Computational Systems Biology
Principal Investigator: Assist. Prof. Athanasia PAVLOPOULOU
In the post-genomics era, there is undoubtedly a plethora of accumulated omics data. In our group, we apply and develop computational approaches in the study of complex biological systems by taking advantage of the publicly available high-throughput technologies. We also set up systems biology workflows for integrating, processing, analyzing, and interpreting this overwhelming information in a biologically and clinically meaningful way. Our purpose is to develop diagnostic markers and therapeutic targets for a range of diseases. To this end, we create a great arsenal of methods, including meta-analysis of epidemiological data, biological networks, machine learning, and in silico drug discovery.
Research Areas
- Analysis of biological sequences
- Analysis of high-throughput biological data
- Biological Networks
- Computer-aided Drug Design
- Development of bioinformatics pipelines for the analysis of biological data
- Machine learning
- Meta-analysis of epidemiological data
- Natural Language Processing
- Nutraceuticals
- Phylogenetics & Comparative Genomics
Publications
Bigiş EZ, Yıldız E, Tagka A, Pavlopoulou A*, Chrousos GP, Geronikolou S. (2025) “Novel Minimal Absent Words Detected in Influenza A Virus” Viruses 17:659.
Logotheti S, Vasilopoulos SN, Tremi I, Gkikoudi A, Fragkos M, Pavlopoulou A, Havaki S, Georgakilas AG (2025) “The DNA Damage Response as an Auxiliary Indicator of Senescence in Cancer: A User-Friendly Toolkit of Markers and Detection Methods” Methods in Molecular Biology 2906:83-112
Asfa SS, Arshinchi Bonab R, Önder O, Uça Apaydın M, Döşeme H, Küçük C, Georgakilas AG, Stadler BM, Logotheti S, Kale S, Pavlopoulou A (2024) “Computer-Aided Identification and Design of Ligands for Multi-Targeting Inhibition of a Molecular Acute Myeloid Leukemia Network” Cancers 16:3607
Kafalı Y, Pavlopoulou A (2024) "From Hydra to Human: In Silico Investigation of the Atavistic Model of Cancer " Cukurova Medical Journal 49: 863-880
Geronikolou S, Pavlopoulou A, Koutelekos I, Kalogirou D, Bacopoulou F, Cokkinos DV. (2024) “Polycystic Ovary Syndrome and Ferroptosis: Following Ariadne’s Thread” Biomedicines 12:2280
Projects & Patents
Completed projects:
The Scientific and Technological Research Council of Turkey - TÜBİTAK 1001 - RD : Characterization of SOX7 transcription factor that is located in recurrently deleted 8p23.1 locus on developmentand drug resistance of multiple myeloma through molecular, epigenomic, and transcriptomic approaches, Finished
The Scientific and Technological Research Council of Turkey - TÜBİTAK 1001 - RD : Using Crispr/Cas9 Genome Wide Sequencing in Determination of Anoikis Resistance Genes in Colon Carcinoma Cells, Finished
The Scientific and Technological Research Council of Turkey - TÜBİTAK 1001 - RD : Development of New Multifunctional Intelligent Artificial Virus Carrier Systems and Targeting Afatinib Resistance Genes Identified in Triple Negative Breast Cancer Cells by Crispr/Cas9 Genome-Wide Sequencing and Obtaining TNBC Treatment Response, Finished
General Secretariat for Research and Innovation of Greece - ARISTEIA II - RD : IntDaMuS: Integration of Data from Multiple Sources, Finished
European Union - INSPIRE - RD : INtegrating the emerging research Potential of the University of Athens Cancer Research Group in the European research area, Finished
European Union - BioExplore - RD : Biotechnology for the exploitation of microalgae, Finished
Ongoing Projects:
Turkish Society of Medical Oncology - P-TTOD-2022-165 - RD : Investigation of the Effect of Natural Compounds Obtained by NaturaProDB Database Analysis and Increasing Treatment Response on HER-2 (+) Breast Cancer Cell,.
General Secretariat for Research and Innovation of Greece - DEKA UTH - RD : Analysis of complex biological networks in systems biology.
Patents:
Kossida S, Vlachakis D, Tsiliki G, Pavlopoulou A (May 2012) “3D PHARMACOPHORE FOR THE DESIGN OF HUMAN POLYADENOSINE RIBONUCLEASE (PARN) INHIBITORS” GR/2012/0100266 – 21.05.2012 (Pub) – 201201605 – 21.05.2012
Staff
Active Members
Merve UÇA APAYDIN (Researcher)
Didem ÖKMEN (PhD Student)
Egemen Erdem GÜLER (PhD Student)
Ahenk ER UĞURCAN (PhD Student)
Elif YILDIZ (PhD Student)
İlayda KELEŞ (MSc Student)
Elif Zülal BİGİŞ (MSc Student)
Eren ÖZ (MSc Student)
Former Members
Işıl TAKAN (PhD Student)
Halil İbrahim TOY (PhD Student)
Merve UÇA APAYDIN (PhD Student)
Halil İbrahim PAZARBAŞI (PhD Student)
Yağmur KAFALI (MSc Student)
Hande YILMAZ (MSc Student)
Melih ÖZBEK (MSc Student)
Seyedehsadaf ASFA (MSc Student)
Reza ARSHINCI BONAB (MSc Student)
