2012 Publications

  1. Aitchison JD, Rout MP. “The yeast nuclear pore complex and transport through it.” Genetics. 2012 Mar;190(3):855-83. PMC3296253
  2. Domanski M, Molloy K., Jiang H, Chait BT, Rout MP, Jensen TH and LaCava J. “Improved Methodology for the Affinity Isolation of Human Protein Complexes Expressed at Near Endogenous Levels”. Biotechniques, May 2012, pp. 1–6. PMC3605737
  3. Donlin LT, Andresen C, Just S, Rudensky E, Pappas CT, Kruger M, Jacobs EY, Unger A, Zieseniss A, Dobenecker MW, Voelkel T, Chait BT, Gregorio CC, Rottbauer W, Tarakhovsky A, Linke WA. “Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization.” Genes Dev. 2012 Jan 15;26(2):114-9. Epub 2012 Jan 12. PMC3273835
  4. DuBois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD, Navarro M, Horn D, Aitchison JD, Rout MP, Field MC. “NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions.” PLoS Biol. 2012 Mar;10(3):e1001287. Epub 2012 Mar 27. PMC3313915
  5. Fernandez-Martinez J, Phillips J, Sekedat MD, Diaz-Avalos R, Velazquez-Muriel J, Franke JD, Williams R, Stokes DL, Chait BT, Sali A, Rout MP. “Structure-function mapping of a heptameric module in the nuclear pore complex.”  J Cell Biol 2012 Feb 20;196(4):419-434. PMC3283990
  6. Fernandez-Martinez J, Rout MP. “A jumbo problem: mapping the structure and functions of the nuclear pore complex.” Curr Opin Cell Biol. 2012 Feb;24(1):92-9. Epub 2012 Feb 8. PMC3472030
  7. Field MC, Horn D, Alsford S, Koreny L, Rout MP. “Telomeres, tethers and trypanosomes.” Nucleus. 2012 Sep 19;3(6). [Epub ahead of print] PMC3515529
  8. Field MC, Adung'a V, Obado S, Chait BT, Rout MP. “Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes.” Parasitology. 2012 Feb 6:1-10. [Epub ahead of print] PMID: 22309600
  9. Frazier Z, Alber F. “A computational approach to increase time scales in Brownian dynamics based reaction-diffusion modeling.” J Comput Biol. 2012 Jun;19(6):606-18. PMC3375646
  10. Heller EA, Zhang W, Selimi F, Earnheart JC, Ślimak MA, Santos-Torres J, Ibañez-Tallon I, Aoki C, Chait BT, Heintz N. “The biochemical anatomy of cortical inhibitory synapses.” PLoS One. 2012;7(6):e39572. Epub 2012 Jun 29. PMC3387162
  11. Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. “Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.” Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1380-7. Epub 2012 Jan 23. PMC3277140
  12. Li X, He L, Che KH, Funderburk SF, Pan L, Pan N, Zhang M, Yue Z, Zhao Y. “Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG.” Nat Commun. 2012 Feb 7;3:662. doi: 10.1038/ncomms1648. PMC3293417
  13. Li X, He L, Zhang M, Yue Z. and Zhao Y.  “The Beclin 1 coiled coil domain: an “imperfect” homodimer interface that facilitates Atg14L and UVRAG binding.” Autophagy 2012 Aug;8(8):1258-60. doi: 10.4161/auto.20750. Epub 2012 May 31. PMC3679240
  14. Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A. “A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.” Nature. 2012 Oct 18;490(7420):421-5. doi: 10.1038/nature11428. Epub 2012 Sep 16. PMC3556990
  15. Obado SO, Rout MP. “Ciliary and nuclear transport: different places, similar routes?” Dev Cell. 2012 Apr 17;22(4):693-4. PMID: 22516195
  16. Oeffinger M. “Two Steps Forward – One Step Back: Advances in Affinity Purification Mass spectrometry of Macromolecular Complexes.” Proteomics. 2012 May;12(10):1591-608. doi: 10.1002/pmic.201100509. PMID: 22592981
  17. Oeffinger M, Zenklusen D. “To the pore and through the pore: A story of mRNA export kinetics.” 2012 Jun;1819(6):494-506. doi: 10.1016/j.bbagrm.2012.02.011. Epub 2012 Feb 22. PMC3345096
  18. Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD. “Asymmetric positive feedback loops reliably control biological responses.” Mol Syst Biol. 2012 Apr 24;8:577. doi: 10.1038/msb.2012.10. PMC3361002
  19. Russel D, Lasker K, Webb B, Velázquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. “Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.” PLoS Biol. 2012 Jan;10(1):e1001244. Epub 2012 Jan 17. PMC3260315
  20. Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley SK. “Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.” Proteins. 2012 Aug;80(8):2110-6. PMC3686472
  21. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A. “A method for integrative structure determination of protein-protein complexes.” Bioinformatics. 2012 Dec 1;28(24):3282-3289. Epub 2012 Oct 23. PMC3519461
  22. Schneidman-Duhovny D, Kim SJ, Sali A. “Integrative structural modeling with small angle X-ray scattering profiles.” BMC Struct Biol. 2012 Jul 16;12:17. doi: 10.1186/1472-6807-12-17. Review. PMC3427135
  23. Tetenbaum-Novatt J, Hough LE, Mironska R, McKenney AS, Rout MP. “Nucleocytoplasmic transport: A role for non-specific competition in karyopherin-nucleoporin interactions.” Mol Cell Proteomics. 2012 Feb 22. [Epub ahead of print] PMC3418842
  24. Tjong H, Gong K, Chen L, Alber F. “Physical tethering and volume exclusion determine higher order genome organization in budding yeast.” Genome Res. 2012 Jul;22(7):1295-305. Epub 2012 May 22. PMC3396370
  25. Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A. “Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.” Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18821-6. Epub 2012 Oct 29. PMC3503186
  26. Xu M, Beck M, Alber F. “High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching.” J Struct Biol. 2012 May;178(2):152-64. Epub 2012 Mar 7. PMC3821800
  27. Xu M, Alber F. “High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization.” BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S18. doi: 10.1186/1752-0509-6-S1-S18. Epub 2012 Jul 16. PMC3403359
  28. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. “UCSF Chimera, MODELLER, and IMP: an integrated modeling system.” J Struct Biol. 2012 Sep;179(3):269-78. Epub 2011 Sep 22. PMC3410985
  29. Zhou XJ, Alber F. “Zooming in on genome organization.”  Nature Methods. 2012 Oct; 9 (10), 961-963. PMC3806477