Cancer Congress, 1.
  2. Gkekas, C. N., Psomopoulos, F. E., & Mitkas, P. A. (2008). A Parallel Data Mining Methodology for Protein Function Prediction Utilizing Finite State Automata. 2nd Electrical and Computer Engineering Student Conference, 6.
  3. Gkekas, C. N., Psomopoulos, F. E., & Mitkas, P. A. (2008). Exploiting parallel data mining processing for protein annotation. Student EUREKA 2008: 2nd Panhellenic Scientific Student Conference, 242–252.
  4. Gkekas, C. N., Psomopoulos, F. E., & Mitkas, P. A. (2008). A Parallel Data Mining Application for Gene Ontology Term Prediction. 3rd EGEE User Forum, 1.
  5. Mitkas, P. A., Maramis, C., Delopoulos, A. N., Symeonidis, A. L., Diplaris, S., Falelakis, M., Psomopoulos, F. E., Batzios, A., Maglaveras, N., Lekka, I., Koutkias, V., Agorastos, T., Mikos, T., & Tatsis, A. (2008). ASSIST: Employing Inference and Semantic Technologies to Facilitate Association Studies on Cervical Cancer. 6th European Symposium on Biomedical Engineering.
  6. Mprouza, I. K., Psomopoulos, F. E., & Mitkas, P. A. (2008). AMoS: Agent-based Molecular Simulations. Student EUREKA 2008: 2nd Panhellenic Scientific Student Conference, 175–186.
  7. Psomopoulos, F. E., & Mitkas, P. A. (2008). Sizing Up: Bioinformatics in a Grid Context. 3rd Conference of the Hellenic Society For Computational Biology and Bioinformatics - HSCBB ’08, 1.
  8. Psomopoulos, F. E., Mitkas, P. A., Krinas, C. S., & Demetropoulos, I. N. (2008). G-MolKnot: A grid enabled systematic algorithm to produce open molecular knots. 1st HellasGrid User Forum, 24–25.

2007

  1. Gkekas, C. N., Psomopoulos, F. E., & Mitkas, P. A. (2007). Modeling Gene Ontology Terms using Finite State Automata. Hellenic Bioinformatics and Medical Informatics Meeting, 1.
  2. Mitkas, P. A., Delopoulos, A. N., Symeonidis, A. L., & Psomopoulos, F. E. (2007). A Framework for Semantic Data Integration and Inferencing on Cervical Cancer. Hellenic Bioinformatics and Medical Informatics Meeting, 1.
  3. Mprouza, I. K., Psomopoulos, F. E., & Mitkas, P. A. (2007). Simulating molecular dynamics through intelligent software agents. Hellenic Bioinformatics and Medical Informatics Meeting, 1.

2006

  1. Polychroniadou, H. E., Psomopoulos, F. E., & Mitkas, P. A. (2006). G-Class: A Divide and Conquer Application for Grid Protein Classification. Proceedings of the 2nd ADMKD 2006: Workshop on Data Mining and Knowledge Discovery (in Conjunction with ADBIS 2006: The 10th East-European Conference on Advances in Databases and Information Systems), 121–132.
  2. Psomopoulos, F. E., & Mitkas, P. A. (2006). PROTEAS: A Finite State Automata based data mining algorithm for rule extraction in protein classification. Proceedings of the 5th Hellenic Data Management Symposium, 118–126.

2005

  1. Psomopoulos, F. E., & Mitkas, P. A. (2005). A protein classification engine based on stochastic finite state automata. Lecture Series on Computer and Computational Sciences VSP/Brill (Proceedings of the Symposium 35: Computational Methods in Molecular Biology in Conjunction with ICCMSE), 4B, 1371–1374.

2004

  1. Psomopoulos, F. E., Diplaris, S., & Mitkas, P. A. (2004). A finite state automata based technique for protein classification rules induction. Proceedings of the Second European Workshop on Data Mining and Text Mining in Bioinformatics (in Conjunction with ECML/PKDD), 54–60.

Other

Short articles

  1. Nicolaidis, A., & Psomopoulos, F. (2019). DNA coding and Gödel numbering. https://arxiv.org/abs/1909.13574
  2. Becker, E. A., Reiter, T., Psomopoulos, F., McKay, S. J., Mizzi, J. E., Williams, J., Hoyt, P. R., Crosby, K., Nederbragt, L., Teal, T., Infante, A., Pierce, T., Michonneau, F., Augustus, G., Harris, R. M., dbmarchant, Thomas, A., Cranston, K., Weitemier, K., … Kretzschmar, W. (2019). datacarpentry/wrangling-genomics: Data Carpentry: Genomics data wrangling and processing, June 2019. https://doi.org/10.5281/zenodo.3260609
  3. Wilson, G., Becker, E., McKay, S., Michonneau, F., Williams, J. J., Mayes, A. C., Silva, R., (hoytpr), P., Crosby, K., Nederbragt, L., NielInfante, Psomopoulos, F. E., Gourlé, H., (gaiusjaugustus), G., dbmarchant, Emonet, R., Cock, P., Banaszkiewicz, P., Teal, T., … gtehennepe. (2017). Data Carpentry Wrangling Genomics Lesson. https://doi.org/10.5281/zenodo.1064254
  4. Psomopoulos, F. E. (2016). International Data Forum Opening Plenary Session: Maintaining Scientific Rigor and Enhancing Discovery. In RDA Newsletter. https://www.rd-alliance.org/blogs/international-data-forum-opening-plenary-session-maintaining-scientific-rigor-and-enhancing
  5. Psomopoulos, F. E. (2016). International Data Forum: Data Stories Session. In RDA Newsletter. https://www.rd-alliance.org/blogs/international-data-forum-data-stories-session.html
  6. Psomopoulos, F. E. (2016). Training life scientists to analyse genomic data – can cloud make life easier? (interview). In @CSC Online Magazine Tells More. https://www.csc.fi/web/atcsc/-/training-life-scientists-to-analyse-genomic-data-can-cloud-make-life-easier
  7. Psomopoulos, F., & Jimenez, R. (2015). EGI-ELIXIR project: Integrating datasets for bioinformatics. In EGI Inspire Newsletter #18 (Number February, pp. 5–6).
  8. Duarte, A., & Psomopoulos, F. (2014). Future opportunities and trends for e-infrastructures and life sciences. In EGI Inspire Newsletter #14 (Number January, p. 1).
  9. Psomopoulos, F. E., Gkekas, C., & Mitkas, P. A. (2008). Data Mining in Bioinformatics using Grid Computing (in Greek). In AUTH Grid Team, Aristotle University of Thessaloniki (Number January, p. 1).

Thesis

  1. Psomopoulos, F. E. (2010). Parallel Data Mining and Analysis Algorithms in a Grid environment and applications in Bioinformatics (p. 184) [PhD Thesis]. Aristotle University of Thessaloniki, Greece.
  2. Psomopoulos, F. E. (2004). A finite state automata algorithm for the extraction of association rules and applications in protein data classification (Greek text only) (p. 108) [Master Thesis]. Aristotle University of Thessaloniki, Greece.