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

Our 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.
  • Computer-aided drug design

NaturaProDB

NaturaProDB is a representative database of diverse natural products with anticancer and chemopreventive activity (https://naturaprodb.web.app/).

 

 

 

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) https://www.fbscience.com/Landmark/articles/10.52586/4944

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

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


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


Yağmur KAFALI MSc Student  yagmur.kafali@ibg.edu.tr


Egemen Erdem GÜLER PhD Student  egemen.guler@ibg.edu.tr


MERVE UÇA APAYDIN PhD Student  merve.uca@ibg.edu.tr


Former Members

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


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


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


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


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


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


Selected Publications

Zanni V, Papakonstantinou D, Kalospyros SA, Karaoulanis D, Biz GM, Manti L, Adamopoulos A, Pavlopoulou A, Georgakilas AG. RadPhysBio: A Radiobiological Database for the Prediction of Cell Survival upon Exposure to Ionizing Radiation.. International journal of molecular sciences. 2024 April ; 25 (9) . doi:10.3390/ijms25094729. Download

Özbek M, Toy HI, Oktay Y, Karakülah G, Suner A, Pavlopoulou A. An in silico approach to the identification of diagnostic and prognostic markers in low-grade gliomas.. PeerJ. 2023 March ; 11 : e15096. doi:10.7717/peerj.15096. Download

Takan I, Karakülah G, Louka A, Pavlopoulou A. "In the light of evolution:" keratins as exceptional tumor biomarkers.. PeerJ. 2023 March ; 11 : e15099. doi:10.7717/peerj.15099. Download

Asfa S, Toy HI, Arshinchi Bonab R, Chrousos GP, Pavlopoulou A, Geronikolou SA. Soft Tissue Ewing Sarcoma Cell Drug Resistance Revisited: A Systems Biology Approach.. International journal of environmental research and public health. 2023 July ; 20 (13) : 6288. doi:10.3390/ijerph20136288. Download

Vasilopoulos SN, Güner H, Uça Apaydın M, Pavlopoulou A, Georgakilas AG. Dual Targeting of DNA Damage Response Proteins Implicated in Cancer Radioresistance.. Genes. 2023 December ; 14 (12) . doi:10.3390/genes14122227. Download

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

Kontou PI; Pavlopoulou A; Dimou N; Theodoropoulou M; Braliou G; Tsaousis G; Pavlopoulos G; Hamodrakas S; Bagos P. The human GPCR signal transduction network . Network Modeling Analysis in Health Informatics and Bioinformatics . 2021 January ; 10 (3) . doi:10.1007/s13721-020-00278-z. 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

Kostandinos Tsaramirsis, Akshet Patel, Pranav Sharma, Nikunj Reddy, Princy Randhawa, Georgios Tsaramirsis, Athanasia Pavlopoulou, Zeynep A. Koçer and Dimitrios Piromalis. Bio-Virus Spread Simulation in Real 3D Space using Augmented Reality. Engineered Science. 2021 November ; 16 : 319-330. doi:10.30919/es8d592. 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 : 41

Selected Book Chapters

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

Total : 1

Selected Proceedings

Asfa S, Arshinchi Bonab R, Pavlopoulou A, Isik Z 2021, 'Algorithm-based approach to uncover potential microRNAs related to cancers of the gastrointestinal track', International Biotechnology Congress, Diyarbakır, Türkiye, Sept. 9, 2021 .

Geronikolou SA, Pavlopoulou A, Cokkinos D, Kanaka-Gantenbein C, Chrousos G, Albanopoulos 2019, 'PUBERTY AND OBESITY: KISSPEPTIN AND ITS RECEPTOR IN THE ANS/INFLAMMATION OBESITY INTERACTOME', 24th World Congress of the International-Federation-for-the-Surgery-of-Obesity-and-Metabolic-Disorders (IFSO) / 21st SECO Congress, Madrid, Spain, Sept. 3, 2019 .

Geronikolou SA, Pavlopoulou A, Chrousos G, Cokkinos D 2018, 'A novel interactome to guide therapy and avoid heart failure in cardiac cancer patients', European Society of Cardiology Congress, Munich, Germany, Aug. 25, 2018 .

Geronikolou S, Albanopoulos K, Cokkinos D, Pavlopoulou A, Chrousos G 2018, 'Kisspeptin and Stress Induced Obesidome', 8th Congress of the International Federation for the Surgery of Obesity and Metabolic Disorders, Athens, Greece, May 17, 2018 .

Geronikolou S, Albanopoulos K, Cokkinos D, Pavlopoulou A, Chrousos G 2018, 'A novel interactome to guide therapy and avoid heart failure in cardiac cancer patients', 8th Congress of the European-Chapter of the International-Federation-for-the-Surgery-of-Obesity-and-Metabolic-Disorders (IFSO-EC), Athens, Greece, May 17, 2018 .

Total : 5

Projects

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

Patents

  • Kossida S, Vlachakis D, Tsiliki G, Pavlopoulou A , 3D PHARMACOPHORE FOR THE DESIGN OF HUMAN POLYADENOSINE RIBONUCLEASE (PARN) INHIBITORS, GR/2012/0100266

Awards

  • Best Poster Award-Işıl TAKAN by 12th International Symposium on Health Informatics and Bioinformatics, 2019
  • Short Term Scientific Mission Scholarship by EuroKUP COST Action, 2010

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