All Publications

    2010

  1. K.V. Pandit, D. Corcoran, H. Yousef, M. Yarlagadda, A. Tzouvelekis, K.F. Gibson, K. Konishi, S.A. Yousem, M. Singh, D. Handley, T. Richards, M. Selman, S.C. Watkins, A. Pardo, A. Ben-Yehudah, D. Bouros, O. Eickelberg,P. Ray, P.V. Benos, N. Kaminski, "Inhibition and role of let-7d in idiopathic pulmonary fibrosis." Am J Resp Crit Care Med, (2010) in press. Abstract (PubMed) and pdf    PMID: 20395559
     
  2. N.A. Temiz, P.V. Benos, C.J. Camacho "Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains." Nucleic Acids Res., (2010) 38:2134-2144. Abstract (PubMed) and pdf    PMID: 20047959
     
  3. 2009

  4. 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    PMID: 19695084   
     
  5. 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    PMID: 19390574
       1 equal contribution,    corresponding authors
     
  6. 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    PMID: 19216739
     
  7. 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    PMID: 19208136
     
  8. 2008

  9. 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] Abstract (PubMed) and pdf    PMID: 18598377   
     
  10. 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.
     
  11. 2007

  12. 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    PMID: 17686852
     
  13. 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    PMID: 17650318
     
  14. 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    PMID: 17646310
     
  15. 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       PMID: 17506886
     
  16. 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    PMID: 17495919
     
  17. 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    PMID: 17397256
     
  18. (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    PMID: 17478497
     
  19. 2006

  20. 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    PMID: 16839740
     
  21. 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    PMID: 16435885
     
  22. 2005

  23. 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    PMID: 16365299
     
  24. 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    PMID: 15961468
     
  25. 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    PMID: 15930494
     
  26. (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    PMID: 15980508
     
  27. (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    PMID: 15980495
     
  28. (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    PMID: 15980532
     
  29. 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) pdf    PMID: 15679090
     
  30. 2004

  31. 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)    PMID: 15693739
     
  32. 2002

  33. 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) and pdf    PMID: 12407183
     
  34. 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    PMID: 12419259
     
  35. 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    PMID: 12384591
     
  36. 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    PMID: 12001270
     
  37. 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) and pdf    PMID: 11751581
     
  38. 2001

  39. 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    PMID: 11262933
     
  40. 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).    PMID: 11337470
     
  41. 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
         PMID: 11230533
     
  42. 2000

  43. 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).    PMID: 10731132
     
  44. 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).    PMID: 10731137
     
  45. 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).    PMID: 10732677
     
  46. 1999

  47. 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) and pdf    PMID: 10100124
     
  48. 1997

  49. 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) and pdf    PMID: 9409831
     
  50. 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) and pdf    PMID: 9305763
     
  51. 1996

  52. 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) and pdf    PMID: 8811100
     
  53. 1995

  54. 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) and pdf    PMID: 7789765
     
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University of Pittsburgh Department of Computational Biology