PUBLICATIONS2018-10-23T17:27:39+00:00
If you are unable to access a full-text copy of any of the following publications, please contact us and we will forward you a copy.

In press:

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling M, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Le Novère N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. (in press)

Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. “SemGen: a tool for semantics-based annotation and composition of biosimulation models.” Bioinformatics (accepted).

  1. Jishage M, Yu X, Shi Y, Ganesan SJ, Chen WY, Sali A, Chait BT, Asturias FJ, Roeder RG “Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1” Nat Struct Mol Biol. 2018 Sep;25(9):859-867. doi: 10.1038/s41594-018-0118-5. Epub 2018 Sep 6. PMID: 30190596
  2. Zinoviev A, Goyal A, Jindal S, LaCava J, Komar AA, Rodnina MV, Hellen CUT, Pestova TV. “Functions of unconventional mammalian translational GTPases GTPBP1 and GTPBP2.” Genes Dev. 2018 Sep 1;32(17-18):1226-1241. doi: 10.1101/gad.314724.118. Epub 2018 Aug 14. PMC6120710
  3. Schrank BR, Aparicio T, Li Y, Chang W, Chait BT, Gundersen GG, Gottesman ME, Gautier J. “Nuclear ARP2/3 drives DNA break clustering for homology-directed repair” Nature. 2018 Jul;559(7712):61-66. doi: 10.1038/s41586-018-0237-5. Epub 2018 Jun 20. PMID: 29925947
  4. Vallat B, Webb B, Westbrook JD, Sali A, Berman HM. “Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.” Structure. 2018 Jun 5;26(6):894-904.e2. doi: 10.1016/j.str.2018.03.011. Epub 2018 Apr 12. PMID: 29657133
  5. Mast FD, Herricks T, Strehler KM, Miller LR, Saleem RA, Rachubinski RA, Aitchison JD. “ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum.” J Cell Biol. 2018 Jun 4;217(6):2087-2102. doi: 10.1083/jcb.201706044. Epub 2018 Mar 27. PMID: 29588378 https://www.ncbi.nlm.nih.gov/pubmed/29588378
  6. Duffy FJ, Thompson E, Downing K, Suliman S, Mayanja-Kizza H, Boom WH, Thiel B, Weiner III J, Kaufmann SHE, Dover D, Tabb DL, Dockrell HM, Ottenhoff THM, Tromp G, Scriba TJ, Zak DE, Walzland G and the GC6-74 Consortium. “A Serum Circulating miRNA Signature for Short-Term Risk of Progression to Active Tuberculosis Among Household Contacts”. Front Immunol. 2018 Apr 13;9:661. doi: 10.3389/fimmu.2018.00661. eCollection 2018. PMID: 29706954
  7. Hayama R, Sparks S, Hecht LM, Dutta K, Cabana CM, Karp JM, Rout MP, Cowburn D. “Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex.” J Biol Chem. 2018 2018 Mar 23;293(12):4555-4563. doi: 10.1074/jbc.AC117.001649. Epub 2018 Jan 26. PMC5868264
  8. Singla J, McClary KM, White KL, Alber F, Sali A, Stevens RC. “Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.” Cell. 2018 Mar 22;173(1):11-19. doi: 10.1016/j.cell.2018.03.014. Review. PMID: 29570991
  9. Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. “Integrative structure and functional anatomy of a nuclear pore complex.” Nature. 2018 Mar 14. doi: 10.1038/nature26003. [Epub ahead of print] PMID: 29539637
  10. Guy AJ, Irani V, Beeson JG, Webb B, Sali A, Richards JS, Ramsland PA. “Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures.” Sci Rep. 2018 Mar 12;8(1):4355. doi: 10.1038/s41598-018-22592-3. PMID: 29531293
  11. Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S. “Modular assembly of the nucleolar pre-60S ribosomal subunit.” Nature. 2018 Mar 5. doi: 10.1038/nature26156. [Epub ahead of print] PMID: 29512650
  12. Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Bart JM, Navarro M, Chait BT, Aitchison JD, Rout MP, Field MC. “Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes.” Mol Biol Cell. 2018 Mar 1. pii: mbc.E17-06-0430. doi: 10.1091/mbc.E17-06-0430. [Epub ahead of print] PMC5921576
  13. Sparks S, Temel DB, Rout MP, Cowburn D. “Deciphering the “Fuzzy” Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering.” Structure. 2018 Jan 29. pii: S0969-2126(18)30010-8. doi: 10.1016/j.str.2018.01.010. [Epub ahead of print] PMID: 29429880
  14. Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O’Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. “Prediction of enzymatic pathways by integrative pathway mapping.” Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/eLife.31097. PMID: 29377793
  15. Kleiner RE, Hang LE, Molloy KR, Chait BT, Kapoor TM. “A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells.” Cell Chem Biol. 2018 Jan 18;25(1):110-120.e3. doi: 10.1016/j.chembiol.2017.10.001. Epub 2017 Nov 5. PMCID: PMC5775914
  16. Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J. “Dissection of affinity captured LINE-1 macromolecular complexes.” Elife. 2018 Jan 8;7. pii: e30094. doi: 10.7554/eLife.30094. [Epub ahead of print] PMC5821459
  17. Winczura K, Schmid M, Iasillo C, Molloy KR, Harder LM, Andersen JS, LaCava J, Jensen TH. “Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions.” Cell Rep. 2018 Jan 2;22(1):44-58. doi: 10.1016/j.celrep.2017.12.037. PMC5770337
  1. Viswanath S, Chemmama IE, Cimermancic P, Sali A. Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.Biophys J. 2017 Dec 5;113(11):2344-2353. doi: 10.1016/j.bpj.2017.10.005. PubMedPMID: 29211988; PubMed Central PMCID: PMC5768525.
  2. Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A. The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria. Front Microbiol. 2017 Nov 16;8:2183. doi: 10.3389/fmicb.2017.02183. eCollection 2017. Review. PubMed PMID: 29201016; PubMed Central PMCID: PMC5696578.
  3. Ma Y, Silveri L, LaCava J, Dokudovskaya S. Tumor suppressor NPRL2 induces ROS production and DNA damage response. Sci Rep. 2017 Nov 10;7(1):15311. doi:10.1038/s41598-017-15497-0. PubMed PMID: 29127423; PubMed Central PMCID: PMC5681675.
  4. Kleiner RE, Hang LE, Molloy KR, Chait BT, Kapoor TM. A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells. Cell Chem Biol. 2018 Jan 18;25(1):110-120.e3. doi: 10.1016/j.chembiol.2017.10.001. Epub 2017 Nov 5. PubMed PMID: 29104064; PubMed Central PMCID: PMC5775914.
  5. Santanach A, Blanco E, Jiang H, Molloy KR, Sansó M, LaCava J, Morey L, DiCroce L. The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity. Nat Commun. 2017 Nov 1;8(1):1235. doi: 10.1038/s41467-017-01464-w. PubMed PMID: 29089522; PubMed Central PMCID: PMC5663739.
  6. Kessler A, Dankwa S, Bernabeu M, Harawa V, Danziger SA, Duffy F, Kampondeni SD, Potchen MJ, Dambrauskas N, Vigdorovich V, Oliver BG, Hochman SE, Mowrey WB, MacCormick IJC, Mandala WL, Rogerson SJ, Sather DN, Aitchison JD, Taylor TE, Seydel KB, Smith JD, Kim K. Linking EPCR-Binding PfEMP1 to Brain Swelling in Pediatric Cerebral Malaria. Cell Host Microbe. 2017 Nov 8;22(5):601-614.e5. doi: 10.1016/j.chom.2017.09.009. Epub 2017 Oct 26. PubMed PMID: 29107642; PubMed Central PMCID: PMC5783720.
  7. Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the Integrative Modeling Platform. Protein Sci. 2018 Jan;27(1):245-258. doi: 10.1002/pro.3311. Epub 2017 Oct 10. PubMed PMID: 28960548; PubMed Central PMCID: PMC5734277.
  8. Wang X, Chemmama IE, Yu C, Huszagh A, Xu Y, Viner R, Block SA, Cimermancic P, Rychnovsky SD, Ye Y, Sali A, Huang L. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J Biol Chem. 2017 Sep 29;292(39):16310-16320. doi: 10.1074/jbc.M117.803619. Epub 2017 Aug 15. PubMed PMID: 28821611; PubMed Central PMCID: PMC5625060.
  9. Domanski M, LaCava J. Affinity Purification of the RNA Degradation Complex, the Exosome, from HEK-293 Cells. Bio Protoc. 2017 Apr 20;7(8). pii: e2238. doi: 10.21769/BioProtoc.2238. PubMed PMID: 28691041; PubMed Central PMCID: PMC5499702.
  10. Domanski M, LaCava J. RNA Degradation Assay Using RNA Exosome Complexes,Affinity-purified from HEK-293 Cells. Bio Protoc. 2017 Apr 20;7(8). pii: e2239. doi: 10.21769/BioProtoc.2239. PubMed PMID: 28670604; PubMed Central PMCID: PMC5493206.
  11. Stecula A, Schlessinger A, Giacomini KM, Sali A. Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer. Biochemistry. 2017 Jul 11;56(27):3475-3483. doi:10.1021/acs.biochem.7b00339.Epub 2017 Jun 29. PubMed PMID: 28661652.
  12. Hayama R, Rout MP, Fernandez-Martinez J. The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. Curr Opin Cell Biol. 2017 Jun;46:110-118. doi: 10.1016/j.ceb.2017.05.003. Epub 2017 Jun 15. Review. PubMed PMID: 28624666; PubMed Central PMCID: PMC5568245.
  13. Obado SO, Field MC, Rout MP. Comparative interactomics provides evidence for functional specialization of the nuclear pore complex. Nucleus. 2017 Jul 4;8(4):340-352. doi: 10.1080/19491034.2017.1313936. Epub 2017 May 2. PubMed PMID: 28463551; PubMed Central PMCID: PMC5597298.
  14. Herricks T, Mast FD, Li S, Aitchison JD. ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth. J Vis Exp. 2017 Jul 3;(125). doi:10.3791/55879. PubMed PMID: 28715382; PubMed Central PMCID: PMC5608540.
  15. Hayama R, Rout MP, Fernandez-Martinez J. The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. Curr Opin Cell Biol. 2017 Jun;46:110-118. doi: 10.1016/j.ceb.2017.05.003. Epub 2017 Jun 15. Review. PubMed PMID: 28624666; PubMed Central PMCID: PMC5568245.
  16. Chen Q, Vieth M, Timm DE, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Zeng W, Lu J, Liu L. Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages. PLoS One. 2017 Apr 13;12(4):e0175758. doi: 10.1371/journal.pone.0175758. eCollection 2017. PubMed PMID: 28406969; PubMed Central PMCID: PMC5391116.
  17. Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex. Elife. 2017 Mar 20;6. pii: e25478. doi: 10.7554/eLife.25478. PubMed PMID: 28318486; PubMed Central PMCID: PMC5386594.
  18. Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics. 2017 May;16(5):840-854. doi: 10.1074/mcp.M116.065326. Epub 2017 Mar 14. PubMed PMID: 28292943; PubMed Central PMCID: PMC5417825.
  19. Rout MP, Obado SO, Schenkman S, Field MC. Specialising the parasite nucleus: Pores, lamins, chromatin, and diversity. PLoS Pathog. 2017 Mar 2;13(3):e1006170. doi: 10.1371/journal.ppat.1006170. eCollection 2017 Mar. Review. PubMed PMID: 28253370; PubMed Central PMCID: PMC5333908.
  20. Manna PT, Obado SO, Boehm C, Gadelha C, Sali A, Chait BT, Rout MP, Field MC. Lineage-specific proteins essential for endocytosis in trypanosomes. J Cell Sci. 2017 Apr 15;130(8):1379-1392. doi: 10.1242/jcs.191478. Epub 2017 Feb 23. PubMed PMID: 28232524; PubMed Central PMCID: PMC5399782.
  21. Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure. 2017 Mar 7;25(3):434-445. doi: 10.1016/j.str.2017.01.006. Epub 2017 Feb 2. PubMed PMID: 28162953; PubMed Central PMCID: PMC5342941.
  22. Boehm CM, Obado S, Gadelha C, Kaupisch A, Manna PT, Gould GW, Munson M, Chait BT, Rout MP, Field MC. The Trypanosome Exocyst: A Conserved Structure Revealing a New Role in Endocytosis. PLoS Pathog. 2017 Jan 23;13(1):e1006063. doi: 10.1371/journal.ppat.1006063. eCollection 2017 Jan. PubMed PMID: 28114397; PubMed Central PMCID: PMC5256885.
  23. Herricks T, Dilworth DJ, Mast FD, Li S, Smith JJ, Ratushny AV, Aitchison JD. One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY! G3 (Bethesda). 2017 Jan 5;7(1):279-288. doi: 10.1534/g3.116.037044. PubMed PMID: 27856698; PubMed Central PMCID: PMC5217116.
  1. Bernabeu M, Danziger SA, Avril M, Vaz M, Babar PH, Brazier AJ, Herricks T, Maki JN, Pereira L, Mascarenhas A, Gomes E, Chery L, Aitchison JD, Rathod PK, Smith JD. “Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass.” Proc Natl Acad Sci U S A. 2016 May 16. pii: 201524294. [Epub ahead of print] PMC4988613
  1. Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. “Revealing Higher Order Protein Structure Using Mass Spectrometry.” J Am Soc Mass Spectrom. 2016 Apr 14. [Epub ahead of print] PMID: 27080007
  1. Domanski M, Upla P, Rice WJ, Molloy KR, Ketaren NE, Stokes DL, Jensen TH, Rout MP, LaCava J. “Purification and analysis of endogenous human RNA exosome complexes.” RNA. 2016 Sep;22(9):1467-75. doi: 10.1261/rna.057760.116. Epub 2016 Jul 11. PMC4986900
  1. Fernandez-Martinez J, LaCava J, Rout MP. “Density Gradient Ultracentrifugation to Isolate Endogenous Protein Complexes after Affinity Capture.” Cold Spring Harb Protoc. 2016 Jul 1;2016(7):pdb.prot087957. doi: 10.1101/pdb.prot087957. PMID: 27371598
  1. Hunziker M, Barandun J, Petfalski E, Tan D, Delan-Forino C, Molloy KR, Kim KH, Dunn-Davies H, Shi Y, Chaker-Margot M, Chait BT, Walz T, Tollervey D, Klinge S. “UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly.” Nat Commun. 2016 Jun 29;7:12090. doi: 10.1038/ncomms12090. PMC4931317
  1. LaCava J, Fernandez-Martinez J, Hakhverdyan Z, Rout MP. “Protein Complex Purification by Affinity Capture.” Cold Spring Harb Protoc. 2016 Jul 1;2016(7):pdb.top077545. doi: 10.1101/pdb.top077545. PMID: 27371601
  1. LaCava J, Fernandez-Martinez J, Rout MP. “Native Elution of Yeast Protein Complexes Obtained by Affinity Capture.” Cold Spring Harb Protoc. 2016 Jul 1;2016(7):pdb.prot087940. doi: 10.1101/pdb.prot087940. PMID: 27371597
  1. LaCava J, Fernandez-Martinez J, Hakhverdyan Z, Rout MP. “Optimized Affinity Capture of Yeast Protein Complexes.” Cold Spring Harb Protoc. 2016 Jul 1;2016(7):pdb.prot087932. doi: 10.1101/pdb.prot087932. PMID: 27371596
  1. Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA. “HIV-host interactome revealed directly from infected cells.” Nat Microbiol. 2016 Jul;1(7). pii: 16068. Epub 2016 May 23. PMC4928716
  1. Lussignol M, Kopp M, Molloy K, Vizcay G, Fleck RA, Dorner M, Bell KL, Chait BT, Rice CM and Catanese MT. “Proteomics of HCV virions reveals an essential role for Nup98 in virus morphogenesis.” Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2484-9. doi: 10.1073/pnas.1518934113. Epub 2016 Feb 16. PMC4780614
  1. Maishman L, Obado SO, Alsford S, Bart JM, Chen WM, Ratushny AV, Navarro M, Horn D, Aitchison JD, Chait BT, Rout MP, Field MC. “Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression.” Nucleic Acids Res. 2016 Sep 12. pii: gkw751. [Epub ahead of print] PMID: 27625397
  1. Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD. “Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum.” J Biol Chem. 2016 Jul 22;291(30):15408-27. doi: 10.1074/jbc.M116.728154. Epub 2016 Apr 29. PMC4957030
  1. Obado SO, Rout MP. “Cilia and Nuclear Pore Proteins: Pore No More?” Dev Cell. 2016 Sep 12;38(5):445-6. doi: 10.1016/j.devcel.2016.08.019. PMID: 27623377
  1. Obado SO, Field MC, Chait BT, Rout MP. “High-Efficiency Isolation of Nuclear Envelope Protein Complexes from Trypanosomes.” Methods Mol Biol. 2016;1411:67-80. doi: 10.1007/978-1-4939-3530-7_3. PMID: 27147034
  1. Obado SO, Brillantes M, Uryu K, Zhang W, Ketaren NE, Chait BT, Field MC, Rout MP. “Interactome mapping reveals the evolutionary history of the nuclear pore complex.” PLoS Biol. 2016 Feb 18;14(2):e1002365. doi: 10.1371/journal.pbio.1002365. eCollection 2016 Feb. PMC4758718
  1. Olinares PD, Dunn AD, Padovan JC, Fernandez-Martinez J, Rout MP, Chait BT. “A robust workflow for native mass spectrometric analysis of affinity-isolated endogenous protein assemblies.” Anal Chem. 2016 Feb 5. [Epub ahead of print] PMC4790104
  1. Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. “Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex.” Proc Natl Acad Sci U S A. 2016 Apr 18. pii: 201522663. [Epub ahead of print] PMC4983827
  1. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. “FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.” Nucleic Acids Res. 2016 Jul 8;44(W1):W424-9. doi: 10.1093/nar/gkw389. Epub 2016 May 5. PMC4987932
  1. Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP, Boeke JD. “Characterization of L1-Ribonucleoprotein Particles.” Methods Mol Biol. 2016;1400:311-38. doi: 10.1007/978-1-4939-3372-3_20. PMID: 26895062
  1. Thompson MK, Fridy PC, Keegan S, Chait BT, Fenyö D, Rout MP. “Optimizing selection of large animals for antibody production by screening immune response to standard vaccines.” J Immunol Methods. 2016 Jan 9. pii: S0022-1759(16)30005-9. doi: 10.1016/j.jim.2016.01.006. [Epub ahead of print] PMC4769958
  1. Aitchison JD, Rout MP. “The interactome challenge.” J Cell Biol. 2015 Nov 23;211(4):729-32. doi: 10.1083/jcb.201510108. Epub 2015 Nov 16. PMC4657177
  2. Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. “Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.” Biophys J. 2015 Aug 18;109(4):793-805. doi: 10.1016/j.bpj.2015.06.065. PMC4547163
  3. Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS. “Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.” BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15. PMC4407105
  4. Dokudovskaya S, Rout MP. “SEA you later alli-GATOR – a dynamic regulator of the TORC1 stress response pathway.” J Cell Sci. 2015 Jun 15;128(12):2219-2228. Epub 2015 May 1. Review. PMC4487016
  5. Fridy PC, Thompson MK, Ketaren NE, Rout MP. “Engineered high-affinity nanobodies recognizing staphylococcal Protein A and suitable for native isolation of protein complexes.” Anal Biochem. 2015 May 15;477:92-4. doi: 10.1016/j.ab.2015.02.013. Epub 2015 Feb 21. PMC4487016
  6. Hakhverdyan Z, Domanski M. Hough L, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy K, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP and LaCava J. “Rapid, Optimized Interactomic Screening.” Nat Methods. 2015 Jun;12(6):553-60. doi: 10.1038/nmeth.3395 PMC4449307
  7. Heider MR, Gu M, Duffy CM, Mirza AM, Marcotte LL, Walls AC, Farrall N, Hakhverdyan Z, Field MC, Rout MP, Frost A, Munson M. “Subunit connectivity, assembly determinants and architecture of the yeast exocyst complex.” Nat Struct Mol Biol. 2016 Jan;23(1):59-66. doi: 10.1038/nsmb.3146. Epub 2015 Dec 14. PMC4752824
  8. 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
  9. Hubin EA, Tabib-Salazar A, Humphrey LJ, Flack JE, Olinares PD, Darst SA, Campbell EA, Paget MS. “Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA.” Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7171-6. doi: 10.1073/pnas.1504942112. Epub 2015 May 26. PMC4466734
  10. Kleiner RE, Verma P, Molloy KR, Chait BT, Kapoor TM. “Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response.” Nat Chem Biol. 2015 Sep 7. doi: 10.1038/nchembio.1908. [Epub ahead of print] PMC4589150
  11. 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
  12. 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
  13. 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
  14. 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
  15. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. “Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.” Mol Cell. 2015 Sep 3;59(5):794-806. doi: 10.1016/j.molcel.2015.07.016. PMC4560838
  16. Morris DH, Yip CK, Shi Y, Chait BT, Wang QJ. “Beclin 1-VPS34 Complex Architecture: Understanding the Nuts and Bolts of Therapeutic Targets.” Front Biol (Beijing). 2015 Oct;10(5):398-426. Epub 2015 Nov 4. PMC4682202
  17. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. “Molecular architecture of the yeast Mediator complex.” Elife. 2015 Sep 24;4. pii: e08719. doi: 10.7554/eLife.08719. PMC4631838
  18. 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
  19. Sun J, Shi Y, Georgescu RE, Yuan Z, Chait BT, Li H, O’Donnell ME. “The architecture of a eukaryotic replisome.” Nat Struct Mol Biol. 2015 Dec;22(12):976-82. doi: 10.1038/nsmb.3113. Epub 2015 Nov 2. PMID: 26524492
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. Mast FD, Ratushny AV, Aitchison JD. “Systems cell biology.” J Cell Biol. 2014 Sep 15;206(6):695-706. Review. PMC4164942
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  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
  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
  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
  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
  2. 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
  3. 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
  4. Eriksson J, Fenyö D. “Modeling experimental design for proteomics.” Methods Mol Biol. 2010;673:223-30. PMC3745767
  5. Fenyö D, Eriksson J, Beavis R. “Mass spectrometric protein identification using the global proteome machine.” Methods Mol Biol. 2010;673:189-202. PMC3757509
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Saleem RA, Aitchison JD. “Systems cell biology of the mitotic spindle.” J Cell Biol, 2010 Jan 11;188(1):7-9.  PMC2812858
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. Lew DJ, Rout MP. “Cell structure and dynamics.” Curr Opin Cell Biol. 2009 Feb;21(1):1-3. PMC2676332
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. Smith JJ and Aitchison JD. “Regulation of peroxisome dynamics.” Curr Opin Cell Biol.  Feb;21(1):119-26. Epub 2009 Jan 31. PMC2681484
  17. 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
  18. 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
  19. 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
  1. 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
  2. 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.
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. Rout MP. “The peroxisome: a production in four acts.” J Cell Biol. 2008 Apr 21;181(2):185-7. PMC2315666
  18. 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
  19. networks regulating fatty acid-induced gene expression and organelle biogenesis.” J Cell Biol. 2008 Apr 21;181(2):281-92. PMC2315675
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. Yue Z, Wang QJ, Komatsu M. “Neuronal autophagy: going the distance to the axon.” 2008 January 1; 4(1): 94–96. PMC2675167
  1. Aitchison JD, Wozniak RW. “Cell biology: pore puzzle.” Nature. 2007 Nov 29;450(7170):621-2. PMID: 18046388
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Robinson CV, Sali A, Baumeister“Molecular sociology of the cell.” Nature 450, 973-982, 2007. PMID: 18075576
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  1. Chait BT. “Mass spectrometry: bottom-up or top-down?” Science. 2006 Oct 6;314(5796):65-6. PMID: 17023639
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. Low A and Muesing MA. “Understanding and inhibiting integrase in the treatment of HIV disease.” PRN Notebook 11: 6-11, Nov. 2006.
  10. 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
  11. Saleem RASmith JJAitchison JD. “Proteomics of the peroxisome.” Biochim Biophys Acta. 2006 Dec;1763(12):1541-51. Epub 2006 Sep 12. PMC1858641
  12. Shen MY, Sali A. “Statistical potential for assessment and prediction of protein structures.” Protein Sci. 2006 Nov;15(11):2507-24. PMC2242414
  13. 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
  14. 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
  15. 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