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  1. Nikolaos G. Sgourakis, Pantelis G. Bagos and Stavros J. Hamodrakas (2005) Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks. Bioinformatics, Vol. 21 no. 22, pages 4101–4106.
  2. Bagos, P.G., Liakopoulos, Th.D., Hamodrakas, S.J. (2005) Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics,2005, 6:7.
  3. Sgourakis, N.G., Bagos, P.G., Papasaikas, P.K. and Hamodrakas, S.J. (2005) A method for the prediction of GPCRs coupling specificity to G proteins using refined profile Hidden Markov Models. BMC Bioinformatics, 6:104.
  4. Bagos, P.G., Liakopoulos, Th.D., Hamodrakas, S.J. (2006) Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics, 7, 189.
  5. I. Emiris, Epam. Fritzilas, D. Manocha (2006) Algebraic Algorithms for Structure Determination in Biological Chemistry. International Journal of Quantum Chemistry, 106, 190–210.
  6. Hamodrakas, S.J., Liappa, C., Iconomidou, V.A. (2007) Consensus prediction of amyloidogenic determinants in amyloid fibril-forming proteins. Int. J. Biol. Macromol., 41(3),295-300.
  7. Karouzou, M.V., Spyropoulos, Y., Iconomidou, V.A., Cornman, R.S., Hamodrakas, S.J., Willis, J.H.(2007) Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences. Insect Biochem Mol Biol., 37(8): 754-60.
  8. Sgourakis, N.G., Bagos, P.G., Hamodrakas, S.J. (2008) Computational methods for the prediction of GPCRs coupling selectivity (Handbook of Research on Systems Biology Applications in Medicine). Medical Information Science, Vol. I, Ch. 9: 167-181.
  9. Frousios, K.K., Iconomidou, V.A., Karletidi, C.M. and Hamodrakas, S.J. (2009) Amyloidogenic determinants are usually not buried. BMC Struct Biol. 9(1): 44.
  10. Anthopoulos, P.G., Hamodrakas, S.J., Bagos, P.G. (2010) Apolipoprotein E polymorphisms and type 2 diabetes: a meta-analysis of 30 studies including 5423 cases and 8197 controls. Mol Genet Metab., 100(3):283-91.
  11. Satagopam, V.P., Theodoropoulou, M.C., Stampolakis, C.K., Pavlopoulos, G.A., Papandreou, N.C., Bagos, P.G., Schneider, R., Hamodrakas, S.J. (2010) GPCRs, G-proteins, Effectors and their interactions: Human-gpDB, a database employing advanced visualization tools and data integration techniques. Database (Oxford),, Vol. 2010, Article ID baq019.
  12. Tsaousis, G.N., Tsirigos, K.D., Andrianou, X.D., Liakopoulos, T.D., Bagos, P.G., Hamodrakas, S.J.(2010) ExTopoDB: A database of experimentally derived topological models of transmembrane proteins. Bioinformatics, 26(19): 2490;2492.
  13. Chatzigeorgiou, K.S., Sergentanis, T.N., Tsiodras, S., Hamodrakas, S.J., Bagos, P.G. (2011) Phoenix 100 versus Vitek 2 in the Identification of Gram-Positive and Gram-Negative Bacteria: a Comprehensive Meta-Analysis. J Clin Microbiol., 49(9): 3284-91.
  14. Stoubos, S., Anthopoulos, P.G., Hamodrakas, S.J., Bagos, P.G. (2012) The association between apolipoprotein E gene polymorphisms and essential hypertension: a meta-analysis of 45 studies including 13940 cases and 16364 controls. Journal of Human Hypertension.
  15. Spyridopoulou, K., Dimou, N.L., Hamodrakas, S.J., Bagos, P.G. (2012) Methylene Tetrahydrofolate Reductase gene polymorphisms and their association with methotrexate toxicity: A meta-analysis. Pharmacogenetics and Genomics, 22(2): 117-33.
  16. Giannopoulos, N.G., Michalopoulos, I., Papandreou, N.C., Malatras, A., Iconomidou, V.A., Hamodrakas, S.J. (2013) LepChorionDB, a database of Lepidopteran chorion proteins and a set of tools useful for the identification of chorion proteins in Lepidopteran proteomes. Insect Biochem Mol Biol. , 43: 189-196.
  17. Michalopoulos, I., Pavlopoulos, G.A., Malatras, A., Karelas, A., Kostadima, M.A., Schneider, R., and Kossida, S.(2012) Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally coexpressed genes. BMC Res Notes 5, 265.
  18. Kotta-Loizou, I., Tsaousis, G.N., Hamodrakas, S.J. (2013) Analysis of Molecular Recognition Features (MoRFs) in membrane proteins. Biochim Biophys Acta., 1834(4): 798-807.
  19. Gypas, F., Tsaousis, G.N., Hamodrakas, S.J. (2013) mpMoRFsDB: a database of molecular recognition features in membrane proteins. Bioinformatics, 29(19):2517-8.
  20. Desiniotis A, Kouvelis VN, Davenport K, Bruce D, Detter C, Tapia R, Han C, Goodwin LA, Woyke T, Kyrpides NC, Typas MA, Pappas KM. Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. J Bacteriol. 2012 Nov;194(21):5966-7
  21. Louros, N.N., Petronikolou N., Karamanos T., Cordopatis P., Iconomidou, V.A., Hamodrakas, S.J. (2014) Structural studies of ‘aggregation-prone’ peptide-analogues of teleostean egg chorion ZPB proteins. Biopolymers doi: 110.1002/bip.22563
  22. Ioannidou, Z.S., Theodoropoulou, M.C., Papandreou, N.C., Willis, J.H., Hamodrakas, S.J. (2014) CutProtFam-Pred: Detection and classification of putative structural cuticular proteins from sequence alone, based on profile Hidden Markov Models. Insect. Biochem. Mol. Biol., Volume 52, September 2014, Pages 51-59. doi: 10.1016/j.ibmb.2014.06.004
  23. Nastou, K.C., Tsaousis, G.N., Kremizas, K.E., Litou, Z.I., Hamodrakas, S.J. (2014) The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions. BioMed Research International, vol. 2014. doi: 10.1155/2014/397145
  24. Papadimitriou, K., Anastasiou, R., Maistrou, E., Plakas, T., Papandreou, N.C., Hamodrakas, S.J., Ferreira, S., Supply, P., Renault, P., Pot, B., Tsakalidou, E.(2015) Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One. 2015 Jan 13;10(1):e0116337. doi: 10.1371/journal.pone.0116337
  25. Skourti E., Logotheti S, Kontos C.K., Pavlopoulou A, Dimoragka P., Trougakos I.P., Gorgoulis V., Scorilas A., Michalopoulos I., Zoumpourlis V. (2015) Progression of Mouse Skin Carcinogenesis Is Associated With the Orchestrated Deregulation of mir-200 Family Members, mir-205 and Their Common Targets. Mol. Carcinog. 1098-2744. doi:10.1002/mc.22365
  26. Louros, N.N., Baltoumas, F.A., Hamodrakas, S.J., Iconomidou, V.A. (2016) A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. J. Comput. Aided. Mol. Des. Feb;30(2):153-64
  27. Rerra, A.I.G., Grimanelli, V.P., Papandreou, N.C., Hamodrakas, S.J. (2016) Optimizing the Aggregation Propensity of Therapeutic Monoclonal Antibodies against Cancer and Autoimmune Diseases: A Computational Study. Int. J. Biochem. Res. Rev. 10(1): 1-15, 2016, Article no.IJBcRR.23216
  28. Kostiou V.D., Theodoropoulou M.C., Hamodrakas S.J. (2016) GprotPRED: Annotation of Gα, Gβ and Gγ subunits of G-proteins using profile hidden Markov models (pHMMs) and application to proteomes. Biochim. Biophys. Acta Volume 1864, Issue 5, pp. 435–440
  29. Nastou, K.C., Tsaousis, G.N., Papandreou, N.C., Hamodrakas, S.J. (2016) MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models. Biochim. Biophys. Acta Volume 1864, Issue 7, pp. 747–754.
  30. Baltoumas, F.A., Theodoropoulou, M.C., Hamodrakas, S.J. (2016) Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. J. Comput. Aided. Mol. Des. Jun;30(6):489-512
  31. Kanost, M.R., (…), Michalopoulos, I., Hamodrakas, S.J., (…), Blissard (2016) Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Bioch. and Mol. Biol. 76 (2016) pp. 118-147.
  32. Pediaditakis I, Kourgiantaki A, Prousis KC, Potamitis C, Xanthopoulos KP, Zervou M, Calogeropoulou T, Charalampopoulos I and Gravanis A (2016) BNN27, a 17-Spiroepoxy Steroid Derivative, Interacts With and Activates p75 Neurotrophin Receptor, Rescuing Cerebellar Granule Neurons from Apoptosis. Front. Pharmacol. 7:512.