All Publications

    2009

  1. A.B. Tchagang, K.V. Bui, T. McGinnis, P.V. Benos, "Extracting biologically significant patterns from short time series gene expression data." BMC Bioinformatics, (2009) 10:255. Abstract (PubMed) and pdf
     
  2. D.L. Corcoran1, K.V. Pandit1, B. Gordon, A. Bhattacharjee, N. Kaminski†, P.V. Benos† "Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data." PLoS ONE, (2009) 4:e5279. Abstract (PubMed) and pdf
     
  3. R. Brower-Sinning, D.M. Carter, C.J. Crevar, E. Ghedin, T.M. Ross, P.V. Benos "The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus." Genome Biol, (2009) 10:R18. Abstract (PubMed) and pdf
     
  4. S. Kadri, V. Hinman, P.V. Benos "HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models." BMC Bioinformatics (Proc APBC), (2009) 10(Suppl 1):S35. Abstract (PubMed) and pdf
     

    5. 2008

  5. Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, "Multiple evidence supporting cyclic assignments", Genome Biol, (2008) 9:403.
    [rebattle article on Jensen et al., Genome Biol (2008), 9:403]
     
  6. A. Tchagang, P.V. Benos, A. Tewfik, "Biological evaluation of biclustering algorithms using gene ontology and chip-chip data", IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), (2008) Las Vegas, NV, March 30 - April 4, 2008.
     

    7. 2007

  7. H. Feng, J.L. Taylor, P.V. Benos, R. Newton, K. Waddell, S.B. Lucas, Y. Chang, P.S. Moore "Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma." J Virol, (2007) 81:11332-11340. Abstract (PubMed) and pdf
     
  8. Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L.L. Breeden, Z. Bar-Joseph "Combined analysis reveals a core set of cycling genes." Genome Biol, (2007) 8:R146. Abstract (PubMed) and pdf
     
  9. S. Mahony, P.E. Auron and P.V. Benos "Inferring protein-DNA dependencies using motif alignments and mutual information." Bioinformatics (Proc ISMB), (2007) 23:i297-i304. Abstract (PubMed) and pdf
     
  10. S. Mahony, D.L. Corcoran, E. Feingold, P.V. Benos "Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome." Genome Biol, (2007) 8:R84. Abstract (PubMed) and pdf   
     
  11. T.S. Mikkelsen(1), ..., P.V. Benos(18), ..., S. Mahony(37), ..., K. Lindblad-Toh(64) "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences." Nature, (2007) 447:167-177. Abstract (PubMed) and pdf
     
  12. S. Mahony, P.E. Auron, P.V. Benos "DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies." PLoS Comput Biol, (2007) 3:e61. Abstract (PubMed) and pdf
     
  13. (Web tool) S. Mahony, P.V. Benos "STAMP: a web tool for exploring DNA-binding motif similarities." Nucl Acids Res, (2007) 35:W253-258. Abstract (PubMed) and pdf
     

    14. 2006

  14. S. Mahony, P.V. Benos, T.J. Smith, and A. Golden "Self-Organizing Neural Networks to Support the Discovery of DNA-Binding Motifs." Neural Networks, (2006) 19:950-962. Abstract (PubMed) and pdf
     
  15. K. Belov, J.E. Deakin, A.T. Papenfuss, M.L. Baker, S.D. Melman, H.V. Siddle, N. Gouin, D.L. Goode, T.J. Sargeant, M.D. Robinson, M.J. Wakefield, S. Mahony, J.G.R. Cross, P.V. Benos, P.B. Samollow, T.P. Speed, J.A.M. Graves, and R.D. Miller "Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial MHC." PLoS Biology, (2006) 4:e46. Abstract (PubMed) and pdf
     

    16. 2005

  16. K.R. Rogulski, D.E. Cohen, D.L. Corcoran, P.V. Benos and E.V. Prochownik "Deregulation of common genes by c-Myc and its direct target, MT-MC1." Proc Natl Acad Sci USA, (2005) 102:18968-18973. Abstract (PubMed) and pdf
     
  17. S. Mahony, A. Golden, T.J. Smith and P.V. Benos "Improved detection of DNA motifs using a self-organized clustering of familial binding profiles." Bioinformatics (Proc ISMB), (2005) 21 Suppl:i283-i291. Abstract (PubMed) and pdf
     
  18. D.L. Corcoran, E. Feingold, J. Dominick, M. Wright, J. Harnaha, M. Trucco, N. Giannoukakis and P.V. Benos "Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements." Genome Res, (2005) 15:840-847. Abstract (PubMed) and pdf
     
  19. (Web tool) D.L. Corcoran, E. Feingold, and P.V. Benos "FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting." Nucl Acids Res, (2005) 33:W442-446. Abstract (PubMed) and pdf
     
  20. (Web tool) C.T. Workman, Y. Yin, D.L. Corcoran, T. Ideker, G.D. Stormo and P.V. Benos "EnoLOGOS: a versatile web tool for energy normalized sequence logos." Nucl Acids Res, (2005) 33:W389-392. Abstract (PubMed) and pdf
     
  21. (Web tool) S. Ringquist, C. Pecoraro, C. Gilchrist, A. Styche, W. Rudert, P.V. Benos, and M. Trucco "SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms." Nucl Acids Res, (2005) 33:W548-552. Abstract (PubMed) and pdf
     
  22. A.M. Alexander, C. Pecoraro, A. Styche, W.A. Rudert, P.V. Benos, S. Ringquist, M. Trucco, "SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing", Biotechniques, (2005) 38:87-94. Abstract (PubMed)
     

    23. 2004

  23. J.K. Vries, R. Munshi, D. Tobi, J. Klein-Seetharaman, P.V. Benos, I. Bahar, "A sequence alignment-independent method for protein classification", Appl Bioinformatics, (2004) 3:137-148. Abstract (PubMed)
     

    24. 2002

  24. 13. D.G. Peters, X.C. Zhang, P.V. Benos, E. Heidrich-O’Hare, R.E. Ferrell, "Genomic analysis of the immediate/early response to shear stress in human coronary artery endothelial cell", Physiol Genomics, (2002) 12:25-33. Abstract (PubMed)
     
  25. 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
     
  26. 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
     
  27. 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
     
  28. 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, M. Ashburner, H.J. Bellen, H. Jaeckle, U. Schaefer, "Mapping and identification of essential gene functions on the X chromosome of Drosophila", EMBO Reports (2002) 3:34-38. Abstract (PubMed)
     

    29. 2001

  29. 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
     
  30. 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).
     
  31. 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
     
     

    32. 2000

  32. 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).
     
  33. 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).
     
  34. 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).
     

    35. 1999

  35. R. Gessmann, P. Benos, H. Brueckner, M. Kokkinidis, "The crystal structures of the synthetic C-terminal Octa- and Dodecapeptides of Trichovirin", J Peptide Sci (1999) 5:83-95. Abstract (PubMed)
     

    36. 1997

  36. P. Deak, M.M. Omar, R.D. Saunders, M. Pal, O. Komonyi, J. Szidonya, P. Maroy, Y. Zhang, M. Ashburner, P. Benos, C. Savakis, I. Siden-Kiamos, C. Louis, V.N. Bolshakov, F.C. Kafatos, E. Madueno, J. Modolell, D.M. Glover, "P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: correlation of physical and cytogenetic maps in chromosomal region 86E-87F", Genetics (1997) 147:1697-1722. Abstract (PubMed)
     
  37. C. Louis, E. Madueno, J. Modolell, M.M. Omar, G. Papagiannakis, R.D. Saunders, C. Savakis, I. Siden-Kiamos, L. Spanos, P. Topalis, Y.Q. Zhang, M. Ashburner, P. Benos, V.N. Bolshakov, P. Deak, D.M. Glover, S. Herrmann, F.C. Kafatos "One-hundred and five new potential Drosophila melanogaster genes revealed through STS analysis", Nucleic Acids Res (1997) 24:3437-3438. Abstract (PubMed)
     

    38. 1996

  38. M. Tabler, P. Benos, M. Dörr, "Representation of unique sequences in libraries of randomized nucleic acids", Nucleic Acids Res (1996) 24:3437-3438. Abstract (PubMed)
     

    39. 1995

  39. E. Madueno Amor, G. Papagiannakis, G. Rimington, R.D.C. Saunders, C. Savakis, I. Siden-Kiamos, G. Skavdis, L. Spanos, J. Trennear, P. Adam, M. Ashburner, P. Benos, V. Bolshakov, D. Coulson, D.M. Glover, S. Herrmann, F.C. Kafatos, C. Louis, T. Majerus, J. Modolell, "A physical map of the X chromosome of Drosophila melanogaster: Cosmid contigs and sequence tagged sites", Genetics (1995) 139:1631-1647. Abstract (PubMed)
     
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University of Pittsburgh Department of Computational Biology