Photo Vasilis Promponas

Postdoctorate research assistant

2004 (Jan) Defended PhD thesis

1997-2004 PhD student in the Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens. Title: "Prediction of protein function from aminoacid sequence" Supervisor: Professor Stavros J. Hamodrakas

1991-1996 Undergraduate studies in the Faculty of Physics, University of Athens. Diploma Thesis: "Structural studies of possible inhibitors of Dihydrofolate Reductase (DHFR)" Supervisor: Professor Stavros J. Hamodrakas

My research interests are oriented towards the interpretation of Large Scale Genomic Data, and the use of computational methods in order to reveal the principles governing the Molecular Basis of Life. In particular, I am mainly interested in the elucidation of protein sequence to structure/function relationships by statistical and machine learning techniques.

1. Sequence repeats, low complexity/compositionally biased regions
- Relation to protein structure
- Assosiation to protein (mis)function
- Evolution of protein repeats
- Correlation to the nucleic acid sequence features

2. Transmembrane Protein topology and structure prediction
- Prediction of structrural features of membrane proteins
- Evolution of transmembrane protein topology/structure/function

3. Sequence-based structural/functional classification of proteins

4. Computer-aided and automatic Genome Annotation

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. [Abstract] [PDF]

Bagos, P.G., Liakopoulos, T.D., Promponas, V.J., Hamodrakas, S.J. (2004) Topology prediction of beta-barrel outer membrane proteins. Proceedings of the Indian National Sciences Academy-Biological Sciences (PINSA-B) [In Press]

Vernikos G.S., Gkogkas C.G., Promponas V.J., Hamodrakas S.J. (2003) GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. BMC Bioinformatics, 4, 53 [Abstract] [PDF]

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. [Abstract] [PDF]

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. [Abstract] [PDF]

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. [Abstract] [PDF]

Promponas, V. J., Palaios, G., Pasquier, C. M., Hamodrakas, J. S. and Hamodrakas S. J. (1999) CoPreTHi: A Web tool which combines transmembrane protein segment prediction methods, In Silico Biology, 3, 1-4. [Abstract]

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. [Abstract] [PDF]

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. [Abstract] [PDF]