Selected Publications
Petr Holub, Florian Kohlmayer, Fabian Prasser, Michaela Th. Mayrhofer, Irene Schlünder, Gillian M. Martin, Sara Casati, Lefteris Koumakis, et al. Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health. Biopreservation and Biobanking. February 2018 (Ahead of print) doi: 10.1089/bio.2017.0110
Lefteris Koumakis, Panos Roussos, George Potamias; minepath.org: a free interactive pathway analysis web server. Nucleic Acids Res 2017; 45 (W1): W116-W121. doi: 10.1093/nar/gkx278
Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias. "MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways." PLOS Comput Biol 12.11 (2016): e1005187
Laine, M. L., V. Moustakis, L. Koumakis, G. Potamias, and B. G. Loos. "Modeling susceptibility to periodontitis." Journal of dental research 92, no. 1 (2013): 45-50. doi:10.1177/0022034512465435.
Potamias, George, Lefteris Koumakis, and Vassilis Moustakis. "Gene selection via discretized gene-expression profiles and greedy feature-elimination." In Methods and Applications of Artificial Intelligence, pp. 256-266. Springer Berlin Heidelberg, 2004
Shaveta Mehta, Nick P. Hughes, Sonia Li, Adrian Jubb, Rosie Adams, Simon Lord, Lefteris Koumakis et al. "Radiogenomics Monitoring in Breast Cancer Identifies Metabolism and Immune Checkpoints as Early Actionable Mechanisms of Resistance to Anti-angiogenic Treatment." EBioMedicine 10 (2016): 109-116
Haridimos Kondylakis, Lefteris Koumakis, Stephanie Hänold, Iheanyi Nwankwo, Nikolaus Forgó, Kostas Marias, Manolis Tsiknakis, Norbert Graf. "Donor’s support tool: Enabling informed secondary use of patient’s biomaterial and personal data." International Journal of Medical Informatics (2016).
Sfakianaki, Pepi, Lefteris Koumakis, Stelios Sfakianakis, Galatia Iatraki, Giorgos Zacharioudakis, Norbert Graf, Kostas Marias, and Manolis Tsiknakis. "Semantic biomedical resource discovery: a Natural Language Processing framework." BMC medical informatics and decision making 15, no. 1 (2015): 77
Haridimos Kondylakis, Brecht Claerhout, Mehta Keyur, Lefteris Koumakis, Jasper van Leeuwen, Kostas Marias, David Perez-Rey, Kristof de Schepper, Manolis Tsiknakis, Anca Bucur. "The INTEGRATE Project: Delivering solutions for efficient multi-centric clinical research and trials." Journal of biomedical informatics 62 (2016): 32-47
Kondylakis, H., Koumakis, L., Tsiknakis, M., Marias, K., Genitsaridi, E., Pravettoni, G., Gorini, A. and Mazzocco, K., 2013. Smart recommendation services in support of patient empowerment and personalized medicine. In Multimedia Services in Intelligent Environments (pp. 39-61). Springer International Publishing
Full list of publications can found at Google Scholar
Research Projects
MyPal (H2020-SC1-2018-Single-Stage-RTD No. 825872)
Work package leader on behalf of CBML at the project MyPal (Fostering Palliative Care of Adults and Children with Cancer through Advanced Patient Reported Outcome Systems) and leader of the software architecture. Total budget of the project 4 Million euros (FORTH budget 330.000)
Bounce (H2020-SC1-2017-CNECT-2 No. 643529)
Technical coordinator on behalf of CBML at the Bounce EU Horizon2020 project. Total budget of the project 5 Million euros (CBML-FORTH budget 725.000).
iManageCancer (H2020-PHC-26-2014 No. 643529)
Scientific coordinator on behalf of CBML at the EU Horizon2020 project and leader of the Smart analytical data services work package. Total budget of the project 4.8 Million euros (CBML-FORTH budget 750.000).
EURECA - Enabling information re-Use by linking clinical REsearch and Care (FP7-ICT-2011.7 No 288048)
Leader of the evaluation and validation work package. Worked and coordinated the verification, validation and evaluation activities of the EURECA components and the clinical scenarios
ENCCA - EUROPEAN NETWORK for CANCER research in CHILDREN and ADOLESCENTS (ENCCA project FP7-HEALTH-F2-2011 No. 261474)
Member of the biological research IT team of the EUROPEAN NETWORK for CANCER research in CHILDREN and ADOLESCENTS (ENCCA project FP7-HEALTH-F2-2011 No. 261474). Worked on the definition of the minimum common dataset for biobanks and on the implementation of a knowledge discovery algorithm for gene regulatory network.
P-Medicine (FP7-ICT-IP-270089) 2011-2015
Implemented bioinformatics and systems biology algorithms for miRNA datasets and their combination with gene regulatory networks. Designed and implemented a natural language processing framework for semantic biomedical resource discovery.
REACTION - Remote Accessibility to Diabetes Management and Therapy in Operational Healthcare Networks (FP7-IP-No 248590)
Design and implementation of predictive models and risk assessment for diabetes. Developed new general algorithms for predictive modelling and participated in the design of the predictive model platform.
ACGT - Advancing Clinico-Genomic Clinical Trials on Cancer: Open Grid Services for Improving Medical Knowledge Discovery (EU-FP6-IST-026996)
Worked on the design and implementation of a web based scientific workflow editor for the orchestration of bioinformatics web services and scripts. Integration of clinical (from clinical trials) and genomic data and implementation of bioinformatics algorithms for (i) gene selection (ii) classification.
InfoBioMed - Structuring European Biomedical Informatics to Support Individualized Healthcare (EU-FP6-IST-507585)
Design and implementation of the online (web based) biobank database. Implementation of text mining algorithms for plain text data.
Gen2Phen - Genotype-to-Phenotype Databases: A Holistic Solution (EU-FP7-HEALTH-200754)
Research and evaluation of web based scientific workflow platforms for distributed environments.
MIMP - Development of curriculum for a Master’s degree in Medical Informatics in Egypt (TEMPUS JEP-31053-2003)
Professor’s assistant for the Master’s degree in Medical Informatics in Egypt.
WS-Talk - Web Services Communicating in the Language of Their User Community (EU-FP6-COOP-CT-00602615)
Worked on natural language processing algorithms and web services orchestration.
Teaching Experience
Adjunct Instructor
1 semester (Spring 2019): Adjunct professor - course “Bioinformatics and Simulation of Physiological Systems” at the Department of Informatics Engineering, Technological Education Institute of Crete.
Adjunct Instructor
1 semester (Spring 2019): Adjunct professor - course “Mathematical Models in Biology” at the M.Sc. Bioinformatics and Neuroinformatics, Hellenic Open University
Adjunct Instructor
1 semester (Spring 2019): Adjunct professor - course “Introduction to Biomedical Signals and Applications” at the Department of Informatics Engineering, Technological Education Institute of Crete.
Adjunct Instructor
1 semester (Spring 2018): Adjunct professor - course “Bioinformatics and Simulation of Physiological Systems” at the Department of Informatics Engineering, Technological Education Institute of Crete.
Adjunct Instructor
1 semester (Fall 2017): Adjunct professor - course "Multimedia eHealth Services" at the Department of Ιnformatics Engineering of the Technological Educational Institute of Crete
Adjunct Instructor
1 semester (Spring 2017): Adjunct professor - course "Bioinformatics and Simulation of Physiological Systems" at the Department of Ιnformatics Engineering of the Technological Educational Institute of Crete
Adjunct Laboratory Collaborator/Instructor
1 semester (Spring 2010): Adjunct Laboratory Collaborator/Instructor at the Department of Informatics Engineering, Technological Education Institute of Crete, course “Object-oriented programming”
8 semesters (Fall 2005, Spring 2006, Fall 2006, Spring 2007, Fall 2007, Spring 2008, Fall 2008, Spring 2009): Adjunct Laboratory Collaborator/Instructor at Department of Sciences, Technological Education Institute of Crete for the course “Advanced programming” at Civil Engineering department
Teaching assistant
2 semesters (Spring 2002 & spring 2003) : Teaching assistant at Computer Science Department, University of Crete for the course “Digital Design”
1 semester (Fall 2002): Teaching assistant at Computer Science Department, University of Crete for the course “Logic”
1 semester (Fall 2001): Teaching assistant at Computer Science Department, University of Crete for the course “Machine learning”
