Short Description

The research interest of the laboratory is based on the field of Molecular Biology - Systems Biology. Specifically, we study complex developmental processes and/or differentiation processes in various biological systems. We also study the bimodal role and dynamics of complex networks of transcription factors and epigenetic mechanisms, in relation to their (combined) role in the regulation of gene expression as well as in the spatiotemporal organization of chromatin architecture. We also study the richness and diversity of the microbial community through the study of the microbiome, with the aim of understanding it, revealing its properties, as well as discovering any microbial signature of specific products. Furthermore, we use eDNA to study the spatiotemporal biodiversity dynamics of marine environment. We also analyze the genomes of bacteria, so that we can classify them phylogenetically, categorize them in silico, as well as predict in silico their potential probiotic properties or properties related to our health.

To achieve all of the above goals, in addition to experimental procedures, we use programming languages, computational biology, and bioinformatics approaches for data analysis and processing.

Using holistic approaches, we can redesign the way we approach the dynamic interactions between cell components and between the cell and its environment, leading to the creation of biological networks and elucidating the properties of biological systems.

  • Study of the dynamics of transcription factors
  • Spatiotemporal organization of chromatin architecture
  • Epigenetics and its relationship to the regulation of gene expression
  • Study of microorganisms (genome analysis/mapping, etc.) and microbiome analysis
  • Microbiome and genome analysis of microorganisms
  • Bioinformatics
  • eDNA

  • 2024-present, Sus.Agri.Food, PI for DUTH: Professor Ioannis Kourkoutas, PK: Project team member
  • 2024-present BIOSHIELD, PI for DUTH: Professor Ioannis Kourkoutas, PK: Project team member
  • 2023-2025 Application of eDNA technology for the monitoring of fish stocks and genetic resources of the aquatic environment of the Thracian Sea as a tool for sustainable management (ECOeDNA), Green Fund. PK: PI
  • 2023-2025 Improving the conservation status of Pinus Heldreichii at the national level through traditional (propagation) and innovative methods (genotyping), Green Fund. PI for DUTH: Professor Aristotle Papageorgiou, PK: Project team member
  • 2022-2023 EMBO Workshop entitled “Systems biology: Linking chromatin and epigenetics to disease and development” PK: PI
  • 2022-2023 DRAMA TERROIR, PI for DUTH: Professor Marirena Grigoriou PK: Project team member
  • 2021 Bilateral relations of the Democritus University of Thrace with the Matis Research Institute in Iceland, Ministry of Education and Science , PI for DUTH: Professor Rafael Sandaltzopoulos,  PK: Project team member – Alternate PI
  • 2021-2023 PAZL, PI for DUTH Professor Marirena Grigoriou PK: Project team member – Alternate PI
  • 2021-2023 AGRO4+, PI for DUTH Professor Marirena Grigoriou PK: Project team member – Alternate PI
  • 2021-2023 Foodbiomes, PI for DUTH: Professor Ioannis Kourkoutas, PK: Project team member
  • 2021-2023 PavlidisTerroir, Professor Marirena Grigoriou PK: Project team member – Alternate PI

  1.  Picco G, Cetin R, Bindels E, van Beek G, van IJcken WFJ, van den Hout M, Kolovos P, Mulugeta E, Huylebroeck D, Grosveld F. (2026). Functional analysis of two uncharacterized genes, C130074G19Rik and I830077J02Rik, during early hematopoietic development. J Cell Sci. Jan 15;139(2)
  2. Seufert I, Gerosa I, Varamogianni-Mamatsi V, Vladimirova A, Sen E, Mantz S, Rademacher A, Schumacher S, Liakopoulos P, Kolovos P, Anders S, Mallm JP, Papantonis A, Rippe K. (2026) Two distinct chromatin modules regulate proinflammatory gene expression. Nat Cell Biol. Jan;28(1):182-196
  3. Tsikitis M, Diokmetzidou A, Liakopoulos P, Karipidou M, Kokkinopoulos I, Vatsellas G, Kloukina I, Kolovos P, Capetanaki Y. (2025). Molecular insights into the role of desmin intermediate filament network in chromatin landscape, cardiomyocyte differentiation, and maturation. Cell Death Dis. Oct 16;16(1):723.
  4. Tokamani M, Liakopoulos P, Tegopoulos K, Zigkou AM, Triantaphyllidis G, Kamidis N, Grigoriou ME, Sandaltzopoulos R, Kolovos P. # (2025). Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding. Microorganisms. Oct 15;13(10):2373.
  5. Papatheodorou I, Blažková G, Bosáková V, Tomášiková Z, Spearing E, Klieber R, Ostašov P, Štíchová J, Dvončová M, Mýtniková A, Emmer J, Bendíčková K, Tomáš T, Šrámek V, Kolovos P, Holubová M, Helán M, Vlková M, Frič J, Hortová-Kohoutková M. (2025). Redefining the role of IL-18 in post-surgical recovery and sepsis: a key mediator of inflammation resolution. J Transl Med. Jul 2;23(1):728.
  6. Bartusel M, Kim SX, Rehimi R, Darnell AM, Nikolić M, Heggemann J, Kolovos P, van Ijcken WFJ, Varineau J, Crispatzu G, Mangold E, Brugmann SA, Vander Heiden MG, Laugsch M, Ludwig KU, Rada-Iglesias A, Calo E. (2025). A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies. Am J Hum Genet.  May 1;112(5):1097-1116.
  7. Tegopoulos, K., Polychronidou, S.V., Voumvouraki, A., Kolovos, P., Skavdis, G., Grigoriou, M.E. (2025). Precise Identification of Vitis vinifera L. Varieties Using Cost-Effective NGS-Based SNP Genotyping.Horticulturae 11(4), 375;
  8. Bosáková, V., Papatheodorou, I., Kafka, F., Tomášiková, Z., Kolovos, P., Hortová Kohoutková, M., & Frič, J. (2025). Serotonin attenuates tumor necrosis factor-induced intestinal inflammation by interacting with human mucosal tissue. Experimental & molecular medicine Feb;57(2):364-378
  9. Tasis, A., Papaioannou, N. E., Grigoriou, M., Paschalidis, N., Loukogiannaki, K., Filia, A,…, Liakopoulos, P., Liapis, K., Kolovos, P., Chavakis, T., Alissafi, T., Kotsianidis, I., Mitroulis, I. (2024). Single-cell analysis of bone marrow CD8+ T cells in Myeloid Neoplasms predicts response to treatment with Azacitidine. Cancer research communications, 4(12),
  10. Tegopoulos, K., Tsirka, T., Stekas, C., Gerasimidi, E., Skavdis, G., Kolovos, P.#, Grigoriou, M.E.#. (2024) Spatiotemporal Dynamics of Assyrtiko Grape Microbiota. Microorganisms, 12(3):577.
  11. Tsetsos, F., Topaloudi, A., Jain, P., Yang, Z., Yu, D., Kolovos, P., Tumer, Z., … Paschou, P. (2024). Genome-wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome. Biological psychiatry, 96(2), 114–124.
  12. Tegopoulos, K., Fountas, D.V., Andronidou, E-M., Bagos, P.G., Kolovos, P., Skavdis, G., Pergantas, P., Braliou, G.G., Papageorgiou, A.C., Grigoriou, M.E. (2023) Assessing Genetic Diversity and Population Differentiation in Wild Hop (Humulus lupulus) from the Region of Central Greece via SNP-NGS Genotyping. Diversity, 15(12):1171.
  13. Varsamis, G. D., Karafyllidis, I. G., Gilkes, K. M., Arranz, U., Martin-Cuevas, R., Calleja, G., Dimitrakis, P., Kolovos, P., Sandaltzopoulos, R., Jessen, H. C., & Wong, J. (2023). Quantum gate algorithm for reference-guided DNA sequence alignment. Computational biology and chemistry, 107, 107959.
  14. Varsamis, G. D., Karafyllidis, I. G., Gilkes, K. M., Arranz, U., Martin-Cuevas, R., Calleja, G., Wong, J., Jessen, H. C., Dimitrakis, P., Kolovos, P., & Sandaltzopoulos, R. (2023). Quantum algorithm for de novo DNA sequence assembly based on quantum walks on graphs. Bio Systems, 233, 105037.
  15. Mitropoulou, G., Prapa, I., Nikolaou, A., Tegopoulos, K., Tsirka, T., Chorianopoulos, N., Tassou, C., Kolovos, P., Grigoriou, M. E., & Kourkoutas, Y. (2022). Effect of Free or Immobilized Lactiplantibacillus plantarum T571 on Feta-Type Cheese Microbiome. Frontiers in bioscience (Elite edition), 14(4), 31.
  16. Foutadakis, S., Roupakia, E., Liakopoulos, P., Kolovos, P.#, & Kolettas, E#. (2022). An Expanded Interplay Network between NF-κB p65 (RelA) and E2F1 Transcription Factors: Roles in Physiology and Pathology. Cancers, 14(20), 5047.
  17. Kiousi, D. E., Efstathiou, C., Tegopoulos, K., Mantzourani, I., Alexopoulos, A., Plessas, S., Kolovos, P., Koffa, M., & Galanis, A. (2022). Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. Frontiers in microbiology, 13, 922689.
  18. Schilders, K. A. A., Edel, G. G., Eenjes, E., Oresta, B., Birkhoff, J., Boerema-de Munck, A., Buscop-van Kempen, M., Liakopoulos, P., Kolovos, P., Demmers, J. A. A., Poot, R., Wijnen, R. M. H., Tibboel, D., & Rottier, R. J. (2022). Identification of SOX2 Interacting Proteins in the Developing Mouse Lung With Potential Implications for Congenital Diaphragmatic Hernia. Frontiers in pediatrics, 10, 881287.
  19. Tegopoulos, K., Stergiou, O. S., Kiousi, D. E., Tsifintaris, M., Koletsou, E., Papageorgiou, A. C., Argyri, A. A., Chorianopoulos, N., Galanis, A.#, & Kolovos, P.#  (2021). Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells. Biomedicines, 9(11), 1718.
  20. Stergiou, O. S., Tegopoulos, K., Kiousi, D. E., Tsifintaris, M., Papageorgiou, A. C., Tassou, C. C., Chorianopoulos, N., Kolovos, P.#, & Galanis, A.# (2021). Whole-Genome Sequencing, Phylogenetic and Genomic Analysis of Lactiplantibacillus pentosus L33, a Potential Probiotic Strain Isolated From Fermented Sausages. Frontiers in microbiology, 12, 746659.
  21. Boltsis, I., Grosveld, F., Giraud, G.#, & Kolovos, P.# (2021). Chromatin Conformation in Development and Disease. Frontiers in cell and developmental biology, 9, 723859.
  22. Giraud, G.*, Kolovos, P.*, Boltsis, I., van Staalduinen, J., Guyot, B., Weiss-Gayet, M., IJcken, W. V., Morlé, F., & Grosveld, F. (2021). Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis. iScience, 24(3), 102210.
  23. Boltsis I, Nowosad K, Brouwer RWW, Tylzanowski P, van IWFJ, Huylebroeck D, Grosveld F, Kolovos P.(2021). Low Input Targeted Chromatin Capture (Low-T2C). Methods Mol Biol 2351: 165-179.
  24. Birkhoff, J. C., Brouwer, R. W. W., Kolovos, P., Korporaal, A. L., Bermejo-Santos, A., Boltsis, I., Nowosad, K., van den Hout, M. C. G. N., Grosveld, F. G., van IJcken, W. F. J., Huylebroeck, D., & Conidi, A. (2020). Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation. Human molecular genetics, 29(15), 2535–2550.
  25. Kolovos, P.*, Nishimura, K.*, Sankar, A.*, Sidoli, S., Cloos, P. A., Helin, K., & Christensen, J. (2020). PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination. Genome research, 30(8), 1119–1130.
  26. Yu, X., Martella, A., Kolovos, P., Stevens, M., Stadhouders, R., Grosveld, F. G., & Andrieu-Soler, C. (2020). The dynamic emergence of GATA1 complexes identified in in vitro embryonic stem cell differentiation and in vivo mouse fetal liver. Haematologica, 105(7), 1802–1812.
  27. Laugsch, M., Bartusel, M., Rehimi, R., Alirzayeva, H., Karaolidou, A., Crispatzu, G., Zentis, P., Nikolic, M., Bleckwehl, T., Kolovos, P., van Ijcken, W. F. J., Šarić, T., Koehler, K., Frommolt, P., Lachlan, K., Baptista, J., & Rada-Iglesias, A. (2019). Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. Cell stem cell, 24(5), 736–752.e12.
  28. Kolovos, P.#, Brouwer, R. W. W., Kockx, C. E. M., Lesnussa, M., Kepper, N., Zuin, J., Imam, A. M. A., van de Werken, H. J. G., Wendt, K. S., Knoch, T. A.#, van IJcken, W. F. J., & Grosveld, F.# (2018). Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C. Nature protocols, 13(3), 459–477.
  29.  Zuin, J., Casa, V., Pozojevic, J., Kolovos, P., van den Hout, M. C. G. N., van Ijcken, W. F. J., Parenti, I., Braunholz, D., Baron, Y., Watrin, E., Kaiser, F. J., & Wendt, K. S. (2017). Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element. PLoS genetics, 13(12), e1007137.
  30. Chondrou, V., Kolovos, P., Sgourou, A., Kourakli, A., Pavlidaki, A., Kastrinou, V., John, A., Symeonidis, A., Ali, B. R., Papachatzopoulou, A., Katsila, T., & Patrinos, G. P. (2017). Whole transcriptome analysis of human erythropoietic cells during ontogenesis suggests a role of VEGFA gene as modulator of fetal hemoglobin and pharmacogenomic biomarker of treatment response to hydroxyurea in β-type hemoglobinopathy patients. Human genomics, 11(1), 24.
  31. Cruz-Molina, S., Respuela, P., Tebartz, C., Kolovos, P., Nikolic, M., Fueyo, R., van Ijcken, W. F. J., Grosveld, F., Frommolt, P., Bazzi, H., & Rada-Iglesias, A. (2017). PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation. Cell stem cell, 20(5), 689–705.e9.
  32. Knoch, T. A., Wachsmuth, M., Kepper, N., Lesnussa, M., Abuseiris, A., Ali Imam, A. M., Kolovos, P., Zuin, J., Kockx, C. E. M., Brouwer, R. W. W., van de Werken, H. J. G., van IJcken, W. F. J., Wendt, K. S., & Grosveld, F. G. (2016). The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes. Epigenetics & chromatin, 9, 58.
  33. Brant, L., Georgomanolis, T., Nikolic, M., Brackley, C. A., Kolovos, P., van Ijcken, W., Grosveld, F. G., Marenduzzo, D., & Papantonis, A. (2016). Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Molecular systems biology, 12(12), 891.
  34. Kolovos, P.#, Georgomanolis, T., Koeferle, A., Larkin, J. D., Brant, L., Nikolicć, M., Gusmao, E. G., Zirkel, A., Knoch, T. A., van Ijcken, W. F., Cook, P. R., Costa, I. G., Grosveld, F. G., & Papantonis, A.#(2016). Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome research, 26(11), 1478–1489.
  35. Stadhouders, R., Cico, A., Stephen, T., Thongjuea, S., Kolovos, P., Baymaz, H. I., Yu, X., Demmers, J., Bezstarosti, K., Maas, A., Barroca, V., Kockx, C., Ozgur, Z., van Ijcken, W., Arcangeli, M. L., Andrieu-Soler, C., Lenhard, B., Grosveld, F., & Soler, E. (2015). Control of developmentally primed erythroid genes by combinatorial co-repressor actions. Nature communications, 6, 8893.
  36. Ferri, F., Parcelier, A., Petit, V., Gallouet, A. S., Lewandowski, D., Dalloz, M., van den Heuvel, A., Kolovos, P., Soler, E., Squadrito, M. L., De Palma, M., Davidson, I., Rousselet, G., & Romeo, P. H. (2015). TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation. Nature communications, 6, 8900.
  37. Caputo, L., Witzel, H. R., Kolovos, P., Cheedipudi, S., Looso, M., Mylona, A., van IJcken, W. F., Laugwitz, K. L., Evans, S. M., Braun, T., Soler, E., Grosveld, F., & Dobreva, G. (2015). The Isl1/Ldb1 Complex Orchestrates Genome-wide Chromatin Organization to Instruct Differentiation of Multipotent Cardiac Progenitors. Cell stem cell, 17(3), 287–299.
  38. Tresini, M., Warmerdam, D. O., Kolovos, P., Snijder, L., Vrouwe, M. G., Demmers, J. A., van IJcken, W. F., Grosveld, F. G., Medema, R. H., Hoeijmakers, J. H., Mullenders, L. H., Vermeulen, W., & Marteijn, J. A. (2015). The core spliceosome as target and effector of non-canonical ATM signalling. Nature, 523(7558), 53–58.
  39. Diermeier, S.*, Kolovos, P.*, Heizinger, L., Schwartz, U., Georgomanolis, T., Zirkel, A., Wedemann, G., Grosveld, F., Knoch, T. A., Merkl, R., Cook, P. R., Längst, G., & Papantonis, A. (2014). TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome biology, 15(12), 536.
  40. Kolovos, P., van de Werken, H. J., Kepper, N., Zuin, J., Brouwer, R. W., Kockx, C. E., Wendt, K. S., van IJcken, W. F., Grosveld, F., & Knoch, T. A. (2014). Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics & chromatin, 7, 10.
  41. Stadhouders, R., de Bruijn, M. J., Rother, M. B., Yuvaraj, S., Ribeiro de Almeida, C., Kolovos, P., Van Zelm, M. C., van Ijcken, W., Grosveld, F., Soler, E., & Hendriks, R. W. (2014). Pre-B cell receptor signaling induces immunoglobulin κ locus accessibility by functional redistribution of enhancer-mediated chromatin interactions. PLoS biology, 12(2), e1001791.
  42. Zuin, J., Dixon, J. R., van der Reijden, M. I., Ye, Z., Kolovos, P., Brouwer, R. W., van de Corput, M. P., van de Werken, H. J., Knoch, T. A., van IJcken, W. F., Grosveld, F. G., Ren, B., & Wendt, K. S. (2014). Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proceedings of the National Academy of Sciences of the United States of America, 111(3), 996–1001.
  43. Stadhouders, R.*, Kolovos, P.*, Brouwer, R.*, Zuin, J., van den Heuvel, A., Kockx, C., Palstra, R. J., Wendt, K. S., Grosveld, F., van Ijcken, W., & Soler, E. (2013). Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nature protocols, 8(3), 509–524.
  44. Stadhouders, R., van den Heuvel, A., Kolovos, P., Jorna, R., Leslie, K., Grosveld, F., & Soler, E. (2012). Transcription regulation by distal enhancers: who’s in the loop?. Transcription, 3(4), 181–186.
  45. van den Driesche, S., Kolovos, P., Platts, S., Drake, A. J., & Sharpe, R. M. (2012). Inter-relationship between testicular dysgenesis and Leydig cell function in the masculinization programming window in the rat. PloS one, 7(1), e30111.
  46. Kolovos, P., Knoch, T. A., Grosveld, F. G., Cook, P. R., & Papantonis, A. (2012). Enhancers and silencers: an integrated and simple model for their function. Epigenetics & chromatin, 5(1), 1.

Name Title Supervisor Year Status
Konstantinos Tegopoulos Genomic and metagenomic analysis of species of economic importance in agrobiology Marirena Grigoriou - Petros Kolovos 2025 Completed

Name Capacity
Papagiotis Liakopoulos PhD student
Aleksandra Gerou PhD student
Katia Koufonikola PhD student
Konstantina Karamitsou Master's Student
Nikos Giannakopoulos Master's Student
Ioannis Nasopoulos Master's Student
Trifon Dimitriou Undergraduate Student
Ethimia - Danai Tzana Undergraduate Student
Panagiotis Xristodoulopoulos Undergraduate Student

Name Capacity
Konstantinos Tegopoulos PhD student
Christos Kirgios Master's Student
Dimitris Kospanos Master's Student
Maria Andreadou Master's Student
Pelagia Chondrou Master's Student
Ethimia Vasilina Katsika Master's Student
Paraskevi Koutra Master's Student
Nikolaos Lotsios Master's Student
Ioanna Papatheodorou Master's Student
Stavros Virvilis Master's Student
Marianna Griniezaki Master's Student
Eliza Kotridou Master's Student
Souzana Logotheti Master's Student
Maria Gaitanidou Master's Student
Athanasia Gkika Master's Student
Maria Melissourgou Master's Student
Anastasia Boutsika Master's Student
Raphaela Mylona Master's Student
Katerina Skeva Master's Student
Odysseas Stergiou Undergraduate Student
Elizavet Kapetanou Undergraduate Student
Aggeliki Panetsou Undergraduate Student
Spiridoula Sagropoulou Undergraduate Student
Markella Ilidaki Undergraduate Student
Eleni Mpalla Undergraduate Student
Christos Kitsopoulos Undergraduate Student
Pavlos Tsiartas Undergraduate Student
Sara Gkiolena Undergraduate Student
Spiridon Mimtsoudis Undergraduate Student
Konstantina Zampouridou Undergraduate Student

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Information

Director

Kolovos Petros, Associate Professor

https://systems.mbg.duth.gr

+30 25510 30385

pkolovos@mbg.duth.gr

Department of Molecular Biology and Genetics, DUTH, Fotis Kafatos Building, University Campus, Dragana area, 68100 Alexandroupoli