Pavlopoulou Lab. on Computational Systems Biology

OVERVIEW

In the post-genomics era, there is undoubtedly a plethora of accumulated genomic, genetic and proteomic data. However, there is a growing gap between the biological molecules (DNA, RNA and proteins) with experimentally determined function/structure and the ones that have not been assigned to any functional/structural annotation. To handle this overwhelming amount of information, we apply bioinformatics and systems biology methods for processing, analyzing, and interpreting biological data in a meaningful way.

RESEARCH INTERESTS

My main research interests include:

  • Application of bioinformatics methods for the analysis and meta-analysis of cancer genetics and genomics data.
  • Phylogenetics & Comparative genomics.
  • Analysis of biological sequences
  • Biological networks.
  • Development of bioinformatics pipelines for the analysis of biological data.

Group Members

Pavlopoulou Lab. on Computational Systems Biology

Research Group Leader

Athanasia PAVLOPOULOU
athanasia.pavlopoulou@ibg.edu.tr
+90 232 299 41 00 (5231)
+9 0 (232) 299 41 73

Hande YILMAZ MSc Student  hande.yilmaz@msfr.ibg.edu.tr


Işıl TAKAN PhD Student  isil.takan@msfr.ibg.edu.tr


Halil İbrahim PAZARBAŞI PhD Student  halil.pazarbasi@msfr.ibg.edu.tr


Halil İbrahim TOY MSc Student  ibrahim.toy@msfr.ibg.edu.tr


Selected Publications

Dimitriou NM; Pavlopoulou A; Tremi I; Koukoulias V; Georgakilas AG. Prediction of Gold Nanoparticle and Microwave-Induced Hyperthermia Effects on Tumor Control via a Simulation Approach. Nanomaterials. 2019 February ; 9 (2) : E167. doi:10.3390/nano9020167.

Düzgün MB, Theofilatos K, Georgakilas AG, Pavlopoulou A. A Bioinformatic Approach for the Identification of Molecular Determinants of Resistance/Sensitivity to Cancer Thermotherapy.. Oxidative medicine and cellular longevity. 2019 November ; 2019 : 4606219. doi:10.1155/2019/4606219.

Pavlopoulou A, Karaca E, Balestrazzi A, Georgakilas AG. In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. Oxidative medicine and cellular longevity. 2019 July ; 2019 : 8683054. doi:10.1155/2019/8683054.

Toy HI, Okmen D, Kontou PI, Georgakilas AG, Pavlopoulou A. HOTAIR as a Prognostic Predictor for Diverse Human Cancers: A Meta- and Bioinformatics Analysis. Cancers. 2019 June ; 11 (6) . doi:10.3390/cancers11060778.

Kontou PI; Pavlopoulou A; Braliou G; Bogiatzi S; Dimou NL; Bangalore S; Bagos P. Identification of Gene Expression Profiles in Myocardial Infarction: a Systematic Review and Meta-analysis. BMC Medical Genomics. 2018 September ; 11 : 109. doi:10.1186/s12920-018-0427-x.

Pavlopoulou A. RecA: a universal drug target in pathogenic bacteria. Frontiers in bioscience (Landmark edition). 2018 January ; 23 : 36-42. doi:10.2741/4580.

Nikolaou M, Pavlopoulou A, Georgakilas AG, Kyrodimos E. The challenge of drug resistance in cancer treatment: a current overview. Clin Exp Metastasis. 2018 April ; 35 (4) : 309-318. doi:10.1007/s10585-018-9903-0.

Pavlopoulos GA; Kontou PI; Bouyioukos C; Markou E; Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. GigaScience. 2018 April ; 7 (4) : 1-31. doi:10.1093/gigascience/giy014.

Karakülah G, Pavlopoulou A. In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. Genes. 2018 June ; 9 (6) : 284. doi:10.3390/genes9060284.

Nikitaki Z; Holá M, Doná M; Pavlopoulou A; Michalopoulos I; Angelis KJ; Georgakilas AG; Macovei A; Balestrazzi A . Integrating plant and animal biology for the search of novel DNA damage biomarkers. Mutat Res. 2018 March ; 775 : 21-38. doi:10.1016/j.mrrev.2018.01.001.

Pavlopoulou A, Bagos PG, Koutsandrea V, Georgakilas AG. Molecular determinants of radiosensitivity in normal and tumor tissue: A bioinformatic approach. Cancer Letters. 2017 September ; 403 : 37-47. doi:10.1016/j.canlet.2017.05.023.

Pavlopoulou, Athanasia; Oktay, Yavuz; Vougas, Konstantinos; Louka, Maria; Vorgias, Constantinos E.; Georgakilas, Alexandros G.. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. CANCER LETTERS. 2016 October ; 380 (2) : 485-493. doi:10.1016/j.canlet.2016.07.018.

Total : 12

Selected Book Chapters

Methods of Analysis and Meta-Analysis for Identifying Differentially Expressed Genes (2018). Genetic Epidemiology. Humana Press.

Total : 1

Academic Memberships

  • Hellenic Society for Computational Biology and Bioinformatics (HSCBB) , 2015
  • Türk Toraks Derneği, 2018

Contact

Pavlopoulou Lab. on Computational Systems Biology

Research Group Leader

Athanasia PAVLOPOULOU
athanasia.pavlopoulou@ibg.edu.tr
+90 232 299 41 00 (5231)
+9 0 (232) 299 41 73