- NCDIR

2015

Hough LE, Dutta K, Sparks S, Temel DB, Kamal A, Tetenbaum-Novatt J, Rout MP, Cowburn D. “The molecular mechanism of nuclear transport revealed by atomic-scale measurements.” Elife. 2015 Sep 15;4. pii: e10027. doi: 10.7554/eLife.10027. PMC4621360
Krutchinsky AN, Padovan JC, Cohen H, Chait BT. “Optimizing electrospray interfaces using slowly diverging conical duct (ConDuct) electrodes.” J Am Soc Mass Spectrom. 2015 Apr;26(4):659-67. doi: 10.1007/s13361-014-1063-0. Epub 2015 Feb 10. PMC4361383
Krutchinsky AN, Padovan JC, Cohen H, Chait BT. “Maximizing Ion Transmission from Atmospheric Pressure into the Vacuum of Mass Spectrometers with a Novel Electrospray Interface.” J Am Soc Mass Spectrom. 2015 Apr;26(4):649-58. doi: 10.1007/s13361-014-1062-1. Epub 2015 Jan 15. PMC4361285
LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. “Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives.” Biotechniques. 2015 Mar 1;58(3):103-19. doi: 10.2144/000114262. eCollection 2015 Mar. PMC4465938
Lord CL, Timney BL, Rout MP, Wente SR. “Altering nuclear pore complex function impacts longevity and mitochondrial function in S. cerevisiae.” J Cell Biol. 2015 Mar 16;208(6):729-44. doi: 10.1083/jcb.201412024. PMC4362458
Mast FD, Rachubinski RA, Aitchison JD. Signaling dynamics and peroxisomes. Current opinion in cell biology. 2015;35:131-136. doi:10.1016/j.ceb.2015.05.002. PMC4529763
Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. “A strategy for dissecting the architectures of native macromolecular assemblies.” Nat Methods. 2015 Dec;12(12):1135-8. doi: 10.1038/nmeth.3617. Epub 2015 Oct 5. PMC4803312
Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ. “Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.” Curr Protoc Bioinformatics. 2015 Mar 9;49:8.19.1-16. doi: 10.1002/0471250953.bi0819s49. PMC4378866

2014

Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S. “Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.” Mol Cell Proteomics. 2014 Nov;13(11):2855-70. doi: 10.1074/mcp.M114.039388. Epub 2014 Jul 29. PMC4223477
Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. “Determining protein complex structures based on a Bayesian model of in vivo FRET data.” Mol Cell Proteomics. 2014 Nov;13(11):2812-23. doi: 10.1074/mcp.M114.040824. Epub 2014 Aug 19. PMC4223474
Bretes H, Rouviere JO, Leger T, Oeffinger M, Devaux F, Doye V and Palancade B. “Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs.” Nucleic Acids Res. 2014 Apr;42(8):5043-58. doi: 10.1093/nar/gku124. Epub 2014 Feb 5. PMC4005672
Carpp LN, Rogers RS, Moritz RL, Aitchison JD. “Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection.” Mol Cell Proteomics. 2014 Nov;13(11):2836-54. doi: 10.1074/mcp.M114.038984. Epub 2014 May 22. PMC4223476
Cevher MA, Shi Y, Li D, Chait BT, Malik S, Roeder RG. Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol. 2014 Dec;21(12):1028-34. doi: 10.1038/nsmb.2914. Epub 2014 Nov 10. PMC4259101
Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD. “Molecular mechanisms of system responses to novel stimuli are predictable from public data.” Nucleic Acids Res. 2014 Feb;42(3):1442-60. doi: 10.1093/nar/gkt938. Epub 2013 Oct 31. PMC3919619
Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. “Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex.” Cell. 2014 Aug 28;158(5):1123-35. doi: 10.1016/j.cell.2014.07.044. PMC4151992
Field MC, Koreny L, Rout MP. “Enriching the pore: splendid complexity from humble origins.” Traffic. 2014 Feb;15(2):141-56. doi: 10.1111/tra.12141. Epub 2014 Jan 8. PMC3906644
Finney OC, Danziger SA, Molina DM, Vignali M, Takagi A, Ji M, Stanisic DI, Siba PM, Liang X, Aitchison JD, Mueller I, Gardner MJ, Wang R. “Predicting antidisease immunity using proteome arrays and sera from children naturally exposed to malaria.” Mol Cell Proteomics. 2014 Oct;13(10):2646-60. doi: 10.1074/mcp.M113.036632. Epub 2014 Jul 14. PMC4188993
Fridy PC, Li Y, Keegan S, Thompson MK, Nudelman I, Scheid JF, Oeffinger M, Nussenzweig MC, Fenyö D, Chait BT, and Rout MP. “A robust pipeline for rapid production of versatile nanobody repertoires.” Nature Methods. 2014 Dec;11(12):1253-60. doi: 10.1038/nmeth.3170. Epub 2014 Nov 2. PMC4272012
Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Chiang JH, Kelly S, Chait BT, Aitchison JD, Rout MP, Field MC. “Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity.” Mol Biol Cell. 2014 Mar 5. [Epub ahead of print] PMC40045926
Holden JM, Koreny L, Kelly S, Chait BT, Rout MP, Field MC, Obado SO. “Touching from a distance: Evolution of interplay between the nuclear pore complex, nuclear basket, and the mitotic spindle.” Nucleus. 2014 Jul 31;5(4). [Epub ahead of print] Review. PMC4152344
Jovanovic-Talisman T, Chait BT, Rout MP. “NPC Mimics: Probing the Mechanism of Nucleocytoplasmic Transport.” Methods Cell Biol. 2014;122:379-93. doi: 10.1016/B978-0-12-417160-2.00017-5. PMC4272007
Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss T, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Almo SC, Rout M, Sali A. “Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.” Mol Cell Proteomics. 2014 Nov;13(11):2911-26. doi: 10.1074/mcp.M114.040915. Epub 2014 Aug 19. PMC4223481
Li Y, Cross FR, Chait BT. “Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes.” Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11323-8. doi: 10.1073/pnas.1409666111. Epub 2014 Jul 21. PMC4128132
Mast FD, Ratushny AV, Aitchison JD. “Systems cell biology.” J Cell Biol. 2014 Sep 15;206(6):695-706. Review. PMC4164942
Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. “Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.” Structure. 2014 Sep 2;22(9):1239-51. doi: 10.1016/j.str.2014.04.019. Epub 2014 Jul 31. PMC4322757
Ptak C, Aitchison JD, Wozniak RW. “The multifunctional nuclear pore complex: a platform for controlling gene expression.” Curr Opin Cell Biol. 2014 Mar 20;28C:46-53. doi: 10.1016/j.ceb.2014.02.001. [Epub ahead of print] Review. PMC4061258
Rout MP, Karpen GH. “Editorial overview: Cell nucleus: the nucleus: a dynamic organelle. “Curr Opin Cell Biol. 2014 Jun;28:iv-vii. doi: 10.1016/j.ceb.2014.05.005. Epub 2014 Jun 4. No abstract available. PMID: 24908378
Schneidman-Duhovny D, Pellarin R, Sali A. “Uncertainty in integrative structural modeling.” Curr Opin Struct Biol. 2014 Aug 27;28C:96-104. doi: 10.1016/j.sbi.2014.08.001. [Epub ahead of print] Review. PMC4252396
Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM. “Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.” Nature. 2014 Jan 30;505(7485):691-5. doi: 10.1038/nature12862. Epub 2013 Nov 27. PMC4077721
Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman D, Sali A, Rout MP, Chait BT. “Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.” Mol Cell Proteomics. 2014 Nov;13(11):2927-43. doi: 10.1074/mcp.M114.041673. Epub 2014 Aug 26. PMC4223482
Simon DN, Rout MP. “Cancer and the nuclear pore complex.” Adv Exp Med Biol. 2014;773:285-307. doi: 10.1007/978-1-4899-8032-8_13. PMID: 24563353
Subbotin RI, Chait BT. “A Pipeline for Determining Protein-Protein Interactions and Proximities in the Cellular Milieu.” 2014 Nov;13(11):2824-35. doi: 10.1074/mcp.M114.041095. Epub 2014 Aug 29. PMC4223475
Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. “Modeling of proteins and their assemblies with the Integrative Modeling Platform.” Methods Mol Biol. 2014;1091:277-95. doi: 10.1007/978-1-62703-691-7_20. Humana Press, London, UK, 2014. PMID: 24203340
Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS. “An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.” Mol Microbiol. 2014 Apr;92(2):369-82. doi: 10.1111/mmi.12564. Epub 2014 Mar 19. PMC4060883
Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. “Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.” J Mol Biol. 2014 Aug 19. pii: S0022-2836(14)00425-2. doi: 10.1016/j.jmb.2014.07.033. [Epub ahead of print] PMC4253074
Zhong Y, Morris DH, Jin L, Patel MS, Karunakaran SK, Fu YJ, Matuszak EA, Weiss HL, Chait BT, Wang QJ. “Nrbf2 Suppresses Autophagy by Modulating Atg14L-containing Beclin 1-Vps34 Protein Complex Architecture and Reducing Intracellular Phosphatidylinositol-3 Phosphate Levels.” J Biol Chem. 2014 Sep 19;289(38):26021-37. doi: 10.1074/jbc.M114.561134. Epub 2014 Aug 1. PMC4176228

2013

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Smith JJ and Aitchison JD. “Peroxisomes take shape.” Nature Reviews Molecular Cell Biology, 2013 Dec;14(12):803-17. doi: 10.1038/nrm3700. PMC4060825
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
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
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
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
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
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
Ward AB, Sali A, Wilson IA. “Integrative structural biology.” Science. 2013 Feb 22;339(6122):913-5. doi: 10.1126/science.1228565. PMC3633482
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
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

2012

Aitchison JD, Rout MP. “The yeast nuclear pore complex and transport through it.” Genetics. 2012 Mar;190(3):855-83. PMC3296253
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
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
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
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
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
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
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
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
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
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
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
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
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
Obado SO, Rout MP. “Ciliary and nuclear transport: different places, similar routes?” Dev Cell. 2012 Apr 17;22(4):693-4. PMID: 22516195
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
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
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
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
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
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
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
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
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
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
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
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
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
Zhou XJ, Alber F. “Zooming in on genome organization.” Nature Methods. 2012 Oct; 9 (10), 961-963. PMC3806477

2011

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
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
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
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
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
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
Eriksson J, Fenyö D. “Modeling mass spectrometry-based protein analysis.” Methods Mol Biol. 2011;694:109-17. PMC3757507
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
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
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
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
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
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
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
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
Ratushny AV, Ramsey SA, Aitchison JD. “Mathematical modeling of biomolecular network dynamics.” Methods Mol Biol. 2011;781:415-33 PMID: 21877294
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
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
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
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
Smith JJ, Saleem RA, Aitchison JD. “Statistical analysis of dynamic transcriptional regulatory network structure.” Methods Mol Biol. 2011;781:337-52. PMID: 21877289
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
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
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
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
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

2010

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
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
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
Eriksson J, Fenyö D. “Modeling experimental design for proteomics.” Methods Mol Biol. 2010;673:223-30. PMC3745767
Fenyö D, Eriksson J, Beavis R. “Mass spectrometric protein identification using the global proteome machine.” Methods Mol Biol. 2010;673:189-202. PMC3757509
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
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
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
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
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
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
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
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
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
Saleem RA, Aitchison JD. “Systems cell biology of the mitotic spindle.” J Cell Biol, 2010 Jan 11;188(1):7-9. PMC2812858
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
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
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
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
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
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
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

2009

DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT. “Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.” Mol Cell Proteomics. 2009 Sep;8(9):2119-30. PMC2742445
Fernandez-Martinez J, Rout MP. “Nuclear pore complex biogenesis.” Curr Opin Cell Biol. 2009 Aug;21(4):603-12. Epub 2009 Jun 11. Review. PMC2749478
Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. “ModLink+: improving fold recognition by using protein-protein interactions.” Bioinformatics. 2009 Jun 15;25(12):1506-12. doi: 10.1093/bioinformatics/btp238. Epub 2009 Apr 8. PMC2687990
Förster F, Lasker K, Beck F, Nickell S, Sali A, Baumeister W. “An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.” Biochem Biophys Res Commun 388, 228-233, 2009. PMC2771176
Gradolatto A, Smart SK, Byrum S, Blair LP, Rogers RS, Kolar EA, Lavender H, Larson SK, Aitchison JD, Taverna SD, Tackett AJ. “A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.” Mol Cell Biol. 2009 Sep;29(17):4604-11. Epub 2009 Jul 6. PMC2725702
Jovanovic-Talisman T, Tetenbaum-Novatt J, McKenney AS, Zilman A, Peters R, Rout MP, Chait BT. “Artificial nanopores that mimic the transport selectivity of the nuclear pore complex.” Nature. 2009 Feb 19;457(7232):1023-7. PMC2764719
Lasker K, Topf M, Sali A, Wolfson HJ. “Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly.” J Mol Biol 2009 Apr 24;388(1):180-94. Epub 2009 Feb 20. PMC2680734
Lew DJ, Rout MP. “Cell structure and dynamics.” Curr Opin Cell Biol. 2009 Feb;21(1):1-3. PMC2676332
Lezon T, Sali A, Bahar I. “Global motions of the nuclear pore complex: Insights from Elastic Network Models.” PLoS Comp Biol 5, e1000496, 2009. PMC2725293
Low A, Prada N, Topper M, Vaida F, Castor D, Mohri H, Hazuda D, Muesing M, Markowitz M. “Natural polymorphisms of human immunodeficiency virus type 1 integrase and inherent susceptibilities to a panel of integrase inhibitors.” Antimicrob Agents Chemother, 2009 Oct;53(10):4275-82. Epub 2009 Aug 3. PMC2764199
Nickell S, Beck F, Scheres SHW, Korinek A, Forster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko J, Carazo J.-M, Mann M, Baumeister W. “Insights into the Molecular Architecture of the 26S Proteasome.” Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):11943-7. Epub 2009 Jul 6. PMC2715492
Oeffinger M, Zenklusen D, Ferguson A, Wei KE, El Hage A, Tollervey D, Chait BT, Singer RH, Rout MP. “Rrp17p is a eukaryotic exonuclease required for 5′ end processing of Pre-60S ribosomal RNA.” Mol Cell. 2009 Dec 11;36(5):768-81. PMC2806520
Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velazquez-Muriel JA, Sali A. “The structural dynamics of macromolecular processes.” Curr Opin Cell Biol 21, 97-108, 2009. PMC2774249
Selimi F, Cristea IM, Heller E, Chait BT, Heintz N. “Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse.” PLoS Biology, 2009 Apr 14;7(4):e83. PMC2672601
Shmulevich I, Aitchison JD. “Deterministic and stochastic models of genetic regulatory networks.” Methods Enzymol. 2009;467:335-56. doi: 10.1016/S0076-6879(09)67013-0. PMC2725293
Smith JJ and Aitchison JD. “Regulation of peroxisome dynamics.” Curr Opin Cell Biol. Feb;21(1):119-26. Epub 2009 Jan 31. PMC2681484
Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD. “Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes.” Mol Cell Biol, 2009 May;29(9):2346-58. Epub 2009 Mar 9. PMC2668375
Yue Z, Holstein G, Chait BT, Wang QJ. “Using genetic mouse models to study the biology and pathology of autophagy in the central nervous system.” Methods in Enzymology. 2009;453:159-80. PMID: 19216906
Zhong Y, Wang QJ, Li X, Chait BT, Heintz N, Yue Z. “Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex.” Nature Cell Biology. 2009 Apr;11(4):468-76. Epub 2009 Mar 8. PMC2664389

2008

Alber F, Förster F, Korkin D, Topf M, Sali A. “Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.” Annual Review in Biochemistry 77: 443-477. 2008a. PMID: 18318657
Alber F, Chait BT, Rout MP, Sali A. “Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints. In: Protein-protein interactions and networks: identification, characterization and prediction.” Ed: Panchenko, A. and Przytycka, T. Cambridge University Press, Cambridge, p. 99-114, Springer-Verlag, London, UK, 2008b.
Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. “Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.” Nat Struct Mol Biol 15, 746-753, 2008. PMC2546500
Chandramouli P, Topf M, Menetret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. “Structure of the mammalian 80S ribosome at 8.7 A resolution.” Structure 16, 535-548, 2008. PMC2775484
Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF. “Crystallographic conformers of actin in a biologically active bundle of filaments.” J. Mol. Biol. 375, 331-336, 2008. PMC2680129
Degrasse JA, Chait BT, Field MC, Rout MP. “High-yield isolation and subcellular proteomic characterization of nuclear and subnuclear structures from trypanosomes.” Methods Mol Biol. 2008;463:77-92. PMID: 18951162
Eramian D, Eswar N, Shen MY, Sali A. “How well can the accuracy of comparative protein structure models be predicted?” Protein Sci. 2008 Nov;17(11):1881-93. doi: 10.1110/ps.036061.108. Epub 2008 Oct 1. PMC2578807
Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A. “Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.” J. Mol. Biol. 382, 1089-1106, 2008. PMC2745287
Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ. “Saccharomyces cerevisiae Yta7 regulates histone gene expression.” Genetics 2008 May;179(1):291-304. PMC2390607
Hood L, Rowen L, Galas DJ, Aitchison JD. “Systems biology at the Institute for Systems Biology.” Brief Funct Genomic Proteomic. 2008 Jul;7(4):239-48. Epub 2008 Jun 25. PMID: 18579616
Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA. “Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.” Structure 16, 755-765, 2008. PMC2600884
Lee DJ, Busby SJ, Westblade LF, Chait BT. “Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex.” J Bacteriol. 2008 Feb;190(4):1284-9. Epub 2007 Dec 14. PMC2238195
Marelli M, Nesvizhskii AI, Aitchison JD. “Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions: an example in peroxisomes.” Methods Mol Biol. 2008;432:357-71. PMID: 18370030
Moorman NJ, Cristea IM, Terhune SS, Rout MP, Chait BT, Shenk T. “Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex.” Cell Host Microbe. 2008 Apr 17;3(4):253-62. PMC2759192
Postow L, Ghenoiu C, Woo EM, Krutchinsky AN, Chait BT, Funabiki H. “Ku80 removal from DNA through double strand break-induced ubiquitylation.” J Cell Biol. 2008 Aug 11;182(3):467-79. Epub 2008 Aug 4. PMC2500133
Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD. “Control of transcriptional variability by overlapping feed-forward regulatory motifs.” Biophys J. 2008 Oct;95(8):3715-23. Epub 2008 Jul 11. PMC2553142
Rout MP. “The peroxisome: a production in four acts.” J Cell Biol. 2008 Apr 21;181(2):185-7. PMC2315666
Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O’Donnell R, Rachubinski RA, Aitchison JD. “Genome-wide analysis of signaling
networks regulating fatty acid-induced gene expression and organelle biogenesis.” J Cell Biol. 2008 Apr 21;181(2):281-92. PMC2315675
Savalia D, Westblade LF, Goel M, Florens L, Kemp P, Akulenko N, Pavlova O, Padovan JC, Chait BT, Washburn MP, Ackermann HW, Mushegian A, Gabisonia T, Molineux I, Severinov K. “Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage.” J Mol Biol. 2008 Mar 28;377(3):774-89. Epub 2008 Jan 11. PMC2587145
Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. “Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.” Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9610-5. Epub 2008 Jul 10. PMC2474495
Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. “Protein structure fitting and refinement guided by cryo-EM density.” Structure 16, 295-307, 2008. PMC2409374
Westblade LF, Minakhin L, Kuznedelov K, Tackett AJ, Chang EJ, Mooney RA, Vvedenskaya I, Wang QJ, Fenyö D, Rout MP, Landick R, Chait BT, Severinov K, Darst SA. “Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions.” J Proteome Res. 2008 Mar;7(3):1244-50. Epub 2008 Feb 14. PMC2612130
Woo EM, Fenyo D, Kwok BH, Funabiki H, Chait BT. “Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting.” Anal Chem. 2008 Apr 1;80(7):2419-25. Epub 2008 Mar 6. PMID: 18321079
Yue Z, Wang QJ, Komatsu M. “Neuronal autophagy: going the distance to the axon.” 2008 January 1; 4(1): 94–96. PMC2675167

2007

Aitchison JD, Wozniak RW. “Cell biology: pore puzzle.” Nature. 2007 Nov 29;450(7170):621-2. PMID: 18046388
Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP. “The molecular architecture of the nuclear pore complex.” Nature 450 (2007) 695-701. PMID: 18046406
Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A. “Determining the architectures of macromolecular assemblies.” Nature 450 (2007) 683-694. PMID: 18046405
Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. “Characterization of protein hubs by inferring interacting motifs from protein interactions.” PLoS Comput Biol. 2007 Sep;3(9):1761-71. Epub 2007 Jul 30. PMC1976338
Berthoux L, Sebastian S, Muesing MA, Luban J (2007). “The role of lysine 186 in HIV-1 integrase multimerization.” Virology Mar 28; [Epub ahead of print]. PMC2149894
Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. “Host pathogen protein interactions predicted by comparative modeling.” Protein Sci. 2007 Dec;16(12):2585-96. Epub 2007 Oct 26. PMC2222825
Komatsu M, Wang QJ, Holstein GR, Friedrich VL, Iwata Jr., J, Kominami E, Chait BT, Tanaka K, Yue Z. “Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration.” Proc Natl Acad Sci, 104 (2007) 14489-14494. PMC1964831
Lloyd AG, Ng YS, Muesing MA, Simon V and Mulder LC. “Characterization of HIV-1 integrase N-terminal mutant viruses.” Virology, 2007 Mar 30;360(1):129-35. Epub 2006 Nov 14. PMC2094525
Oeffinger M, Fatica A, Rout MP, Tollervey D. “Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis.” Nucleic Acids Res. 2007;35(4):1354-66. Epub 2007 Feb 1. PMC1849896
Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP. “Comprehensive analysis of diverse ribonucleoprotein complexes.” Nat Methods. 2007 Nov;4(11):951-6. Epub 2007 Oct 7. PMID: 17922018
Robinson CV, Sali A, Baumeister“Molecular sociology of the cell.” Nature 450, 973-982, 2007. PMID: 18075576
Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD. “Transcriptional responses to fatty acid are coordinated by combinatorial control.” Mol Syst Biol. 2007;3:115. Epub 2007 Jun 5. PMC1911199
Taverna SD, Ueberheide BM, Liu Y, Tackett AJ, Diaz RL, Shabanowitz J, Chait BT, Hunt DF, Allis CD. “Long-distance combinatorial linkage between methylation and acetylation on histone H3N termini.” Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2086-91. Epub 2007 Feb 6. PMC1892956
Topper MB, Luo Y, Zhadina M, Mohammed K, Smith L and Muesing MA. “Post-translational acetylation of the carboxyl-terminal domain of integrase is dispensible for viral replication.” J Virol, 2007 Mar;81(6):3012-7. Epub 2006 Dec 20. PMC1865993
Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, Woolford JL Jr. “Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes.” Genes Dev. 2007 Oct 15;21(20):2580-92. PMC2000323
Zilman A., Di Talia S, Chait BT, Rout MP, Magnasco MO. “Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport.” PLoS Comput Biol. 2007 Jul;3(7):e125. PMC1914370

2006

Chait BT. “Mass spectrometry: bottom-up or top-down?” Science. 2006 Oct 6;314(5796):65-6. PMID: 17023639
Cristea IM, Carroll JW, Rout MP, Rice CM, Chait BT, MacDonald MR. “Tracking and elucidating alphavirus-host protein interactions.” J Biol Chem. 2006 Oct 6;281(40):30269-78. PMID: 16895903
Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan M. “Protein complex compositions predicted by structural similarity.” Nucleic Acids Research 31;34(10), 2943-52, 2006. PMC1474056
Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A. “Simple fold composition and modular architecture of the nuclear pore complex.” Proc Natl Acad Sci U S A. 2006 Feb 14; 103(7): 2172-7. PMC1413685
Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP. “Protease accessibility laddering: a proteomic tool for probing protein structure.” Structure. 2006 Apr;14 (4):653-60. PMID: 16615907
Guermah M, Palhan VB, Tackett AJ, Chait BT, Roeder RG. “Synergistic functions of SII and p300 in productive activator-dependent transcription of chromatin templates.” Cell. 2006 Apr 21;125(2):275-86. PMID: 16630816
Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. “Structural modeling of protein interactions by analogy: application to PSD-95.” PLoS Comput Biol. 2006 Nov 10;2(11):e153. Epub 2006 Oct 4. PMC1635541
Lloyd AG, Tateishi S, Bieniasz PD, Muesing MA, Yamaizumi M and Mulder LC. “Effect of DNA repair protein Rad18 on viral infection.” PLoS Pathog. 2006 May;2(5):e40. Epub 2006 May 19. PMC1463017
Low A and Muesing MA. “Understanding and inhibiting integrase in the treatment of HIV disease.” PRN Notebook 11: 6-11, Nov. 2006.
McBride KM, Gazumyan A, Woo EM, Barreto VM, Robbiani DF, Chait BT, Nussenzweig MC. “Regulation of hypermutation by activation-induced cytidine deaminase phosphorylation.” Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8798-803. Epub 2006 May 24. PMC1482658
Saleem RA, Smith JJ, Aitchison JD. “Proteomics of the peroxisome.” Biochim Biophys Acta. 2006 Dec;1763(12):1541-51. Epub 2006 Sep 12. PMC1858641
Shen MY, Sali A. “Statistical potential for assessment and prediction of protein structures.” Protein Sci. 2006 Nov;15(11):2507-24. PMC2242414
Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD. “Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism.” Mol Syst Biol. 2006;2:2006.0009. Epub 2006 Feb 21. PMC1681483
Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. “Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs.” Mol Cell. 2006 Dec 8;24(5):785-96. PMID: 17157260
Wang QJ, Ding Y, Kohtz DS, Mizushima N, Cristea IM, Rout MP, Chait BT, Zhong Y, Heintz N, Yue Z. “Induction of autophagy in axonal dystrophy and degeneration.” J Neurosci. 2006 Aug 2;26(31):8057-68. PMID: 16885219