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
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
Elif Zülal BİGİŞ
MSc Student
zulal.bigis@std.ibg.edu.tr
Ahenk ER UĞURCAN
PhD Student
ahenk.er@ibg.edu.tr
Elif YILDIZ
PhD Student
elif.yildiz@ibg.edu.tr
MERVE UÇA APAYDIN
Researcher
merve.uca@ibg.edu.tr
0 (232) 299 _ _
İlayda KELEŞ
MSc Student
ilayda.keles@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
Halil İbrahim PAZARBAŞI
PhD Student
halil.pazarbasi@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
MERVE UÇA APAYDIN
PhD Student
merve.uca@ibg.edu.tr
0 (232) 299 _ _
Selected Publications
Logotheti S, Vasilopoulos SN, Tremi I, Gkikoudi A, Fragkos M, Pavlopoulou A, Havaki S, Georgakilas AG. 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 (Clifton, N.J.). 2025 January ; 2906 : 83-112. doi:10.1007/978-1-0716-4426-3_6.
Bigiş EZ, Yıldız E, Tagka A, Pavlopoulou A, Chrousos GP, Geronikolou S. Novel Minimal Absent Words Detected in Influenza A Virus.. Viruses. 2025 April ; 17 (5) . doi:10.3390/v17050659.
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) : 4729. doi:10.3390/ijms25094729.
Logotheti S, Pavlopoulou A, Rudsari HK, Galow AM, Kafali Y, Kyrodimos E, Giotakis AI, Marquardt S, Velalopoulou A, Verginadis II, Koumenis C, Stiewe T, Zoidakis J, Balasingham I, David R, Georgakilas AG. Intercellular pathways of cancer treatment-related cardiotoxicity and their therapeutic implications: The paradigm of radiotherapy.. Pharmacology & therapeutics. 2024 May : 108670. doi:10.1016/j.pharmthera.2024.108670.
Geronikolou SA, Pavlopoulou A, Uça Apaydin M, Albanopoulos K, Cokkinos DV, Chrousos G. Non-Hereditary Obesity Type Networks and New Drug Targets: An In Silico Approach.. International journal of molecular sciences. 2024 July ; 25 (14) . doi:10.3390/ijms25147684.
Geronikolou S, Pavlopoulou A, Koutelekos I, Kalogirou D, Bacopoulou F, Cokkinos DV. Polycystic Ovary Syndrome and Ferroptosis: Following Ariadne's Thread.. Biomedicines. 2024 October ; 12 (10) . doi:10.3390/biomedicines12102280.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Geronikolou SA, Pavlopoulou A, Chrousos GP, Cokkinos DV. Interactions Networks for Primary Heart Sarcomas.. Cancers. 2021 August ; 13 (15) : 3882. doi:10.3390/cancers13153882.
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.
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.
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.
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.
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.
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.
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.
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.
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 : 46
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