Saez-Rodriguez Group

Systems biomedicine

Angeliki Kalamara, M.Sc.

After obtaining my Diploma in Computer Engineering from the Polytechnic School at University of Patras I continued my Master studies with specialization in Bioinformatics at National and Kapodistrian University. During the last year of my master’s degree I spent half of my research term at INRIA Sophia-­Antipolis, as an intern in the Algorithms Biology Structure (ABS) team where I dealt with Cryo­–Electron Microscopy maps segmentation to detect the individual protein complex's subunits by heavily relying on computational geometry methods. Afterwards, I joined Dr. Julio Saez-Rodriguez’s group at the European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI) as an intern where my main project was the analysis of microarray gene expression profiles of primary tumours and cell lines from colorectal cancer using consensus-based unsupervised clustering and association to drug response. Currently, I conduct my PhD research at Dr. Julio Saez-Rodriguez’s group at the Joint Research Center for Computational Biomedicine where I am working on the development of physiologically-based pharmacokinetic/pharmacodynamic (PBPK/PD) models.

Research Interests

Currently, my research interests cover the areas of physiologically-based pharmacokinetic/pharmacodynamic (PBPK/PD) modeling, drug combination therapies and drug-drug interactions (DDI’s) in cancer research. A full PBPK/PD model is taking into account the physiology of an individual or a population and links dose-concentration (Pharmacokinetics) and concentration-effect (Pharmacodynamics) relationships thereby facilitating the description and prediction of the time-course of the drug effects resulting from a certain dose regimen. In the context of cancer, I am interested in integrating patient-specific molecular characteristics (e.g genomic) in order to understand inter-subject variability in drug response. The main goal is the coupling of drug exposure to tumor drug response. Moreover, the development of PBPK models can help dealing with complex DDI’s and predict patients’ response to drug combination therapies.

Professional Career

2014-2015 Internship at European Bioinformatics Institute (EMBL-EBI), Systems Biomedicine Group
2013 Internship at INRIA Sophia-Antipolis, Structural Bioinformatics


2015-present PhD student in mechanistic modeling at JRC Combine, RWTH Aachen, Germany
2011-2014 MSc in Bioinformatics, National and Kapodistrian University of Athens
2005-2011 5-year Diploma in Computer Engineering and Informatics, University of Patras