Greek version

Short CV of Professor Stavros J. Hamodrakas 

 

Personal:

Name: Stavros J. Hamodrakas
Birth: March 10, 1947
Place: Kalamata, Greece

Address: Faculty of Biology,
Department of Cell Biology and Biophysics
University of Athens, Athens 15701
Greece
Phone: +30-210-7274545 , +30-210-7274931
Fax: +30-210-7274254
e.mail: shamodr@biol.uoa.gr
web: http://biophysics.biol.uoa.gr , http://bioinformatics.biol.uoa.gr/msc

Present Position: Professor

Education: 

1970-1974, Ph.D Astbury Dept. of Biophysics, University of Leeds, U.K

1965-1970, B.Sc Physics Dept., University of Athens, Greece 

Research experience: 

1976-present

Faculty of Biology, University of Athens
2008 1 month visit, University of Colorado at Boulder, USA

1 month visit, EMBL, Heidelberg, Germany
2007 1 month visit, University of Colorado at Boulder, USA
2006 1 month visit, EMBL, Heidelberg, Germany
2005 1 month visit, EMBL, Heidelberg, Germany
2004 1 month visit, EMBL, Heidelberg, Germany
2003 1 month visit, EMBL, Heidelberg, Germany
2002 1 month visit, EMBL, Heidelberg, Germany
2001 1 month visit, EMBL, Heidelberg, Germany
2000 1 month visit, EMBL, Heidelberg, Germany
1999 1 month visit, EMBL, Heidelberg, Germany
1998 2 month visit, EMBL, Heidelberg, Germany
1995-96 5 month visit, EMBL, Heidelberg, Germany
1994-95 3 month visit, EMBL, Heidelberg, Germany
1994 3 month visit Dept. of Biochemistry University of Mississippi, USA
1990-91 7 month visit, Dept. of Medical Biophysics
University of Toronto, Canada
1987 1 month visit, EMBL, Heidelberg, Germany
1985 2 months visit, EMBL, Heidelberg
1984 1 month visit, Astbury Dept. Biophysics, U.K
1983 2 months visit, EMBL, Heidelberg
1982 2 months visit, EMBL, Heidelberg
1980 1 month visit , EMBL, Heidelberg
15 days visit, MRC, Cambridge, U.K
1979 2 months visit , Rosenstiel Basic Medical Sciences Research Center, Brandeis University, USA and the Biological Laboratories, Harvard University, USA
1977 2 months visit , Astbury Dept. of Biophysics,
Leeds University, U.K
1976 Environmental Pollution Control Project for Athens
(4 months as a research assoc.)
1975-1976 Nuclear Research Center "Demokritos",
Athens, Greece (Research Scientist)
1970-1974 Astbury Dept. of Biophysics, University of Leeds, U.K (research assistant)

 Research activity: 

The scientific research interests of our laboratory are focused in the fields of Structural Biology / Molecular Biophysics and Computational Biology / Bioinformatics. More specifically, we are dealing with:

 Teaching experience: 

I am teaching a full (one semester) Biophysics course to 3rd year Physics and Biology students since 1976.

I have published a book (in Greek) on Molecular Biophysics (1st edition 1987, 2nd edition 1993) which includes topics such as:

  1. X-ray Diffraction studies of Biological Micro- and Macromolecules

  2. Applications of Neutron Diffraction in Studies of BiologicalStructures

  3. Use of Molecular Models- Conformational Analysis of Biomolecules using Energy Calculations and modeling

  4. Principles of Stereochemistry. Applications in biomolecules and and Biological Structures

  5. Principles of Protein Structure

  6. Protein Folding and Structure Prediction

  7. The structure of Fibrous Proteins

  8. Image Analysis- Optical Diffraction and Reconstruction- 3D-reconstruction of Biological Structures from Electron Micrographs

  9. Principles and Applications of Infrared Spectroscopy, Laser-Raman spectroscopy NMR , O.R.D and C.D in studies of biomolecules and biological structures

  10.  Molecular Recognition: Structure and Function of biomicromolecules (drugs, neurotransmitters, antibiotics e.t.c) and their receptors

  11.  Photoreceptors: Rhodopsin and Bacteriorhodopsin (structure and function) 

I am also teaching a full (one semester) course to 2nd year Biology students, since 1986, entitled "Computers in Biology".

I was a visiting professor at the Department of Medicine of the University of Crete during the period 1984-85

List of publications:

    1. Hamodrakas, S. J., Geddes, A. J. and Sheldrick, B. (1974) X-ray analysis of disodium cromoglycate, Journal of Pharmacy and Pharmacology, 26, 54.
    2. Hamodrakas, S. J., Geddes, A. J. and Sheldrick, B. (1974) The crystal structure of â-methylphenylcholine ether bromide, Acta Cryst., B30, 881.
    3. Geddes, A. J., Hamodrakas, S. J. and Sheldrick, B. (1974) (The crystal structure of) N-acetyl methionine methyl ester, C8H15NO3S, Cryst. Struct. Comm., 3, 97.
    4. S. J. Hamodrakas (1974) X-ray crystallographic studies of disodium cromoglycate, â-methylphenylcholine ether bromide and N-acetyl methionine methyl ester, Ph.D Thesis, University of Leeds (U.K).
    5. Hamodrakas, S. J., Filippakis, S. E. and Sheldrick, B. (1977) (The crystal structure of) 2-carboxamidomethyl-4,5-dimethoxy-phenyl diethyl sulfonamide, C14H22N2O5S, Cryst. Struct. Comm., 6, 209.
    6. Hamodrakas, S. J. and Filippakis, S. E. (1977) (The crystal structure of) N-morpholine-4,5 dimethoxy-2-carboxymethyl benzene sulfonamide, C14H19NO7S, Cryst. Struct. Comm., 6, 301.
    7. Hamodrakas, S. J., Akrigg, D. and Sheldrick, B. (1978) (The crystal structure of) Methyl dehydroabietate, C21H30O2, Cryst. Struct. Comm., 7, 429.
    8. Hamodrakas, S. J., Akrigg, D., Sheldrick, B. and Camoutsis, C. (1978) (The crystal structure of) Ethyl-3-[4,5-Dimethoxy-2-(5-methyl-2pyridylsulfamoyl) phenyl] propionate, Acta Cryst., B34, 3426.
    9. Hamodrakas, S. J., Margaritis, L. H. and Nixon, P. E. (1982) Crystalline layer in Drosophila melanogaster eggshell: Arrangement of components as revealed by negative staining and reconstruction, Int. J. Biol. Macromol., 4, 25-31.
    10. Hamodrakas, S. J., Jones, C. W. and Kafatos, F. C. (1982) Secondary structure predictions for silkmoth chorion proteins, Biochim. Biophys. Acta, 700, 42-51.
    11. Hamodrakas, S. J., Asher, S. A., Mazur, G. D., Regier, J. C. and Kafatos, F. C. (1982) Laser-Raman studies of protein conformation in the Silkmoth chorion, Biochim. Biophys. Acta , 703, 216-222.
    12. Regier, J. C., Kafatos, F. C. and Hamodrakas, S. J. (1983) Silkmoth chorion multigene families constitute a superfamily:Comparison of C and B family sequences, Proc. Natln. Acad. Sci. USA, 80, 1043-1047.
    13. Hamodrakas, S. J., Paulson, J. R., Rodakis, G. C. and Kafatos F. C. (1983) X-ray Diffraction studies of a silkmoth chorion, Int. J. Biol. Macromol., 5, 149-153.
    14. Eliopoulos, E. E., Sheldrick, B. and Hamodrakas, S. J. (1983) The crystal structure of Ethyl 3-[4,5-Dimethoxy-2-(4- methyl-2-pyridylsulfamoyl)phenyl] propionate, C19H24N2O8S, Acta Cryst., C39, 743.
    15. Eliopoulos, E. E., Sheldrick, B. and Hamodrakas, S. J. (1983) The crystal structure of Ethyl 3-[4,5-Dimethoxy-2-(3-methyl-2-pyridylsulfamoyl)phenyl] propionate), C19H24N2O8S, Acta Cryst., C39, 1693.
    16. Margaritis, L. H., Hamodrakas, S. J., Arad, T. and Leonard, K. R. (1984) Three Dimensional Reconstruction of Innermost Chorion Layer from Drosophila melanogaster, Biol. Cell, 52 (3), 279-284.
    17. Hamodrakas, S. J. (1984) Twisted ?â-pleated sheet: The Molecular Conformation which possibly dictates the formation of the Helicoidal Architecture of several proteinaceous eggshells, Int. J. Biol. Macromol., 6, 51.
    18. Hamodrakas, S. J. and Kafatos, F. C. (1984) Structural Implications of Primary Sequences from a family of Balbiani Ring-Encoded Proteins in Chironomus, J. Mol. Evol., 20, 296-303.
    19. Hamodrakas, S. J., Kamitsos, E. I. and Papanicolaou, A. (1984) Laser-Raman spectroscopic studies of the Eggshell (Chorion) of Bombyx mori, Int. J. Biol. Macromol., 6, 333-336.
    20. Hamodrakas, S. J., Etmektzoglou, Th. and Kafatos, F. C. (1985) Amino acid Periodicities and Their Structural Implications for the Evolutionarily Conservative Central Domain of Some Silkmoth Chorion Proteins, J. Mol. Biol., 186, 583-589.
    21. Hamodrakas, S. J., Margaritis, L. H., Papassideri, I. and Fowler, A. (1986) Fine structure of the silkmoth Antheraea polyphemus chorion as revealed by X-ray diffraction, and freeze fracturing, Int. J. Biol. Macromol., 8, 237-242.
    22. Papanicolaou, A., Margaritis, L. H. and Hamodrakas, S. J. (1986) Ultrastructural analysis of chorion formation in the silkmoth Bombyx mori, Can. J. Zool., 64, 1158-1173.
    23. Hamodrakas, S. J., Kamitsos, E. I. and Papadopoulou, P. (1987) Laser-Raman and infrared spectroscopic studies of protein conformation in the eggshell of the fish Salmo gairdneri, Biochim. Biophys. Acta, 913, 163-169.
    24. Hamodrakas, S. J. (1988) A protein secondary structure prediction scheme for the IBM-PC and compatibles, Computer applications in the Biosciences, 4 (4), 473-477.
    25. Hamodrakas, S. J., Bosshard, H. E. and Carlson, C. N. (1988) Structural models of the evolutionarily conservative central domain of silkmoth chorion proteins, Protein Engineering, 2 (3), 201-207.
    26. Hamodrakas, S. J., Alexandraki, E., Troganis, A. and Stassinopoulou, C.I. (1989) Models of binding of 4'-nitrophenyl á-D-mannopyranoside to the lectin concanavalin A, Int. J. Biol. Macromol., 11 (1), 17-22.
    27. Hamodrakas, S. J., Batrinou, A. and Christophoratou, T. (1989) Structural and functional features of Drosophila chorion proteins s36 and s38 from analysis of primary structure and infrared spectroscopy, Int. J. Biol. Macromol., 11 (5), 307-313.
    28. Eliopoulos, E., Sheldrick, B. and Hamodrakas, S. J. (1991) (The crystal structure of) 4,5-Dimethoxy-2-[3-(1,4-oxazinan-4-yl)-3-oxopropyl]-N-(2-pyridyl)-benzenesulfonamide Methanol solvate, Acta Cryst., C47, 1212-1215.
    29. Aggeli, A., Hamodrakas, S. J., Komitopoulou, K. and Konsolaki, M. (1991) Tandemly repeating peptide motifs and their secondary structure in Ceratitis capitata eggshell proteins Ccs36 and Ccs38, Int. J. Biol. Macromol., 13, 307-315.
    30. Margaritis, L. H., Hamodrakas, S. J., Papassideri, I. Arad, T. and Leonard, K. R. (1991) Three-dimensional reconstruction of innermost chorion layer of Drosophila grimshawi and Drosophila melanogaster eggshell mutant fs(1)384, Int. J. Biol. Macromol., 13, 247-253.
    31. Orfanidou, C. C., Hamodrakas, S. J., Margaritis, L. H., Galanopoulos, V.K., Dedieu, J. C., and Gulik-Krzywicki, T. (1992) Fine structure of the chorion of Manduca sexta and Sesamia nonagrioides as revealed by scanning electron microscopy and freeze-fracturing, Tissue & Cell, 24(5), 735-744.
    32. Wellman, S. E., Hamodrakas, S. J., Kamitsos, E. I.·and Case, S. T. (1992) Secondary structure of synthetic peptides derived from the repeating unit of a giant secretory protein from Chironomus tentans, Biochim. Biophys. Acta, 1121, 279-285.
    33. Gessman, R., Petratos, K., Hamodrakas, S. J., Tsitsa, P. and Antoniadou-Vyza, E. (1992) Structure of 2-Amino-6-dimethylamino-4-(tricyclo [3.3.1.1.3,7] decyl-1-yl)-1,3,5-triazine, Acta Cryst., C48, 347-350.
    34. Hamodrakas, S. J., Hempel, A., Camerman, N., Ottensmeyer, F. P., Tsitsa, P., Antoniadou-Vyzas, E. and Camerman, A. (1992) Molecular and crystal structure of 2-amino-4-(tricyclo[3.3.1.1.3,7] decyl-1)-6-N-methyl-piperazino-1,3,5-triazine, J. Cryst. Spectrosc. Res., 22, 607-614.
    35. Hamodrakas, S. J. (1992) Molecular architecture of helicoidal proteinaceous eggshells in "Results and Problems in Cell Differentiation", Vol. 19, (S.T. Case ed.), Ch. 6, pp. 116-186 Springer-Verlag, Berlin-Heidelberg (rev. article).
    36. Hempel, A., Camerman, N., Hamodrakas, S. J., Ottensmeyer, F. P., Troganis, A., Stassinopoulou, C. I. and Camerman, A. (1993) 2,2,6,6-Tetramethylpiperidine-1-oxyl-4-yl-á-D-glucopyranoside, Acta Cryst., C49, 298-300.
    37. Kolocouris, A., Kolocouris, N., Foscolos, G. B., Fytas, G., Hempel, A., Camerman, N., Camerman, A. and Hamodrakas, S. J. (1993) Molecular and crystal structures of a tricyclic ã-lactam ketone and its Mannich base, J. Cryst. Spectrosc. Res., 23, 663-668.
    38. Tsitsa, P., Antoniadou-Vyza, E., Hamodrakas, S. J., Eliopoulos, E. E., Tsantili-Kakoulidou, A., Lada-Hytiroglou, E., Roussakis, C., Chinou, I., Hempel, A., Camerman, N., Ottensmeyer, F. P., and Van den Berghe, D. A. (1993) Synthesis, Crystal Structure and Biological Properties of a new Series of Lipophilic s-Triazines, Dihydrofolate Reductase (DHFR) Inhibitors, Eur. J. Med. Chem., 28, 149-158.
    39. Perrakis, A., Hempel, A., Hamodrakas, S. J., Camerman, N., Tsitsa, P., Antoniadou-Vyzas E. and Camerman, A. (1993) Molecular and crystal structure of 2-amino-6-dimethyl amino-4-(-tricyclo[3.3.1.13,7]dec-1-yl) methyl-1,3,5-triazine, J. Cryst. Spectrosc. Res., 23, 821-824.
    40. Perrakis, A., Constantinides, C., Athanasiades, A. and Hamodrakas, S. J. (1995) PBM: A software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible, PCs Computer Applications in the Biosciences (CABIOS), 11(2), 141-145.
    41. Orfanidou, C. C., Chryssikos, G. D., Kamitsos, E. I., Wellman, E., Case, S. T. and Hamodrakas, S. J. (1995) Spectroscopic studies of Manduca sexta and Sesamia nonagrioides chorion protein structure, Int. J. Biol. Macromol., 17(2), 93-98.
    42. Hamodrakas, S. J., Perrakis, A. and Antoniadou-Vyzas, E. (1996) A de novo designed possible 5-lipoxygenase inhibitor: a-acetoxy-N-[1-(1-(tricyclo[3.3.1.13,7]dec-1-yl)ethyl]benzene acetamide, Acta Cryst., C52, 677-679.
    43. Perrakis, A., Schneider, T. S., Antoniadou-Vyzas, E., Dauter, Z. and Hamodrakas, S. J. (1996) Refinement of 2-amino-6-(4-methyl-1-piperazinyl)-4-tricyclo[3.3.1.13,7]dec-1-yl)-1,3,5-triazine at three different temperatures using image-plate data, J. Appl. Cryst., 29, 261-264.
    44. Agianian, B., Perrakis, A., Kanellopoulos, P. N., Sheldrick B. and Hamodrakas, S. J. (1997) The crystal and molecular structure of p-nitrophenyl-á-D-mannopyranoside ethanol solvate, Acta Cryst., C53, 811-814.
    45. Papadopoulou, P., Galanopoulos, V. K. and Hamodrakas, S. J. (1996) Molecular and supramolecular architecture of the Salmo gairdneri proteinaceous eggshell during development, J. Struct. Biology, 116, 399-412.
    46. Kanellopoulos, P. N., Pavlou, K., Perrakis, A., Agianian, B., Vorgias, C., Mavrommatis, C., Soufi, M., Tucker, P. A. and Hamodrakas, S. J. (1996) The crystal structure of the complexes of Concanavalin A with 4'-nitrophenyl-á-D-mannopyranoside and 4'-nitrophenyl-á-D-glucopyranoside, J. Struct. Biology, 116, 345-355.
    47. Kanellopoulos, P. N., Pavlou, K., Agianian, B., Tucker, P. A. and Hamodrakas, S. J. (1996) A triclinic crystal form of the lectin Concanavalin A, J. Struct. Biol., 117, 16-23.
    48. Hamodrakas, S. J., Kanellopoulos, P. N., Pavlou, K. and Tucker, P. A. (1997) The crystal structure of the complex of Concanavalin A with 4'- methylumbelliferyl-á-D-glucopyranoside, J. Struct. Biol., 118, 23-30.
    49. Benaki, D. C., Aggeli, A., Chryssikos, G. D., Yiannopoulos, Y. D., Brumley, E., Case, S. T., Boden, N. and Hamodrakas, S. J. (1998) Laser-Raman and FT-IR spectroscopic studies of peptide-analogues of silkmoth chorion protein segments, Int. J. Biol. Macromol., 23(1), 49-59.
    50. Pasquier, C. M., Promponas, V. I., Varvayannis, N. J. and Hamodrakas, S. J. (1998) A web server to locate periodicities in a sequence, Bioinformatics, 14(8), 749-50.
    51. Iconomidou, V. A., Willis, J. H. and Hamodrakas, S. J. (1999) Is beta-pleated sheet the molecular conformation which dictates formation of helicoidal cuticle? Insect Biochem. Mol. Biol., 29(3), 285-92.
    52. Promponas, V. J., Palaios, G., Pasquier, C. M., Hamodrakas, J. S. and Hamodrakas S. J. (1999) CoPreTHi: A Web tool which combins transmembrane protein segment prediction methods, In Silico Biology, 3, 1-4.
    53. Pasquier, C., Promponas, V. J., Palaios, G. A., Hamodrakas, J. S., and Hamodrakas, S. J. (1999) A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm, Protein Eng., 12(5), 381-5.
    54. Pasquier, C., and Hamodrakas, S. J. (1999) An hierarchical artificial neural network system for the classification of transmembrane proteins, Protein Eng., 12(8), 631-4.
    55. Perrakis, A., Antoniadou-Vyzas, E., Tsitsa, P., Lamzin, V. S., Wilson, K. S. and Hamodrakas, S. J. (1999) Molecular, crystal and solution structure of a â-cyclodextrin complex with ADM-10, a potent antimicrobial drug, Carbohydrate Res., 317(1-4), 19-28.
    56. Iconomidou, V. A.; Vriend, G.A. and Hamodrakas, S. J. (2000) Amyloids protect the silkmoth oocyte and embryo, FEBS Letters, 479, 141-5.
    57. Promponas, V. J.; Enright, A. J.; Tsoka, S.; Kreil, D. P.; Leroy, C. and Hamodrakas, S. J.; Sander, C.; Ouzounis, C. A. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics, 16(10), 915-922.
    58. Iconomidou, V. A., Chryssikos, G. D., Gionis, V., Pavlidis, M. A., Paipetis, A. and Hamodrakas, S. J. (2000) Secondary structure of chorion proteins of the teleostean fish Dentex dentex by ATR FT-IR and FT-Raman spectroscopy, J. Struct. Biol., 132, 112-122.
    59. Iconomidou, V. A., Chryssikos, G. D., Gionis, V., Willis, J. H. and Hamodrakas, S. J. (2001) "Soft"-cuticle protein secondary structure as revealed by FT-Raman, ATR FT-IR and CD spectroscopy, Insect Biochem. Mol. Biol., 31, 877-885.
    60. Liakopoulos, T. D., Pasquier, C. and Hamodrakas, S. J. (2001) A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm, Protein Eng, 14, 387-390.
    61. Karmirantzou, M. and Hamodrakas, S. J. (2001) A database of DNA-binding proteins: an approach for protein family classification, Protein Eng., 14(7), 465-472.
    62. Iconomidou, V. A., Chryssikos, G. D., Gionis, V., Vriend, G., Hoenger, A. and Hamodrakas, S. J. (2001) Amyloid-like fibrils from an 18-residue peptide-analogue of a part of the central domain of the B-family of silkmoth chorion proteins, FEBS Letters, 499, 268-273.
    63. Pasquier, C., Promponas, V. I. and Hamodrakas, S. J. (2001) PRED-CLASS: Cascading neural networks for generalized protein classification and genome-wide applications, Proteins, 44, 361-369.
    64. Iconomidou, V.A. and Hamodrakas, S.J. (2001) Amyloid-like fibrils from a peptide-analogue of the central domain of silkmoth chorion proteins. In A. Aggeli, N. Boden, S, Zhang"Self-Assembling Peptide Systems in Biology, Medicine, and Engineering" , Chapter 12, 161-169, Kluwer Press.
    65. Hamodrakas, S.J., Willis, J.H. and Iconomidou, V.A. (2002) A structural model of the chitin-binding domain of cuticle proteins, Insect Biochem. Mol. Biol., 32,1577-1583.
    66. Papandreou, N. C., Makedonopoulou, S., Antoniadou-Vyza, E. A., Mavridis, I. M. and Hamodrakas, S. J. (2002) 2,4-Diamino-5-(1-naphthyl)-3,5-diaza-1-azoniaspiro[5.5]undeca-1,3-diene chloride, Acta Cryst., C58, 730-732.
    67. Iliopoulos, I., Tsoka, S., Andrade, M., Enright, A.J., Carroll, M., Poullet, P., Promponas, V., Liakopoulos, T., Palaios, G., Pasquier, C., Hamodrakas, S., Tamames, J., Yagnik, A., Tramontano, A., Devos, D., Blaschke, C., Valencia, A., Brett, D., Martin, D., Leroy, C., Rigoutsos, I., Sander, C., Ouzounis, C.A. (2003) Evaluation of Annotation Strategies using an Entire Genome Sequence. Bioinformatics, 19 (6), 717-726.
    68. Iconomidou, V.A., Chryssikos, G.D., Gionis, V., Hoenger, A., Hamodrakas, S.J. (2003) FT-Raman Spectroscopy as diagnostic tool of Congo red binding to amyloids. Biopolymers (Biospectroscopy), 72, 185-192.
    69. Benaki, D.C, Mikros, E., Hamodrakas, S.J. (2003) Conformational Analysis of Peptide Analogues of Silkmoth Chorion Protein Segments Using CD, NMR and Molecular Modelling. Journal of Peptide Science.
    70. Papasaikas, P.K., Bagos, P.G., Litou, Z.I. and Hamodrakas, SJ. (2003) A novel method for GPCR recognition and family classification, from sequence alone, using signatures derived from profile Hidden Markov models, S.A.R-Q.S.A.R Environmen. Research, 14(5-6), 413-420.
    71. Vernikos, G.S., Gkogkas, C.G., Promponas, V.J. and Hamodrakas, S.J. (2003) GeneViTo: visualizing gene-product functional and structural features in genomic datasets, BMC Bioinformatics, 4:53.
    72. Hamodrakas, S.J., Hoenger, A., Iconomidou, V.A. (2004) Amyloid fibrillogenesis of silkmoth chorion protein peptide-analogues via a liquid crystalline intermediate phase. J. Struct. Biol., 145, 226-235.
    73. Pashou, E.E., Litou, Z.I., Liakopoulos, Th.D. and Hamodrakas, S.J. (2004) waveTM: Wavelet-based transmembrane segment prediction. In Silico Biol.4, 0012.
    74. Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C., Hamodrakas, S.J. (2004) A Hidden Markov Model capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics, 2004, 5:29.
    75. Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C., Hamodrakas, S.J. (2004) PRED-TMBB: A web server for predicting the topology of â-barrel outer membrane proteins Nucleic Acids Res, 32, W400-404.
    76. Bagos, P.G., Liakopoulos, T.D., Hamodrakas, S.J. (2004) Maximum Likelihood and Conditional Maximum Likelihood learning algorithms for Hidden Markov Models with labeled data. Journal of Computational Methods in Sciences and Engineering, In Press.
    77. Papasaikas, P.K., Bagos, P.G., Litou, Z.I., Promponas V.J. and Hamodrakas, S.J. (2004) PRED-GPCR: GPCR recognition and family classification server. Nucleic Acids Res, 32, W380-382.
    78. Spyropoulos, I.C., Liakopoulos, T.D., Bagos, P.G., Hamodrakas, S.J. (2004) TMRPres2D: high quality visual representation of transmembrane protein models. Bioinformatics, 20(17), 3258-3260.
    79. Magkrioti, C.K., Spyropoulos, I.C., Iconomidou, V.A., Willis, Hamodrakas, S.J. (2004) CuticleDB: a relational database of Arthropod cuticular proteins. BMC Bioinformatics, 5: 138.
    80. Elefsinioti, A.L., Bagos, P.G., Spyropoulos, I.C., Hamodrakas, S.J. (2004) A database for G proteins and their interaction with GPCRs. BMC Bioinformatics, 5(1), 208.
    81. Bagos, P.G., Liakopoulos, Hamodrakas, S.J. (2004) Finding beta-barrel outer membrane proteins with a markov chain model. WSEAS Transactions on Biology and Biomedicine, 2(1), 186-189.
    82. Bagos, P.G., Liakopoulos, Hamodrakas, S.J. (2004) Faster Gradient Descent Training of Hidden Markov Models, Using Individual Learning Rate Adaptation. Proceedings of ICGI 2004 Lecture Notes In Artificial Intelligence, 2(1), Vol. 3264, pp. 40-52.
    83. Bagos, P.G., Liakopoulos, T.D., Promponas, V.J., Hamodrakas, S.J. (2004) Topology prediction of â-barrel outer membrane proteins. Proc Indian Natl Sci Acad., B71(1), 19-41.
    84. 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, 6:7.
    85. Iconomidou, V.A., Willis, J.H., Hamodrakas, S.J. (2005) Unique features of the structural model of hard cuticle proteins: implications for chitin-protein interactions and cross-linking in cuticle. Insect Biochem. Mol. Biol., 35(6), 553-60.
    86. Willis, J.H., Iconomidou, V.A., Smith, R.F. Hamodrakas, S.J. (2005) Cuticular Proteins in 'Comprehensive Insect Science', (L. I. Gilbert, K. Iatrou, and S. Gill, Eds.). Elsevier, Oxford, Vol. 4, Ch. 2, 79-110.
    87. 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.
    88. Sgourakis, N.G., Bagos, P.G., Hamodrakas, S.J. (2005) Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks. Bioinformatics, 21(22), 4101-6.
    89. 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.
    90. Petsalaki, E.I., Bagos, P.G., Litou, Z.I., Hamodrakas, S.J. (2006) PredSL: A Tool for the N-terminal Sequence-based Prediction of Protein Subcellular Localization. Geno. Prot. Bioinfo., 4, 1.
    91. Iconomidou, V.A., Chryssikos, G.D., Gionis V, Galanis, A.S., Cordopatis, P., Hoenger, A., Hamodrakas, S.J. (2006) Amyloid fibril formation propensity is inherent into the hexapeptide tandemly repeating sequence of the central domain of silkmoth chorion proteins of the A-family. J. Struct. Biol., 156, 480-488.
    92. Bagos, P.G., Karnaouri, A.C., Nikolopoulos, G.K., Hamodrakas, S.J. (2007) No evidence for association of CTLA-4 gene polymorphisms with the risk of developing Multiple Sclerosis: a meta-analysis. Multiple Sclerosis. 13, 156-168.
    93. Iconomidou, V.A., Georgaka, M.E., Chryssikos, G.D., Gionis, V., Megalofonou, P., Hamodrakas, S.J. (2007) Dogfish egg case structural studies by ATR FT-IR and FT-Raman spectroscopy. Int. J. Biol. Macromol., 41(1), 102-108.
    94. Hamodrakas, S.J., Christina Liappa, C. Iconomidou, V.A. (2007) Consensus prediction of amyloidogenic determinants in amyloid fibril-forming proteins. Int. J. Biol. Macromol., 41(3),295-300.
    95. Kastritis, P.L., Papandreou, N.C., Hamodrakas, S.J. (2007) Haloadaptation: Insights from comparative modeling studies of halophilic archaeal DHFRs. Int. J.Biol. Macromol., 41(4),447-53.
    96. 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.
    97. Litou, Z.I., Bagos, P.G., Tsirigos, K.D., Liakopoulos, Th.D., Hamodrakas, S.J. (2008) Prediction of Cell Wall sorting signals in Gram-positive bacteria with a Hidden Markov Model: application to complete genomes. IJBCB, 6(2), 387-401.
    98. Iconomidou, V.A. and Hamodrakas, S.J. (2008) Natural Protective Amyloids. Curr. Prot. Pept. Sci., 9(3), 291-309.
    99. Nikolopoulos, G.K., Dimou, N.L., Hamodrakas, S.J., Bagos, P.G. (2008) Cytokine gene polymorphisms in periodontal disease: a meta-analysis of 53 studies including 4178 cases and 4590 controls. J Clin Periodontol, 35(9), 754-767.
    100. Theodoropoulou, M.C., Bagos, P.G., Spyropoulos, I.C., Hamodrakas, S.J. (2008) gpDB: a database of GPCRs, G-proteins, effectors and their interactions. Bioinformatics, 24(12), 1471-1472.
    101. Bagos, P.G., Tsirigos, K.D., Liakopoulos, T.D., Hamodrakas, S.J. (2008) Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model. J Proteome Res, 7(12), 5082-5093.
    102. Skopeliti, M., Iconomidou, V.A., Derhovanessian, E., Pawelec, G., Voelter, W., Kalbacher, H., Hamodrakas, S.J., Tsitsilonis, O.E. (2009) Prothymosin alpha immunoactive carboxyl-terminal peptide TKKQKTDEDD stimulates lymphocyte reactions, induces dendritic cell maturation and adopts a beta-sheet conformation in a sequence-specific manner. Mol Immunol, 46(5), 784-792.
    103. Bagos, P.G., Tsirigos, K.D. Plessas, S.K., Liakopoulos, T.D., Hamodrakas, S.J . (2009) Prediction of signal peptides in archaea. Protein Eng Des Sel, 22(1), 27-35.
    104. Frousios, K.K., Iconomidou, V.A., Karletidi, C.M., Hamodrakas, S.J. (2009) Amyloidogenic determinants are usually not buried. BMC Struct Biol., 9(1), 44.