2013 Publications

  1. Adams RL, Wente SR. “Uncovering nuclear pore complexity with innovation.” Cell. 2013 Mar 14;152(6):1218-21. doi: 10.1016/j.cell.2013.02.042. Review. PMC3672239
  2. Andersen PR, Domanski M, Kristiansen MS, Storvall H, Ntini E, Verheggen C, Schein A, Bunkenborg J, Poser I, Hallais M, Sandberg R, Hyman A, Lacava J, Rout MP, Andersen JS, Bertrand E, Jensen TH. “The human cap-binding complex is functionally connected to the nuclear RNA exosome.” Nat Struct Mol Biol. 2013 Dec;20(12):1367-76. doi: 10.1038/nsmb.2703. Epub 2013 Nov 24. PMC3923317
  3. Baker LA, Ueberheide BM, Dewell S, Chait BT, Zheng D, Allis CD. “The yeast snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress.” Mol Cell Biol. 2013 Oct;33(19):3735-48. doi: 10.1128/MCB.00025-13. Epub 2013 Jul 22. PMC3811877
  4. Bao Y, Waldemarson S, Zhang G, Wahlander A, Ueberheide B, Myung S, Reed B, Molloy K, Padovan JC, Eriksson J, Neubert TA, Chait BT, Fenyö D. “Detection and Correction of Interference in SRM Analysis.” Methods. 2013 Jun 15;61(3):299-303. doi: 10.1016/j.ymeth.2013.05.008. Epub 2013 May 23. PMC3771650
  5. Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. “Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data.” J Am Chem Soc. 2013 Oct 28. [Epub ahead of print] PMC3902174
  6. Chen WM, Danziger SA, Chiang JH, Aitchison JD. “PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.” Bioinformatics. 2013 Oct 1;29(19):2435-44. doi: 10.1093/bioinformatics/btt387. Epub 2013 Jul 5. PMC3777105
  7. Danziger SA, Ratushny AV, Smith JJ, Saleem R, Wan Y, Arens CE, Armstrong A, Sitko K, Chen W-M, Chiang J-H, Reiss DJ, Baliga NS, Aitchison JD. “Molecular mechanisms of responses to novel stimuli are predictable by integrating public datasets.” Nucleic Acids Res. 2013 Oct 31. [Epub ahead of print] PMC3919619
  8. Di Virgilio M, Callen E, Yamane A, Zhang W, Jankovic M, Gitlin AD, Feldhahn N, Resch W, Oliveira TY, Chait BT, Nussenzweig A, Casellas R, Robbiani DF, Nussenzweig MC. “Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching.” Science. 2013 Feb 8;339(6120):711-5. doi: 10.1126/science.1230624. Epub 2013 Jan 10. PMC3815530
  9. Guttman M, Weinkam P, Sali A, Lee KK. “All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins.” Structure. 2013 Mar 5;21(3):321-31. doi: 10.1016/j.str.2013.02.004. PMC3840220
  10. LaCava J, Chandramouli N, Jiang H, Rout MP. “Improved native isolation of endogenous protein a-tagged protein complexes.” Biotechniques. 2013 Apr;54(4):213-6. doi: 10.2144/000114012. PMC3667664
  11. Li X, Foley EA, Kawashima SA, Molloy KR, Li Y, Chait BT, Kapoor TM. “Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach.” Protein Sci. 2013 Mar;22(3):287-95. doi: 10.1002/pro.2210. Epub 2013 Jan 27. PMC3595459
  12. Natalizio BJ, Wente SR. “Postage for the messenger: designating routes for nuclear mRNA export.” Trends Cell Biol. 2013 Aug;23(8):365-73. doi: 10.1016/j.tcb.2013.03.006. Epub 2013 Apr 11. PMC3729607
  13. Niepel M, Molloy KR, Williams R, Farr JC, Meinema AC, Vecchietti N, Cristea IM, Chait BT, Rout MP, Strambio-De-Castillia C. “The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome.” Mol Biol Cell. 2013 Oct 23. [Epub ahead of print] PMC3861087
  14. Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS. “Metallochaperones regulate intracellular copper levels.” PLoS Comput Biol. 2013 Jan;9(1):e1002880. doi: 10.1371/journal.pcbi.1002880. Epub 2013 Jan 17. PMC3551603
  15. Peterson SE, Li Y, Wu-Baer F, Chait BT, Baer R, Yan H, Gottesman ME, Gautier J. “Activation of DSB processing requires phosphorylation of CtIP by ATR.” Mol Cell. 2013 Feb 21;49(4):657-67. PMC3582837
  16. Ryan CJ, Cimermančič P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. “High-resolution network biology: connecting sequence with function.” Nat Rev Genet. 2013 Dec;14(12):865-79. doi: 10.1038/nrg3574. Epub 2013 Nov 7. Review. PMC4023809
  17. Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC. “Structure, Dynamics, Evolution, and Function of a Major Scaffold Component in the Nuclear Pore Complex.” 2013 Apr 2;21(4):560-71. doi: 10.1016/j.str.2013.02.005. Epub 2013 Mar 14. PMC3755625
  18. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. “Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments.” Biophys J. 2013 Aug 20;105(4):962-74. doi: 10.1016/j.bpj.2013.07.020. PMC3752106
  19. Smith JJ and Aitchison JD. “Peroxisomes take shape.” Nature Reviews Molecular Cell Biology, 2013 Dec;14(12):803-17. doi: 10.1038/nrm3700. PMC4060825
  20. Smith TC, Fridy PC, Li Y, Basil S, Arjun S, Friesen RM, Leszyk J, Chait BT, Rout MP, Luna EJ. “Supervillin Binding to Myosin II and Synergism with Anillin Are Required for Cytokinesis”, Mol Biol Cell. 2013 Dec;24(23):3603-19. doi: 10.1091/mbc.E12-10-0714. Epub 2013 Oct 2. PMC3842989
  21. Taylor MS, Lacava J, Mita P, Molloy KR, Huang CR, Li D, Adney EM, Jiang H, Burns KH, Chait BT, Rout MP, Boeke JD, Dai L. “Affinity Proteomics Reveals Human Host Factors Implicated in Discrete Stages of LINE-1 Retrotransposition.” Cell. 2013 Nov 21;155(5):1034-48. doi: 10.1016/j.cell.2013.10.021. PMC3904357
  22. Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M. “Conformational States of macromolecular assemblies explored by integrative structure calculation.” Structure. 2013 Sep 3;21(9):1500-8. doi: 10.1016/j.str.2013.08.006. PMC3988990
  23. Trewhella J, Hendrickson W, Kleywegt G, Sali A, Sato M, Schwede T, Svergun D, Tainer J, Westbrook J, Berman H. “Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB”. Structure. 2013 Jun 4;21(6):875-81. doi: 10.1016/j.str.2013.04.020. PMID: 23747111
  24. van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC. Huynen MA. “Evolution of modular intraflagellar transport from a coatomer-like progenitor.” Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6943-8. doi: 10.1073/pnas.1221011110. Epub 2013 Apr 8. PMC3637775
  25. Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW. “A role for the nucleoporin nup170p in chromatin structure and gene silencing.” Cell. 2013 Feb 28;152(5):969-83. doi: 10.1016/j.cell.2013.01.049. PMC3690833
  26. Ward AB, Sali A, Wilson IA. “Integrative structural biology.” Science. 2013 Feb 22;339(6122):913-5. doi: 10.1126/science.1228565. PMC3633482
  27. Xu M, Alber F. “Automated target segmentation and fast alignment methods for highthrouput classification and averaging of crowded cryo electron subtomograms.” Bioinformatics 2013 Jul 1;29(13):i274-82. doi: 10.1093/bioinformatics/btt225. PMC3694676
  28. Xue JZ, Woo EM, Postow L, Chait BT, Funabiki H, “Chromatin-Bound Xenopus Dppa2 Shapes the Nucleus by Locally Inhibiting Microtubule Assembly.” Dev Cell. 2013 Oct 14;27(1):47-59. doi: 10.1016/j.devcel.2013.08.002. Epub 2013 Sep 26. PMC3800493