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

Seyedehsadaf ASFA MSc Student  sadaf.asfa@msfr.ibg.edu.tr


REZA ARSHINCI BONAB MSc Student  reza.arshinchi@msfr.ibg.edu.tr


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


Melih ÖZBEK MSc Student  melih.ozbek@msfr.ibg.edu.tr


Didem ÖKMEN PhD Student  didem.okmen@msfr.ibg.edu.tr


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


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


Former Members

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


Selected Publications

Toy HI, Karakülah G, Kontou PI, Alotaibi H, Georgakilas AG, Pavlopoulou A. Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach.. Frontiers in cell and developmental biology. 2021 April ; 9 : 770. doi:10.3389/fcell.2021.620248.

Logotheti S, Marquardt S, Richter C, Sophie Hain R, Murr N, Takan I, Pavlopoulou A, Pützer BM. Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk.. Cancers. 2020 December ; 12 (3789) : 1-21. doi:10.3390/cancers12123789.

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 : 14

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