Pavlopoulou Lab. on Computational Systems Biology


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.


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.
  • Nutraceuticals
  • Development of bioinformatics pipelines for the analysis of biological data.


NaturaProDB is a representative database of diverse natural products with anticancer and chemopreventive activity (



Journal issue cover

The researsch article entitled "Bioinformatic approaches to the investigation of the atavistic genes implicated in cancer" was selected as cover story for the journal Frontiers in Bioscience (Landmark Edition)

Group Members

Pavlopoulou Lab. on Computational Systems Biology

Research Group Leader

+90 232 299 41 00 (5231)
+9 0 (232) 299 41 73

Işıl TAKAN PhD Student

Seyedehsadaf ASFA MSc Student


Yağmur KAFALI MSc Student

Melih ÖZBEK MSc Student

Halil İbrahim PAZARBAŞI PhD Student

Didem ÖKMEN PhD Student

Former Members

Halil İbrahim TOY PhD Student

Hande YILMAZ MSc Student

Selected Publications

Geronikolou SA, Takan I, Pavlopoulou A, Mantzourani M, Chrousos GP. Thrombocytopenia in COVID‑19 and vaccine‑induced thrombotic thrombocytopenia. International Journal of Molecular Medicine. 2022 March ; 49 (3) : 1-19. doi:10.3892/ijmm.2022.5090. Download

Posani E, Dilucca M, Forcelloni S, Pavlopoulou A, Georgakilas AG, Giansanti A. Temporal evolution and adaptation of SARS-CoV-2 codon usage. Frontiers in bioscience (Landmark edition). 2022 January ; 27 (1) : 13. doi:10.31083/j.fbl2701013. Download

Faustino D, Brinkmeier H, Logotheti S, Jonitz-Heincke A, Yilmaz H, Takan I, Peters K, Bader R, Lang H, Pavlopoulou A, Pützer BM, Spitschak A. Novel integrated workflow allows production and in-depth quality assessment of multifactorial reprogrammed skeletal muscle cells from human stem cells.. Cellular and molecular life sciences : CMLS. 2022 April ; 79 (5) : 229. doi:10.1007/s00018-022-04264-8. Download

Ozkur M, Benlier N, Takan I, Vasileiou C, Georgakilas AG, Pavlopoulou A, Cetin Z, Saygili EI. Ginger for Healthy Ageing: A Systematic Review on Current Evidence of Its Antioxidant, Anti-Inflammatory, and Anticancer Properties.. Oxidative Medicine and Cellular Longevity. 2022 May ; 2022 : 4748447. doi:10.1155/2022/4748447. Download

Okay K, Varış PÜ, Miral S, Pavlopoulou A, Oktay Y, Karakülah G. Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment.. Journal of autism and developmental disorders. 2022 June . doi:10.1007/s10803-022-05636-6. Download

Logotheti S, Pavlopoulou A, Marquardt S, Takan I, Georgakilas AG, Stiewe T. p73 isoforms meet evolution of metastasis.. Cancer metastasis reviews. 2022 August . doi:10.1007/s10555-022-10057-z. Download

Arshinchi Bonab R, Asfa S, Kontou P, Karakülah G, Pavlopoulou A. Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach.. PeerJ. 2022 October ; 10 : e14149. doi:10.7717/peerj.14149. Download

Sagkrioti E, Biz GM, Takan I, Asfa S, Nikitaki Z, Zanni V, Kars RH, Hellweg CE, Azzam EI, Logotheti S, Pavlopoulou A, Georgakilas AG. Radiation Type- and Dose-Specific Transcriptional Responses across Healthy and Diseased Mammalian Tissues.. Antioxidants (Basel, Switzerland). 2022 November ; 11 (11) . doi:10.3390/antiox11112286. Download

Özbek M, Toy HI, Takan I, Asfa S, Arshinchi Bonab R, Karakülah G, Kontou PI, Geronikolou SA, Pavlopoulou A. A Counterintuitive Neutrophil-Mediated Pattern in COVID-19 Patients Revealed through Transcriptomics Analysis.. Viruses. 2022 December ; 15 (1) . doi:10.3390/v15010104. Download

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. Download

Geronikolou SA, Pavlopoulou A, Cokkinos DV, Bacopoulou F, Chrousos GP. Polycystic οvary syndrome revisited: An interactions network approach.. European journal of clinical investigation. 2021 May . doi:10.1111/eci.13578. Download

Marquardt S, Pavlopoulou A, Takan I, Dhar P, Pützer BM, Logotheti S. A Systems-Based Key Innovation-Driven Approach Infers Co-option of Jaw Developmental Programs During Cancer Progression.. Frontiers in cell and developmental biology. 2021 June ; 9 : 682619. doi:10.3389/fcell.2021.682619. Download

Moumoulidis PT, Pavlopoulou A, Ünal R, Mavragani I, Georgakilas AG, Kyrodimos E. Nodal tumor volume as a prognostic factor for head and neck squamous cell carcinoma: a systematic review.. Frontiers in bioscience (Landmark edition). 2021 July ; 26 (7) : 235-245. doi:10.52586/4937. Download

Geronikolou SA, Pavlopoulou A, Chrousos GP, Cokkinos DV. Interactions Networks for Primary Heart Sarcomas.. Cancers. 2021 August ; 13 (15) : 3882. doi:10.3390/cancers13153882. Download

Louka A, Takan I, Pavlopoulou A, Georgakilas AG. Bioinformatic approaches to the investigation of the atavistic genes implicated in cancer.. Frontiers in bioscience (Landmark edition). 2021 August ; 26 (8) : 279-311. doi:10.52586/4944. Download

Theofylaktou D, Takan I, Karakülah G, Biz GM, Zanni V, Pavlopoulou A, Georgakilas AG. Mining Natural Products with Anticancer Biological Activity through a Systems Biology Approach.. Oxidative medicine and cellular longevity. 2021 August ; 2021 : 9993518. doi:10.1155/2021/9993518. Download

Yılmaz H, Toy HI, Marquardt S, Karakülah G, Küçük C, Kontou PI, Logotheti S, Pavlopoulou A. In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia.. International journal of molecular sciences. 2021 September ; 22 (17) : 9601. doi:10.3390/ijms22179601. Download

Raje S, Reddy N, Jerbi H, Randhawa P, Tsaramirsis G, Shrivas NV, Pavlopoulou A, Stojmenović M, Piromalis D. Applications of Healthcare Robots in Combating the COVID-19 Pandemic.. Applied bionics and biomechanics. 2021 November ; 2021 : 7099510. doi:10.1155/2021/7099510. Download

Pavlopoulou A, Asfa S, Gioukakis E, Mavragani IV, Nikitaki Z, Takan I, Pouget JP, Harrison L, Georgakilas AG. In Silico Investigation of the Biological Implications of Complex DNA Damage with Emphasis in Cancer Radiotherapy through a Systems Biology Approach. Molecules (Basel, Switzerland). 2021 December ; 26 (24) . doi:10.3390/molecules26247602. Download

S G, Pavlopoulou A, Lambrou GI, Koutelekos J, Cokkinos D, Albanopoulos K, Chrousos GP. Kisspeptin and the Genetic Obesity Interactome. Advances in experimental medicine and biology. 2021 January ; 1339 : 111-117. doi:10.1007/978-3-030-78787-5_15. Download

Dilucca M, Forcelloni S, Georgakilas AG, Giansanti A, Pavlopoulou A. Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes.. Viruses. 2020 April ; 12 (5) . doi:10.3390/v12050498. Download

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. Download

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. Download

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. Download

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. Download

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. Download

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. Download

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

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. Download

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. Download

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

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. Download

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. Download

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. Download

Total : 34

Selected Book Chapters

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

Total : 1


The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Using Crispr/Cas9 Genome Wide Sequencing in Determination of Anoikis Resistance Genes in Colon Carcinoma Cells, Ongoing

Academic Memberships

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


Pavlopoulou Lab. on Computational Systems Biology

Research Group Leader

+90 232 299 41 00 (5231)
+9 0 (232) 299 41 73