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Collaborating Researcher
Computational BioMedicine Lab (CBML) Email: koumakis@ics.forth.gr |
Short CV
Dr. L. Koumakis is an experienced biomedical informatics professional with expertise in computational biology, bioinformatics, data mining and software infrastructures for life science. Expert in design, development and adaptation of methodologies and tools for knowledge discovery from heterogeneous clinico-genomic data to strengthen and support individualized and stratified medicine protocols. L. Koumakis is 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. He is the author of MinePath (www.minepath.org), an interactive pathway analysis web-server for real-time identification of differentially expressed sub-pathways in gene regulatory networks. In the past, he has worked in the design and implementation of service-oriented architectures for life sciences and he has experience in formal validation and evaluation procedures for software. He has participated in various international and national R&D projects and has published more than 60 papers in scientific journals, proceedings of international conferences & workshops, related to his fields of expertise. He serves as a reviewer for journals in the field of bioinformatics, including Plos and frontiers, and as project evaluator for the Greek General Secretary of Research and Technology and for the French National Alliance for Life and Health Sciences (call for proposals in the field of multidisciplinary approaches in modeling complex biological processes applied to cancer field).
Full CV can be found here.
Research Interests
His current research interests are in the following areas:
- Bioinformatics
- Computational Biology
- Data Mining
- Machine Learning
- Natural language processing
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).
- IMIA Yearbook of Medical Informatics – one of the best articles from the literature: The publication entitled Donor’s support tool: Enabling informed secondary use of patient’s biomaterial and personal data has been selected to be included in the IMIA Yearbook of Medical Informatics as one of the best articles from the literature in the ‘Consumer Health Informatics’ subfield of medical informatics published in the past year.
Participation in Research Projects
- MyPal – Fostering Palliative Care of Adults and Children with Cancer through Advanced Patient Reported Outcome Systems H2020-SC1-2018-Single-Stage-RTD Νο. 825872 (accepted, expected start date 12/2018, duration 42 Months)
- OpenBioC – AN OPEN AND INTEGRATED COLLABORATIVE BIOINFORMATICS PLATFORM. Ερευνώ Δημιουργώ Καινοτομώ Τ1ΕΔΚ-05275 (9/7/2018 – 8/7/2021)
- BOUNCE – Predicting Effective Adaptation to Breast Cancer to Help Women to BOUNCE Back. H2020-SC1-2017-CNECT-2 (1/11/2017-31/10/2021)
- iManageCancer – Empowering patients and strengthening self-management in cancer diseases. H2020-PHC-26-2014 No. 643529 (Scientific coordinator on behalf of CBML)
- EURECA – Enabling information re-Use by linking clinical REsearch and Care, FP7-ICT-2011.7 No 288048 (WP leader on behalf of CBML)
- ENCCA – EUROPEAN NETWORK for CANCER research in CHILDREN and ADOLESCENTS, FP7-HEALTH-F2-2011 No. 261474
- P-MEDICINE – From data sharing and integration via VPH models to personalized medicine, FP7-ICT-2009.5.3, No 270089
- REACTION – Remote Accessibility to Diabetes Management and Therapy in Operational Healthcare Networks, FP7-IP-No 248590
- GEN2PHEN – Genotype-to-Phenotype Databases: A Holistic Solution, EU-FP7-HEALTH-200754
- INFOBIOMED – Structuring European Biomedical Informatics to Support Individualized Healthcare EU-FP6-IST-507585
- ACGT – Advancing Clinico-Genomic Clinical Trials on Cancer: Open Grid Services for Improving Medical Knowledge Discovery, EU-FP6-IST-026996
- MIMP – Development of curriculum for a Master s degree in Medical Informatics in Egypt, TEMPUS JEP-31053-2003
- WS-TALK – Web Services Communicating in the Language of Their User Community, EU-FP6-COOP-CT-00602615
- PROGNOCHIP – Development and Establishment of DNA Microarray Technology in Greece: Identification and Validation of Classification and Prognosis Molecular Markers for Breast Cancer, GSRT/Greece-EPAN
- IRAIA – Getting orientation in complex information spaces as an emergent behaviour of autonomous information agents, IST/ 1999-10602