2010 Publications

  1. Cristea IM, Rozjabek H, Molloy KR, Karki S, White LL, Rice CM, Rout MP, Chait BT, MacDonald MR. “Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: role for G3BP1 and G3BP2 in virus replication.” J Virol. 2010 Jul;84(13):6720-32. Epub 2010 Apr 14. PMC2903289
  1. Cristea IM, Moorman NJ, Terhune SS, Cuevas CD, O'Keefe ES, Rout MP, Chait BT, Shenk T. “Human Cytomegalovirus pUL83 Stimulates Activity of the Viral Immediate-Early Promoter through its Interaction with the Cellular IFI16 Protein." J. Virology 2010 May 26. PMC2897612
  1. Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD. “QTIPS: A novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments.” J Am Soc Mass Spectrom. 2010 Aug;21(8):1417-22. Epub 2010 Apr 8. PMC2914207
  1. Eriksson J, Fenyö D. “Modeling experimental design for proteomics.” Methods Mol Biol. 2010;673:223-30. PMC3745767
  1. Fenyö D, Eriksson J, Beavis R. “Mass spectrometric protein identification using the global proteome machine.” Methods Mol Biol. 2010;673:189-202. PMC3757509
  1. Förster F, Lasker K, Nickell S, Sali A, Baumeister W. “Toward an integrated structural model of the 26S proteasome.”  Mol Cell Proteomics. 2010 Aug;9(8):1666-77. Epub 2010 May  PMC2938054
  1. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, Boydston EA, Holmes MC, Gregory PD, Greally JM, Rafii S, Yang C, Scambler PJ, Garrick D, Gibbons RJ, Higgs DR, Cristea IM, Urnov FD, Zheng D, Allis CD. “Distinct factors control histone variant H3.3 localization at specific genomic regions.” Cell. 2010 Mar 5;140(5):678-91. doi: 10.1016/j.cell.2010.01.003. PMC2885838
  1. Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD. “Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress.” J Biol Chem. 2010 Feb 26;285(9):6739-49. Epub 2009 Dec 21. PMC2825468
  1. Lasker K, Phillips JL, Russel D, Velázquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A. “Integrative structure modeling of macromolecular assemblies from proteomics data.”  Mol Cell Proteomics. 2010 Aug;9(8):1689-702. Epub 2010 May 27.  PMC2938050
  1. Lasker K, Sali A, Wolfson HJ. “Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.”  2010 Nov 15;78(15):3205-11.   PMC2952722
  1. Li Y, Stewart NK, Berger AJ, Vos S, Schoeffler AJ, Berger JM, Chait BT, Oakley MG. “Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction.” Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18832-7. Epub 2010 Oct 4.  PMC2973889
  1. Nesić D, Miller MC, Quinkert ZT, Stein M, Chait BT, Stebbins CE. “Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates.”  Nat Struct Mol Biol. 2010 Jan;17(1):130-2. Epub 2009 Dec 6.  PMC3006182
  1. Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD. “Genome-wide analysis of effectors of peroxisome biogenesis.” PLoS One. 2010 Aug 4;5(8):e11953.  PMC2915925
  1. Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. “Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.” Mol Cell Proteomics. 2010 Sep;9(9):2076-88. Epub 2010 Apr 15.  PMC2938103
  1. Saleem RA, Aitchison JD. “Systems cell biology of the mitotic spindle.” J Cell Biol, 2010 Jan 11;188(1):7-9.  PMC2812858
  1. Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK. “Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.” Proteins. 2010 Jun;78(8):1992-8. PMC3136511
  1. Schneidman-Duhovny D, Hammel A, Sali A. “FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles.” Nucleic Acids Res. 2010 Jul;38(Web Server issue):W540-4. Epub 2010 May 27. PMC2896111
  1. Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. “GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.” Mol Syst Biol. 2010;6:353. Epub 2010 Mar 9. PMC2858444
  1. Terhune SS, Moorman NJ, Cristea IM, Savaryn JP, Cuevas-Bennett C, Rout MP, Chait BT, Shenk T. “Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA.” PLoS Pathog. 2010 Jun 24;6(6):e1000965.  PMC2891856
  1. Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD. “Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing.” Nucleic Acids Res, 2010 Mar 1;38(5):1431-40. Epub 2009 Dec 14.  PMC2836552
  1. Westblade LF, Campbell EA, Pukhrambam C, Padovan JC, Nickels BE, Lamour V, Darst SA. “Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.” Nucleic Acids Res. 2010 Dec;38(22):8357-69. doi: 10.1093/nar/gkq692. Epub 2010 Aug. PMC3001067
  1. Zhang G, Ueberheide BM, Waldemarson S, Myung S, Molloy K, Eriksson J, Chait BT, Neubert TA, Fenyö D. “Protein quantitation using mass spectrometry.”  Methods Mol Biol. 2010;673:211-22.  PMC3758905