Οι παρακάτω εργασίες αφορούν έρευνα που έγινε στα πλαίσια του μεταπτυχιακού προγράμματος Βιοπληροφορική και περιλαμβάνουν τουλάχιστον μία/έναν φοιτήτρια/φοιτητή του προγράμματος

1. Baltsavia, I., Theodosiou, T., Papanikolaou, N., Pavlopoulos, G.A., Amoutzias, G.D., Panagopoulou, M., Chatzaki, E., Andreakos, E. and Iliopoulos, I., 2022. Prediction and Ranking of Biomarkers Using multiple UniReD. International Journal of Molecular Sciences, 23(19), p.11112.

2. Karaglani, M., Panagopoulou, M., Baltsavia, I., Apalaki, P., Theodosiou, T., Iliopoulos, I., Tsamardinos, I. and Chatzaki, E., 2022. Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach. International Journal of Molecular Sciences, 23(6), p.2959.

3. Theodorakis, E., Antonakis, A.N., Baltsavia, I., Pavlopoulos, G.A., Samiotaki, M., Amoutzias, G.D., Theodosiou, T., Acuto, O., Efstathiou, G. and Iliopoulos, I., 2021. ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics. Nucleic acids research, 49(W1), pp.W573-W577.

4. Vogiatzi, A., Baltsavia, I., Dialynas, E., Theodorou, V., Zhou, Y., Deligianni, E., Iliopoulos, I., Wilkie, A.O., Twigg, S.R. and Mavrothalassitis, G., 2021. Erf affects commitment and differentiation of osteoprogenitor cells in cranial sutures via the retinoic acid pathway. Molecular and Cellular Biology, 41(8), pp.e00149-21.

5. Vasileiou, D., Karapiperis, C., Baltsavia, I., Chasapi, A., Ahrén, D., Janssen, P.J., Iliopoulos, I., Promponas, V.J., Enright, A.J. and Ouzounis, C.A., 2023. CGG toolkit: Software components for computational genomics. PLOS Computational Biology, 19(11), p.e1011498.

6. Eptaminitaki, G.C., Zaravinos, A., Stellas, D., Panagopoulou, M., Karaliota, S., Baltsavia, I., Iliopoulos, I., Chatzaki, E., Iliopoulos, D. and Baritaki, S., 2023. Genome-Wide Analysis of lncRNA-mRNA Co-Expression Networks in CD133+/CD44+ Stem-like PDAC Cells. Cancers, 15(4), p.1053.

7. Vasilarou, M., Alachiotis, N., Garefalaki, J., Beloukas, A. and Pavlidis, P., 2021. Population genomics insights into the first wave of COVID-19. Life, 11(2), p.129.

8. Kioukis, A., Michalopoulou, V.A., Briers, L., Pirintsos, S., Studholme, D.J., Pavlidis, P. and Sarris, P.F., 2020. Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection. BMC genomics, 21, pp.1-14.

9. Litos, A., Intze, E., Pavlidis, P. and Lagkouvardos, I., 2022. Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time. Frontiers in Bioinformatics, 2, p.866902.

10. Papadantonakis, S., Poirazi, P. and Pavlidis, P., 2016. CoMuS: simulating coalescent histories and polymorphic data from multiple species. Molecular ecology resources, 16(6), pp.1435-1448.

11. Natsidis, P., Tsakogiannis, A., Pavlidis, P., Tsigenopoulos, C.S. and Manousaki, T., 2019. Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. Communications Biology, 2(1), p.400.

12. George Potamias, Polymnia Gkoublia and Alexandros Kanterakis. The two-stage molecular scenery of SARS-CoV-2 infection with implications to disease severity: An in-silico quest”. Frontiers in Immunology-Viral Immunology
    

13. Kyriakis, Dimitrios, Alexandros Kanterakis, Tereza Manousaki, Alexandros Tsakogiannis, Michalis Tsagris, Ioannis Tsamardinos, Leonidas Papaharisis, Dimitris Chatziplis, George Potamias, and Costas S. Tsigenopoulos. "Scanning of genetic variants and genetic mapping of phenotypic traits in gilthead sea bream through ddRAD sequencing." Frontiers in genetics 10 (2019): 675.

14. Astrinaki, Maria, Alexandros Kanterakis, Helen Latsoudis, George Potamias, and Dimitris Kafetzopoulos. "Zazz: Variant Annotation and Exploration of Next Generation Sequencing Variants." In 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE), pp. 856-860. IEEE, 2019.

15. Ioannis Giannoulakis, Alexandros Kanterakis, Konstantina Pityanou, George Potamias, Ioannis Iliopoulos. A graph representation of the individual exome variation with evidence from biomedical text corpora. ISMB/ECCB 2021 conference (virtual).

16. Danai Maria Kotzampasi, Alexandros Kanterakis2, Vangelis Daskalakisand George Potamias. Correlation between CYP2D6 variants and their metabolic activity by Molecular Dynamics Simulations.  ISMB/ECCB 2021 conference (virtual).

17. Kosmara D, Papanikolaou S, Nikolaou C, Bertsias G.  Extensive Alternative Splicing Patterns in Systemic Lupus Erythematosus Highlight Sexual Differences. Cells. 2023 Nov 22;12(23):2678. doi: 10.3390/cells12232678.PMID: 38067106

18. Tassios E, Nikolaou C, Vakirlis N. Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains. Mol Biol Evol. 2023 Mar 4;40(3):msad059. doi: 10.1093/molbev/msad059.PMID: 36917489 

19. Athanasouli P, Balli M, De Jaime-Soguero A, Boel A, Papanikolaou S, van der Veer BK, Janiszewski A, Vanhessche T, Francis A, El Laithy Y, Nigro AL, Aulicino F, Koh KP, Pasque V, Cosma MP, Verfaillie C, Zwijsen A, Heindryckx B, Nikolaou C, Lluis F. The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency. Nat Commun. 2023 Mar 3;14(1):1210. doi: 10.1038/s41467-023-36914-1.PMID: 36869101 

20. Stavropoulou A, Tassios E, Kalyva M, Georgoulopoulos M, Vakirlis N, Iliopoulos I, Nikolaou C. Distinct chromosomal "niches" in the genome of Saccharomyces cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates. NAR Genom Bioinform. 2022 Nov 14;4(4):lqac086. doi: 10.1093/nargab/lqac086. eCollection 2022 Dec.PMID: 36381424 

21. Papanikolaou S, Bertsias GK, Nikolaou C. Extensive Changes in Transcription Dynamics Reflected on Alternative Splicing Events in Systemic Lupus Erythematosus Patients. Genes (Basel). 2021 Aug 18;12(8):1260. doi: 10.3390/genes12081260.PMID: 34440434 

22. Karagianni N, Kranidioti K, Fikas N, Tsochatzidou M, Chouvardas P, Denis MC, Kollias G, Nikolaou C. An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis. PLoS Comput Biol. 2019 May 9;15(5):e1006933. doi: 10.1371/journal.pcbi.1006933. eCollection 2019 May.PMID: 31071076 

23. Tsochatzidou M, Malliarou M, Papanikolaou N, Roca J, Nikolaou C. Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae. Nucleic Acids Res. 2017 Jun 2;45(10):5818-5828. doi: 10.1093/nar/gkx198.PMID: 28369650

24. Malakasis, N., Chavlis, S. and Poirazi, P., 2023. Synaptic turnover promotes efficient learning in bio-realistic spiking neural networks. bioRxiv, pp.2023-05.