TAKIS BENOS


Correspondence  

Center for Computational Biology & Bioinformatics,
University of Pittsburgh,
W1041 Biomedical Sciences Tower,
200 Lothrop Street, Pittsburgh, PA 15213
Phone: (412) 648 3315; Fax: (412) 648 3163
E-mail: benos@pitt.edu
URL: http://www.hgen.pitt.edu/~benos/

Research Interests

The primary focus of my research is in the area of gene regulation and special emphasis is given to the understanding of the mechanisms that govern the specific DNA binding by the regulatory proteins. The recognition of a particular DNA sequence in the proximity of a gene (promoter region) is in the centre of most cellular functions and constitutes a key step towards gene regulation. Moreover, the ability to engineer transcription factors so that they can bind a predetermined DNA target with high affinity is not trivial nowadays. Thus, unravelling the rules behind the specific DNA recognition by transcription factors is of great medical importance, with numerous potential therapeutic applications. Despite its importance, it is still a poorly understood process. Part of our work consists of the development of computational algorithms to model this process. Biochemical experimentation is an essential component of our research too, providing the data that are necessary for training and evaluation of our algorithms.  Another research area that I am interested in is that of genome analysis, with special emphasis to the evolution of protein families and as well as to the whole genomes.

Current Position

Assistant Professor at the Department of Human Genetics, GSPH, with joint appointment at the Center for Computational Biology and Bioinformatics and the Cancer Institute, University of Pittsburgh (2002 - ).

Education

Ph.D. in Molecular Biology, Department of Biology, University of Crete, 1997.
M.S. in Molecular Biology, Department of Biology, University of Crete, 1993.
B.S. in Mathematics, Department of Mathematics, University of Crete, 1990.

Career/Employment

Assistant Professor, Department of Human Genetics, GSPH, University of Pittsburgh, 2002 -
Joint appointments:
Center for Computational Biology and Bioinformatics (CCBB) and
University of Pittsburgh Cancer Institute (UPCI), University of Pittsburgh

Research Associate, Department of Genetics, Washington University, 1999 - 2002.

Research Assistant, European Molecular Biology Laboratory - The EBI, 1997 - 1999.

Selected Recent Publications

  1. P.V. Benos, A.S. Lapedes and G.D. Stormo, "Probabilistic code for DNA recognition by proteins of the EGR-family", J. Mol. Biol., (2002) 323:701-727. Abstract (PubMed) and pdf (publisher).

    2.  
  2. D.G. Peters, X.C. Zhang, P.V. Benos, E. Heidrich-O'Hare and R.E. Ferrell "Genomic analysis of the immediate/early response to shear stress in human coronary artery endothelial cell", Physiol Genomics, (2002) in press. Abstract (PubMed) and pdf (publisher).

    3.  
  3. P.V. Benos, M.L. Bulyk and G.D. Stormo, "Additivity in protein-DNA interactions: how good an approximation is it?", Nucleic Acids Res., (2002) 30:4442-445. Abstract (PubMed) and pdf (publisher).

    4.  
  4. P.V. Benos, A.S. Lapedes and G.D. Stormo, "Is there a code for protein-DNA recognition? Probab(ilistical)ly...", Bioessays, (2002) 24:466-475. (Review article) Abstract (PubMed) and pdf (publisher)

    5.  
  5. A. Peter, P. Schoettler, M. Werner, N. Beinert, G. Dowe, P. Burkert, F. Mourkioti, L. Denzer, Y. He, P. Deak, P.V. Benos, M.K. Gatt, L. Murphy, D. Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demaille, E. Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B. Minana, F.C. Kafatos, S. Bolshakov, I. Siden-Kiamos, G. Papagiannakis, L. Spanos, C. Louis, E. Madueno, B. de Pablos, J. Modolell, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders, A. Billaud, L. Pachter, R. Klapper, W. Janning, D.M. Glover and M. Ashburner, H.J. Bellen, H. Jaeckle and U. Schaefer, "Mapping and identification of essential gene functions on the X chromosome of Drosophila", EMBO Reports, (2002) 3:34-38 Abstract (PubMed) and pdf (publisher).

    6.  
  6. P.V. Benos, M.K. Gatt, L. Murphy, D. Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demaille, E. Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B. Minana, F.C. Kafatos, S. Bolshakov, I. Siden-Kiamos, G. Papagiannakis, L. Spanos, C. Louis, E. Madueno, B. de Pablos, J. Modolell, A. Peter, P. Schoettler, M. Werner, F. Mourkioti, N. Beinert, G. Dowe, U. Schaefer, H. Jaeckle, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders, A. Billaud, L. Pachter, D.M. Glover and M. Ashburner, "From first base: The sequence of the tip of the X chromosome of D. melanogaster, a comparison of two sequencing strategies", Genome Res., (2001) 11:710-730. Abstract (PubMed) and pdf (publisher).

    7.  
  7. S. Brogna*, P.V. Benos*, G. Gasperi, C. Savakis, "The Drosophila alcohol dehydrogenase gene may have evolved independently of the functionally homologous medfly, olive fly and flesh fly genes", Mol. Biol. Evol., (2001) 18:322-329. Abstract (PubMed) and pdf (publisher).
    (*) equal contribution

    8.  
  8. P.V. Benos, A.S. Lapedes, D.S. Fields, G.D. Stormo, "SAMIE: Statistical Algorithm for Modeling Interaction Energies", Pac. Symp. Biocomput. (2001) 6:115-126. Abstract (PubMed) and pdf (publisher).

    9.  
  9. P.V. Benos, M.K. Gatt, M. Ashburner, L. Murphy, D. Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demailles, E. Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B. Minana, F.C. Kafatos, C. Louis, I. Siden-Kiamos, S. Bolshakov, G. Papagiannakis, L. Spanos, S. Cox, E. Madueno, B. de Pablos, J. Modolell, A. Peter, P. Schoettler, M. Werner, F. Mourkioti, N. Beinert, G. Dowe, U. Schaefer, H. Jaeckle, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders and D.M. Glover, "From DNA sequence to chromosome organisation: the tip of the X chromosome of D. melanogaster", Science (2000) 287:2220-2222. Abstract (PubMed) and pdf (publisher).

    10.  
  10. M.D. Adams(1), ..., P.V. Benos(43), ..., J.C. Venter(195), "The genome sequence of Drosophila melanogaster", Science (2000) 287:2185-2195. Abstract (PubMed) and pdf (publisher).

    11.  
  11. P. Benos, N. Tavernarakis, S. Brogna, G. Thireos, C. Savakis, "Acquisition of a potential marker for insect transformation: isolation of a novel alcohol dehydrogenase gene from Bactrocera oleae by functional complementation in yeast", Mol. Gen. Genet. (2000) 263:90-95. Abstract (PubMed) and pdf (publisher).

    12.  

 

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Last Updated: April 2002