Benos Lab Recent Publications (2003-04)

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).

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).

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).

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).  

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).

Alexander, A.M., C. Pecoraro, A. Styche, W.A. Rudert, P.V. Benos, S. Ringquist, and M. Trucco.
"SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing" Biotechniques 38 (2005): 87-94.

Corcoran, D.L., E. Feingold, and P.V. Benos. 2005a.
"FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting"
Nucleic Acids Res 33 (2005a): W442-446.

Corcoran, D.L., E. Feingold, J. Dominick, M. Wright, J. Harnaha, M. Trucco, N. Giannoukakis, and P.V. Benos. 2005b.
"Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements"
 Genome Res 15 (2005b): 840-847.

Mahony, S., A. Golden, T.J. Smith, and P.V. Benos. 2005.
"Improved detection of DNA motifs using a self-organized clustering of familial binding profiles"
Bioinformatics 21 Suppl 1 (2005): i283-i291.

Ringquist, S., C. Pecoraro, C.M. Gilchrist, A. Styche, W.A. Rudert, P.V. Benos, and M. Trucco.
"SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms"
Nucleic Acids Res 33 (2005): W548-552.

Workman, C.T., Y. Yin, D.L. Corcoran, T. Ideker, G.D. Stormo, and P.V. Benos. 2005a.
"EnoLOGOS: a versatile web tool for energy normalized sequence logos"
Nucleic Acids Res 33 (2005a): W389-392.