About

Lefteris Koumakis

I am an informatics professional, expert in design development and adaptation of methodologies and tools for knowledge discovery on heterogeneous data sources. My research interests include biomedical informatics, eHealth, bioinformatics, data mining and systems integration.

I am the IT Architect of the Greek Biobanks network (BBMR-GR), responsible for the coordination and connection of the Greek biobank Centers and their linkage with collections in other European Center via the BBMRI-ERIC. Author of MinePath, an interactive pathway analysis web server for real-time identification of differentially expressed sub-pathways in gene regulatory networks.

  • Computer Science
  • Data Mining
  • BioInformatics
  • Computational Biology

Education

Doctorate of Philosophy (Ph.D.)

Systems biology - Technical University of Crete Greece

Dissertation: Computational methods for knowledge discovery from heterogeneous data sources: methodology and implementation on biological and molecular sources

Advisors: Vassilis Moustakis, George Potamias, Michael Zervakis

2011-2014

Master of Science (M.Sc.)

Computer Science Department, University of Crete, Greece

Thesis: HealthObs: Health Observatory. Uniform Modelling and Intelligent Data Processing in Distributed and Heterogeneous Clinical Information Sources

Advisors: Stelios Orfanoudakis, George Potamias

2002-2004

Bachelor of Science (B.Sc.)

Computer Science Department, University of Crete, Greece

Thesis: Automated Construction and Revision of Semantic Networks.

Advisor: George Potamias

1996-2001

Awards

IADR/AADR William J. Gies Award

The publication entitled Modeling susceptibility to periodontitis received the IADR/AADR William J. Gies Award for the best clinical research paper published in the Journal of Dental Research (JDR) during the preceding year.

The JDR is the top ranked journal (Impact Factor: 4.144) for original scientific articles in dentistry.

Best Student Paper Award

The publication: L. Koumakis, G. Potamias, K. Marias and M. Tsiknakis. “An Algorithmic Approach for the Effect of Transcription Factor Binding Sites over Functional Gene Regulatory Networks” received the Best Student Paper Award at the 15th IEEE International Conference on Bioinformatics & Bioengineering (BIBE).

Scholarships

Heraclitus II

Ph.D. Scholarship (2011-2014): Heraclitus II, Investing in knowledge society through the European Social Fund.

FORTH M.Sc.

M.Sc. Student Research Fellowship (2002-2004), Foundation for Research and Technology – Hellas (FORTH) - Institute of Computer Science (ICS)

Erasmus

Erasmus Program Scholarship (2001) at Universitat Politècnica de Catalunya (Spring 2001)

Work

Web Based systems

Current Projects

Past Projects

Leadership Activities

IT Architect of the Greek Biobanks network (BBMR.gr)

BBMRI-GR will create a network of Greek Biobanks and connect them with the BBMRI-ERIC. The IT architect is responsible for the coordination and connection of all the Greek Centers of biobank collections and their linkage with existing collections in other European Centers, via the BBMRI-ERIC. Furthermore, L. Koumakis represents Greece at the BBMRI-ERIC Common Services IT.

H2020 - Scientific coordinator on behalf of CBML

Scientific coordinator on behalf of CBML at the EU Horizon2020 project iManageCancer - Empowering patients and strengthening self-management in cancer diseases (H2020-PHC-26-2014 No. 643529) and leader of the Smart analytical data services work package. Total budget of the project 4.8 Million euros (CBML-FORTH budget 750.000).

FP7 - Work Package leader

Work package leader on behalf of CBML at the FP7 EU project EURECA - Enabling information re-Use by linking clinical REsearch and Care (FP7-ICT-2011.7 No 288048). Total budget of the project 13 Million euros (CBML-FORTH budget 960.000).

Research Projects

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.

Selected Publications

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

Teaching Experience

Adjunct Instructor

1 semester (Spring 2017): Instructor for the 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”

Skills

Languages

  • Greek : Native
  • English : Full professional proficiency (ILR level 4, C2)
  • Spanish : Basic (ILR level 0)

Programming languages

  • Java : Expert
  • JavaScript : Expert
  • C++, C, C# : Good
  • V.Basic, .net : Good
  • R-statistic : Basic

Other tools/platforms

  • Weka, SPSS
  • Tomcat/servlets, web/rest services
  • Unix