2011 Publications

  1. Beck M, Topf M, Frazier Z, Tjong H, Zhang S, Xu M, Alber F. “Exploring the spatial and temporal organization of a cell’s proteome.” J Struct Biol. 2011 Mar;173(3):483-96. Epub 2010 Nov 19. PMC3784337
  2. Berdygulova Z, Westblade LF, Florens L, Koonin EV, Chait BT, Ramanculov E, Washburn MP, Darst SA, Severinov K, Minakhin L.  “Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45.”  J Mol Biol. 2011 Jan 7;405(1):125-42. Epub 2010 Nov 2.  PMC3018760
  3. Cristea IM, Chait BT. “Conjugation of magnetic beads for immunopurification of protein complexes.”  Cold Spring Harb Protoc. 2011 May 1;2011(5). pii: pdb.prot5610. doi: 10.1101/pdb.prot5610.  PMID: 21536766
  4. Cristea IM, Chait BT. “Affinity purification of protein complexes.” Cold Spring Harb Protoc. 2011 May 1;2011(5). pii: pdb.prot5611. doi: 10.1101/pdb.prot5611. PMID: 21536765
  5. Dokudovskaya S, Rout MP. “A novel coatomer-related SEA complex dynamically associates with the vacuole in yeast and is implicated in the response to nitrogen starvation.” Autophagy. 2011 Nov;7(11):1392-3. Epub 2011 Nov 1. PMC3242801
  6. Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. “A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae.” Mol Cell Proteomics. 2011 Mar 31. [Epub ahead of print] PMC3108837
  7. Eriksson J, Fenyö D. “Modeling mass spectrometry-based protein analysis.” Methods Mol Biol. 2011;694:109-17.  PMC3757507
  8. Field MC, Sali A, Rout MP. “On a bender--BARs, ESCRTs, COPs, and finally getting your coat.” J Cell Biol. 2011 Jun 13;193(6):963-72. PMC3115789
  9. Grünwald D, Singer RH, Rout M. “Nuclear export dynamics of RNA-protein complexes.” Nature. 2011 Jul 20;475(7356):333-41. doi: 10.1038/nature10318. PMC3154952
  10. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ. “Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.” Nature. 2011 Dec 21;481(7381):371-5. doi: 10.1038/nature10693. PMC3310910
  11. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. “Global landscape of HIV-human protein complexes.” Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719. PMC3310911
  12. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. “Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.” Nat Biotechnol. 2011 Dec 25;30(1):90-8. doi: 10.1038/nbt.2057. PMC3782096
  13. Keck JM, Jones MH, Wong CCL, Binkley J, Chen DC, Jaspersen SL, Holinger EP, Xu T, Niepel M, Rout MP, Vogel J, Sidow A, Yates JR III, Winey M.  “A Cell Cycle Phosphoproteome of the Yeast Centrosome.” Science 2011 Jun 24;332(6037):1557-1561. PMC3825980
  14. Li X, Wang QJ, Pan N, Lee S, Zhao Y, Chait BT, Yue Z.  “Phosphorylation-dependent 14-3-3 binding to LRRK2 is impaired by common mutations of familial Parkinson's disease.”  PLoS One. 2011 Mar 1;6(3):e17153. PMC3046972
  15. Peterson SE, Li Y, Chait BT, Gottesman ME, Baer R, Gautier J. “Cdk1 uncouples CtIP-dependent resection and Rad51 filament formation during M-phase double-strand break repair.” J Cell Biol. 2011 Sep 5;194(5):705-20. PMC3171114
  16. Ratushny AV, Ramsey SA, Aitchison JD. “Mathematical modeling of biomolecular network dynamics.” Methods Mol Biol. 2011;781:415-33 PMID: 21877294
  17. Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, 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, Sali A, Sauder JM, Burley SK. “Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.”  Proteins. 2011 May;79(5):1672-7. doi: 10.1002/prot.22973. Epub 2011 Mar 1. PMC3350809
  18. Scheid JF, Mouquet H, Ueberheide B, Diskin R, Klein F, Oliveira TY, Pietzsch J, Fenyo D, Abadir A, Velinzon K, Hurley A, Myung S, Boulad F, Poignard P, Burton DR, Pereyra F, Ho DD, Walker BD, Seaman MS, Bjorkman PJ, Chait BT, Nussenzweig MC. “Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding.” Science. 2011 Sep 16;333(6049):1633-7. Epub 2011 Jul 14. PMC3351836
  19. Schneidman-Duhovny D, Hammel M, Sali A.  “Macromolecular docking restrained by a small angle X-ray scattering profile.”  J Struct Biol. 2011 Mar;173(3):461-71. Epub 2010 Oct 12. PMC3040266
  20. Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD. “Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing.” Mol Syst Biol. 2011 Jan 4;7:455.  PMC3049408
  21. Smith JJ, Saleem RA, Aitchison JD. “Statistical analysis of dynamic transcriptional regulatory network structure.” Methods Mol Biol. 2011;781:337-52. PMID: 21877289
  22. Tetenbaum-Novatt J, Rout MP.  “The Mechanism of Nucleocytoplasmic Transport through the Nuclear Pore Complex.” Cold Spring Harb Symp Quant Biol. 2011 Mar 29. [Epub ahead of print] PMC3418842
  23. Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. “MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.” Nucleic Acids Res. 2011 Jul;39(Web Server issue):W167-70. PMC3125811
  24. Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD.  “Role of the nuclear envelope in genome organization and gene expression.” Wiley Interdiscip Rev Syst Biol Med. 2011 Mar-Apr;3(2):147-66. doi: 10.1002/wsbm.101.  PMC3050641
  25. Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A. “Modeling of proteins and their assemblies with the integrative modeling platform.” Methods Mol Biol. 2011;781:377-97. PMID: 21877292
  26. Xu M, Beck M, Alber F. “Template-free detection of macromolecular complexes in cryo electron tomograms.” Bioinformatics (ISMB). Bioinformatics. 2011 Jul 1;27(13):i69-76. PMC3117359