Listed on this page are publications with contributing work from the NCDIR acknowledging Grant ID: P41 GM109824. Please acknowledge/cite grant ID if using content pertaining to grant.

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For the full list of publications prior to the commencement of the P41-funded NCDIR, please click here.

For a list of of all NCDIR presentations since 2019, please click here.

  1. Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. “Structures, functions, and adaptations of the human LINE-1 ORF2 protein.” Nature. 2024 Feb;626(7997):194-206.doi: 10.1038/s41586-023-06947-z.  Epub 2023 Dec 14. PMC10630966
  2. Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. “Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus.” bioRxiv [Preprint]. 2024 Jan 29:2023.07.14.549041. doi:10.1101/2023.07.14.549041. PMC10369967.
  3. Li W, Li A, Yu B, Zhang X, Liu X, White KL, Stevens RC, Baumeister W, Sali A, Jasnin M, Sun L. “In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography.” Nat Commun. 2024 Feb 12;15(1):1311. doi: 10.1038/s41467-024-45648-7. PMC10861521
  4. Neal ML, Choudhry SK, Aitchison JD. “Deleteome-Tools: Utilizing a compendium of yeast deletion strain transcriptomes to identify co-functional genes.” bioRxiv [Preprint]. 2024 Feb 8:2024.02.05.578946. doi: 10.1101/2024.02.05.578946. PMC10871253
  5. Olivier JF, Langlais D, Jeyakumar T, Polyak MJ, Galarneau L, Cayrol R, Jiang H, Molloy KR, Xu G, Suzuki H, LaCava J, Gros P, Fodil N. “CCDC88B interacts with RASAL3 and ARHGEF2 and regulates dendritic cell function in neuroinflammation and colitis.” Commun Biol. 2024 Jan 10;7(1):77. doi: 10.1038/s42003-023-05751-9. PMC10781698
  6. Ramsey JR, Shelton PMM, Heiss TK, Olinares PDB, Vostal LE, Soileau H, Grasso M, Casebeer SW, Adaniya S, Miller M, Sun S, Huggins DJ, Myers RW, Chait BT, Vinogradova EV, Kapoor TM. “Using a Function-First “Scout Fragment”-Based Approach to Develop Allosteric Covalent Inhibitors of Conformationally Dynamic Helicase Mechanoenzymes.” J Am Chem Soc. 2024 Jan 10;146(1):62-67. doi: 10.1021/jacs.3c10581. Epub 2023 Dec 22. PMID: 38134034
  7. Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. “Integrative spatiotemporal map of nucleocytoplasmic transport.” bioRxiv. 2024 Jan 2:2023.12.31.573409. doi: 10.1101/2023.12.31.573409. Preprint. PMC10802240
  1. Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell. 2023 Sep 21;83(18):3283-3302.e5. doi: 10.1016/j.molcel.2023.08.025. PMC10630966
  2. Berman AY, Wieczorek M, Aher A, Olinares PDB, Chait BT, Kapoor TM. “A nucleotide binding-independent role for γ-tubulin in microtubule capping and cell division.” J Cell Biol. 2023 Mar 6;222(3):e202204102. doi: 10.1083/jcb.202204102. Epub 2023 Jan 25. PMC9930161
  3. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. “RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.” Nucleic Acids Res. 2023 Jan 6;51(D1):D488-D508. doi: 10.1093/nar/gkac1077. PMC9825554
  4. Choudhry SK, Neal ML, Li S, Navare AT, Van Eeuwen T, Wozniak RW, Mast FD, Rout MP, Aitchison JD. “Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chromatin.” J Cell Biol. 2023 Sep 4;222(9):e202207060. doi: 10.1083/jcb.202207060. Epub 2023 Jun 26. PMC10292210
  5. Chua GNL, Watters JW, Olinares PDB, Luo JA, Chait BT, Liu S. “Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes.” bioRxiv. 2023 Jun 5:2023.06.02.543478. doi: 10.1101/2023.06.02.543478. Preprint. PMC10274721 
  1. Cowburn D, Rout MP. “Improving the Hole Picture: Towards a Consensus on the Mechanism of Nuclear Transport.” Biochem Soc Trans. 2023 Apr 26;51(2):871-886. doi: 10.1042/BST20220494. PMC10212546
  2. Cross FR, Fridy P, Ketaren N, Mast F, Li S, Olivier P, Pecani K, Chait BT, Aitchison JD, Rout MP. “Expanding and Improving Nanobody Repertoires Using a Yeast Display Method: Targeting SARS-CoV-2”. J Biol Chem. 2023 Jan 28;102954.doi: 10.1016/j.jbc.2023.102954.  Epub 2023 Jan 28. PMC9884143
  3. Di Stefano LH, Saba LJ, Oghbaie M, Jiang H, McKerrow W, Benitez-Guijarro M, Taylor MS, LaCava J. “Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules.” Methods Mol Biol. 2023;2607:215-256. doi: 10.1007/978-1-0716-2883-6_12. PMID: 36449166
  4. Echeverria I, Braberg H, Krogan NJ, Sali A. “Integrative structure determination of histones H3 and H4 using genetic interactions.” FEBS J. 2023 May;290(10):2565-2575. doi: 10.1111/febs.16435. Epub 2022 Apr 3. PMC9481981
  5. Gkeka A, Aresta-Branco F, Triller G, Vlachou EP, van Straaten M, Lilic M, Olinares PDB, Perez K, Chait BT, Blatnik R, Ruppert T, Verdi JP, Stebbins CE, Papavasiliou FN. “Immunodominant surface epitopes power immune evasion in the African trypanosome.” Cell Rep. 2023 Mar 28;42(3):112262. doi: 10.1016/j.celrep.2023.112262. Epub 2023 Mar 20. PMID: 36943866
  6. Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. “Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.” Nat Struct Mol Biol. 2023 Mar;30(3):296-308. doi: 10.1038/s41594-022-00918-0. Epub 2023 Feb 13. PMC10312659
  7. Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. “Dynamic molecular mechanism of the nuclear pore complex permeability barrier.” bioRxiv. 2023 Apr 14:2023.03.31.535055. doi: 10.1101/2023.03.31.535055. Preprint. PMC10103940
  8. Kumar S, Neal ML, Li S, Navare AT, Van Eeuwen T, Wozniak RW, Mast FD, Rout MP, Aitchison JD. “Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chromatin.” J Cell Biol. 2023 Sep 4;222(9):e202207060. doi: 10.1083/jcb.202207060. Epub 2023 Jun 26. PMC10292210
  9. Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. “Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.” bioRxiv. 2023 Oct 29:2023.10.28.564055. doi: 10.1101/2023.10.28.564055. Preprint. PMC10634877
  10. Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Götte M, Chait BT, Campbell EA, Darst SA. “Structural basis for substrate selection by the SARS-CoV-2 replicase.” Nature. 2023 Feb 1:1-7. doi: 10.1038/s41586-022-05664-3. Online ahead of print. PMC9891196
  11. Markert J, Luger K, Lee H, Hu H, Taylor NMI, Fernandez-Martinez J, Rout M, Alder N. “Depicting protein structures as schematics.” Trends Biochem Sci. 2023 Apr;48(4):307-310. doi: 10.1016/j.tibs.2023.01.006. PMID: 36931235
  12. Moreira CMDN, Kelemen CD, Obado SO, Zahedifard F, Zhang N, Holetz FB, Gauglitz L, Dallagiovanna B, Field MC, Kramer S, Zoltner M. “Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared.” J Biol Chem. 2023 Jan;299(1):102726. doi: 10.1016/j.jbc.2022.102726. Epub 2022 Nov 19. PMC9791439
  13. Obado S, Stein M, Hegedűsová E, Zhang W, Hutchinson S, Brillantes M, Glover L, Paris Z, Chait BT, Field MC, Rout MP. “Mex67 paralogs mediate division of labor in trypanosome RNA processing and export.” bioRxiv 2022.06.27.497849; doi: https://doi.org/10.1101/2022.06.27.497849
  14. Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J. “A quantitative map of nuclear pore assembly reveals two distinct mechanisms.” Nature. 2023 Jan;613(7944):575-581. doi: 10.1038/s41586-022-05528-w. Epub 2023 Jan 4. PMC9849139
  15. Oyong DA, Duffy FJ, Neal ML, Du Y, Carnes J, Schwedhelm KV, Hertoghs N, Jun SH, Miller H, Aitchison JD, De Rosa SC, Newell EW, McElrath MJ, McDermott SM, Stuart KD. “Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge.” PLoS Pathog. 2023 May 17;19(5):e1011051. doi: 10.1371/journal.ppat.1011051. eCollection 2023 May. PMC10228810
  16. Saik NO, Ptak C, Rehman S, Aitchison JD, Montpetit B, Wozniak RW. “SUMOylation at the inner nuclear membrane facilitates nuclear envelope biogenesis during mitosis.” J Cell Biol. 2023 Aug 7;222(8):e202208137. doi: 10.1083/jcb.202208137. Epub 2023 Jul 3. PMC10318406
  17. Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait B, Darst SA, Campbell EA. “Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain.” Mol Cell. 2023 Nov 2;83(21):3921-3930.e7. doi: 10.1016/j.molcel.2023.10.001. Epub 2023 Oct 26. PMID: 37890482
  18. Staheli JP, Neal ML, Navare A, Mast FD, Aitchison JD. “Predicting host-based, synthetic lethal antiviral targets from omics data.” bioRxiv. 2023 Aug 16:2023.08.15.553430. doi: 10.1101/2023.08.15.553430. Preprint. PMC10462099
  19. Taylor MS, Connie W, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cheng WC, Heaps J, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Norden BL, Chait BT, Goggins M, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Jung E, Arora KS, Zukerberg LR, Yilmaz OH, Chi G, Matulonis UA, Song Y, Nieman L, Parikh AR, Strickland M, Corcoran RB, Mustelin T, Eng G, Yilmaz ÃH, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. “Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker.” Cancer Discov. 2023 Sep 12. doi: 10.1158/2159-8290.CD-23-0313. PMID: 37698949
  20. Xu J, Kumar S, Hua N, Kou Y, Lei X, Rout MP, Aitchison JD, Alber F, Chen L. “Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions”. bioRxiv [Preprint]. 2023 Mar 17:2023.01.25.525462. doi: 10.1101/2023.01.25.525462.  PMC9900799
  21. Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. “A general method for quantitative fractionation of mammalian cells.” J Cell Biol. 2023 Jun 5;222(6):e202209062. doi: 10.1083/jcb.202209062. Epub 2023 Mar 15. PMC10040634
  22. Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. “ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.” J Mol Biol. 2023 Feb 23:168021. doi: 10.1016/j.jmb.2023.168021. Epub 2023 Feb 23. PMC10293049
  23. Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. “Conformational Dynamics of the Activated GLP-1 Receptor-Gs Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling.” ACS Cent Sci. 2023 Apr 24;9(5):992-1007. doi: 10.1021/acscentsci.3c00063. eCollection 2023 May 24. PMC10214531
  1. Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. “Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex.” Cell. 2022 Jan 20;185(2):361-378.e25. doi: 10.1016/j.cell.2021.12.015. Epub 2022 Jan 3. PMC8928745
  2. Balasubramanian S, Andreani M, Andrade JG, Saha T, Sundaravinayagam D, Garzón J, Zhang W, Popp O, Hiraga SI, Rahjouei A, Rosen DB, Mertins P, Chait BT, Donaldson AD, Di Virgilio M. “Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region.” Elife. 2022 Apr 13;11:e75047. doi: 10.7554/eLife.75047. PMC9007588
  3. Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali A, Condello C, DeGrado WF. “Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ.” Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2114486119. doi: 10.1073/pnas.2114486119. PMC8812518
  4. Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. “From systems to structure – using genetic data to model protein structures.” Nat Rev Genet. 2022 Jun;23(6):342-354. doi: 10.1038/s41576-021-00441-w. Epub 2022 Jan 10. PMC8744059
  5. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. “RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.” Protein Sci. 2022 Dec;31(12):e4482. doi: 10.1002/pro.4482. PMC9667899
  6. Carter CC, Mast FD, Olivier JP, Bourgeois NM, Kaushansky A, Aitchison JD. “Dengue activates mTORC2 signaling to counteract apoptosis and maximize viral replication.” Front Cell Infect Microbiol. 2022 Sep 12;12:979996. doi: 10.3389/fcimb.2022.979996. eCollection 2022. PMC9510660
  7. Du J, Vandavasi VG, Molloy KR, Yang H, Massenburg LN, Singh A, Kwansa AL, Yingling YG, O’Neill H, Chait BT, Kumar M, Nixon BT. “Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes.” Biomacromolecules. 2022 Sep 12;23(9):3663-3677. doi: 10.1021/acs.biomac.2c00550. Epub 2022 Aug 10. PMID: 35948425
  8. Du Y, Hertoghs N, Duffy FJ, Carnes J, McDermott SM, Neal ML, Schwedhelm KV, McElrath MJ, De Rosa SC, Aitchison JD, Stuart KD. “Systems analysis of immune responses to attenuated P. falciparum malaria sporozoite vaccination reveals excessive inflammatory signatures correlating with impaired immunity.” PLoS Pathog. 2022 Feb 2;18(2):e1010282. doi: 10.1371/journal.ppat.1010282. eCollection 2022 Feb. PMC8843222
  9. Duffy FJ, Hertoghs N, Du Y, Neal ML, Oyong D, McDermott S, Minkah N, Carnes J, Schwedhelm KV, McElrath MJ, De Rosa SC, Newell E, Aitchison JD, Stuart K. “Longitudinal immune profiling after radiation-attenuated sporozoite vaccination reveals coordinated immune processes correlated with malaria protection.” Front Immunol. 2022 Dec 15;13:1042741. doi: 10.3389/fimmu.2022.1042741. eCollection 2022. PMC9798120
  10. Duffy FJ, Olson GS, Gold ES, Jahn A, Aderem A, Aitchison JD, Rothchild AC, Diercks AH, Nemeth J. “Use of a Contained Mycobacterium tuberculosis Mouse Infection Model to Predict Active Disease and Containment in Humans.” J Infect Dis. 2022 May 16;225(10):1832-1840. doi: 10.1093/infdis/jiab130. PMC9113476
  11. Echeverria I, Braberg H, Krogan NJ, Sali A. “Integrative structure determination of histones H3 and H4 using genetic interactions.” FEBS J. 2022 Mar 17. doi: 10.1111/febs.16435. Online ahead of print. PMC9481981
  12. Field MC, Rout MP. “Coatomer in the universe of cellular complexity.” Mol Biol Cell. 2022 Dec 1;33(14):pe8. doi: 10.1091/mbc.E19-01-0012. PMC9727805
  13. Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. “Integration of software tools for integrative modeling of biomolecular systems.” J Struct Biol. 2022 Mar;214(1):107841. doi: 10.1016/j.jsb.2022.107841. Epub 2022 Feb 9. PMC9278553
  14. Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY. “Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA.” Nat Commun. 2022 Aug 15;13(1):4668. doi: 10.1038/s41467-022-32315-y. PMC9378689
  15. Li A, Zhang X, Singla J, White K, Loconte V, Hu C, Zhang C, Li S, Li W, Francis JP, Wang C, Sali A, Sun L, He X, Stevens RC. “Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion.” PLoS One. 2022 Mar 24;17(3):e0265567. doi: 10.1371/journal.pone.0265567. eCollection 2022. PMC8947144
  16. Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Le Gros M, White KL, Larabell CA. “Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.” Structure. 2022 Apr 7;30(4):510-521.e3. doi: 10.1016/j.str.2022.01.006. Epub 2022 Feb 10. PMC9013509
  17. Mickolajczyk KJ, Olinares PDB, Chait BTC, Liu S, Kapoor TM. “The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates.” Elife. 2022 Feb 11;11:e73534. doi: 10.7554/eLife.73534. PMC8837202
  18. Navare AT, Mast FD, Olivier JP, Bertomeu T, Neal ML, Carpp LN, Kaushansky A, Coulombe-Huntington J, Tyers M, Aitchison JD. “Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality.” J Cell Biol. 2022 Nov 7;221(11):e202011050. doi: 10.1083/jcb.202011050. Epub 2022 Oct 28. PMC9623979
  19. Neal ML, Duffy FJ, Du Y, Aitchison JD, Stuart KD. “Preimmunization correlates of protection shared across malaria vaccine trials in adults.” NPJ Vaccines. 2022 Jan 14;7(1):5. doi: 10.1038/s41541-021-00425-1. PMC8760258
  20. Nudelman I, Fernandez-Martinez J, Rout MP. “Affinity Isolation of Endogenous Saccharomyces Cerevisiae Nuclear Pore Complexes.” Methods Mol Biol. 2022;2502:3-34. doi: 10.1007/978-1-0716-2337-4_1. PMC9200140
  21. Obado SO, Rout MP, Field MC. “Sending the message: specialized RNA export mechanisms in trypanosomes.” Trends Parasitol. 2022 Oct;38(10):854-867. doi: 10.1016/j.pt.2022.07.008. Epub 2022 Aug 24. PMC9894534. Review
  22. Serganov AA, Udi Y, Stein ME, Patel V, Fridy PC, Rice CM, Saeed M, Jacobs EY, Chait BT, Rout MP. “Proteomic elucidation of the targets and primary functions of the picornavirus 2A protease.” J Biol Chem. 2022 Mar 30:101882. doi: 10.1016/j.jbc.2022.101882. Epub 2022 Mar 31. PMC9168619
  23. Vijayan K, Arang N, Wei L, Morrison R, Geiger R, Parks KR, Lewis AJ, Mast FD, Douglass AN, Kain HS, Aitchison JD, Johnson JS, Aderem A, Kaushansky A. “A genome-wide CRISPR-Cas9 screen identifies CENPJ as a host regulator of altered microtubule organization during Plasmodium liver infection.” Cell Chem Biol. 2022 Jun 18:S2451-9456(22)00205-7. doi: 10.1016/j.chembiol.2022.06.001. Epub 2022 Jun 22. PMC9481707
  24. Zinder JC, Olinares PDB, Svetlov V, Bush MW, Nudler E, Chait BT, Walz T, de Lange T. “Shelterin is a Dimeric Complex with Extensive Structural Heterogeneity.” Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2201662119. doi: 10.1073/pnas.2201662119. Epub 2022 Jul 26. PMC9351484
  1. Borah S, Thaller DJ, Hakhverdyan Z, Rodriguez EC, Isenhour AW, Rout MP, King MC, Lusk CP. “Heh2/Man1 may be an evolutionarily conserved sensor of NPC assembly state.” Mol Biol Cell. 2021 Jul 15;32(15):1359-1373. doi: 10.1091/mbc. E20-09-0584. Epub 2021 May 19. PMC8694041
  2. Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. “Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis.” Cell. 2021 Jul 16:S0092-8674(21)00824-2. doi: 10.1016/j.cell.2021.06.033. Epub 2021 Jul 22. PMC8382161
  1. Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA. “CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.” Elife. 2021 May 5;10:e65168. doi: 10.7554/eLife.65168. PMC8099430
  1. Duffy FJ, Olson GS, Gold ES, Jahn A, Aderem A, Aitchison J, Rothchild AC, Diercks AH, Nemeth J. “A contained Mycobacterium tuberculosis mouse infection model predicts active disease and containment in humans.” J Infect Dis. 2021 Mar 10:jiab130. doi: 10.1093/infdis/jiab130. Online ahead of print. PMID: 33693706
  2. Fernandez-Martinez J, Rout MP. “One Ring to Rule them All? Structural and Functional Diversity in the Nuclear Pore Complex.” Trends Biochem Sci. 2021 Feb 6:S0968-0004(21)00005-0. doi: 10.1016/j.tibs.2021.01.003. Online ahead of print. PMC8195821
  3. Gennari JH, König M, Misirli G, Neal ML, Nickerson DP, Waltemath D. “OMEX metadata specification (version 1.2).” J Integr Bioinform. 2021 Oct 20;18(3):20210020. doi: 10.1515/jib-2021-0020. PMC8560343
  4. Hakhverdyan Z, Molloy KR, Subbotin RI, Fernandez-Martinez J, Chait BT, Rout MP. “Measuring in vivo protein turnover and exchange in yeast macromolecular assemblies.” STAR Protoc. 2021 Sep 8;2(3):100800. doi: 10.1016/j.xpro.2021.100800. eCollection 2021 Sep 17. PMC8433251
  5. Hakhverdyan Z, Molloy KR, Keegan S, Herricks T, Lepore DM, Munson M, Subbotin RI, Fenyö D, Aitchison JD, Fernandez-Martinez J, Chait BT, Rout MP. “Dissecting the Structural Dynamics of the Nuclear Pore Complex.” Mol Cell. 2021 Jan 7;81(1):153-165.e7. doi: 10.1016/j.molcel.2020.11.032. Epub 2020 Dec 16. PMC8121378
  6. Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. “The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex.” Structure. 2021 May 6;29(5):467-478.e6. doi: 10.1016/j.str.2020.12.006. Epub 2021 Jan 6. PMC8675206
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  1. Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J. “LINE-1 ORF2p expression is nearly imperceptible in human cancers.” Mob DNA. 2019 Dec 31;11:1. doi: 10.1186/s13100-019-0191-2. eCollection 2020. PMC6937734
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  1. Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN Jr, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. “Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.” Structure. 2019 Dec 3;27(12):1745-1759. doi: 10.1016/j.str.2019.11.002. Epub 2019 Nov 25. PMID: 31780431
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  4. Field MC, Rout MP. “Pore timing: the evolutionary origins of the nucleus and nuclear pore complex.” F1000Res. 2019 Apr 3;8. pii: F1000 Faculty Rev-369. doi: 10.12688/f1000research.16402.1. eCollection 2019. Review. PMC6449795
  5. Glennon EKK, Austin LS, Arang N, Kain HS, Mast FD, Vijayan K, Aitchison JD, Kappe SHI, Kaushansky A. “Alterations in Phosphorylation of Hepatocyte Ribosomal Protein S6 Control Plasmodium Liver Stage Infection.” Cell Rep. 2019 Mar 19;26(12):3391-3399.e4. doi: 10.1016/j.celrep.2019.02.085. PMC6447308
  6. Hayama R, Sorci M, Keating Iv JJ, Hecht LM, Plawsky JL, Belfort G, Chait BT, Rout MP. “Interactions of nuclear transport factors and surface-conjugated FG nucleoporins: Insights and limitations.” PLoS One. 2019 Jun 6;14(6):e0217897. doi: 10.1371/journal.pone.0217897. eCollection 2019. PMC6553764
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  9. 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. 2019 May 1;35(9):1600-1602. doi: 10.1093/bioinformatics/bty829. PMC6499248
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  5. 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. PMC5908968
  6. 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. PMC5847524
  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. 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. PMC5921576
  9. Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F. “Producing genome structure populations with the dynamic and automated PGS software.” Nat Protoc. 2018 May;13(5):915-926. doi:1038/nprot.2018.008. Epub 2018 Apr 5. PMC6043163
  10. 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 22;555(7697):475-482. doi: 10.1038/nature26003. Epub 2018 Mar 14. PMC6022767 
  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. 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. PMC5775914
  3. Mast FD, Aitchison JD. “Characterization of Peroxisomal Regulation Networks.” Subcell Biochem. 2018;89:367-382. doi: 10.1007/978-981-13-2233-4_16. PMID: 30378032 (Book Chapter)
  1. 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. PMC5987711
  1. 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 Apr 5;556(7699):126-129. doi: 10.1038/nature26156. Epub 2018 Mar 5. PMC6118127
  2. 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. PMC6145447
  3. 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. PMC6014618
  4. 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 Mar 6;26(3):477-484.e4. doi: 10.1016/j.str.2018.01.010. Epub 2018 Feb 8.PMC5929991
  1. 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. PMC5821459
  2. 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. PMC5990459
  3. 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
  4. Yoshizawa T, Ali R, Jiou J, Fung HYJ, Burke KA, Kim SJ, Lin Y, Peeples WB, Saltzberg D, Soniat M, Baumhardt JM, Oldenbourg R, Sali A, Fawzi NL, Rosen MK, Chook YM. “Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites.”Cell. 2018 Apr 19;173(3):693-705.e22. doi: 10.1016/j.cell.2018.03.003. PMC6234985
  5. 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
  1. Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S. “The complete structure of the small-subunit processome.” Nat Struct Mol Biol. 2017 Nov;24(11):944-953. doi: 10.1038/nsmb.3472. Epub 2017 Sep 25. PMID: 28945246
  2. 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. PMC5256885
  3. 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. PMC5391116
  4. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network. “The 4D nucleome project.” Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. PMC5617335
  5. 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. PMC5499702
  6. 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. PMC5493206
  7. 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. PMC5568245
  8. 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. PMC5608540 Full text links
  9. 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. PMC5217116
  10. 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. PMC5386594
  11. Kazantsev F, Akberdin I, Lashin S, Ree N, Timonov V, Ratushny A, Khlebodarova T, Likhoshvai V. “MAMMOTh: A new database for curated mathematical models of biomolecular systems.” J Bioinform Comput Biol. 2018 Feb;16(1):1740010. doi: 10.1142/S0219720017400108. Epub 2017 Nov 3. PMID: 29172865
  12. 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. PMC5783720
  13. 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. 2017 Oct 25. pii: S2451-9456(17)30358-6. doi:10.1016/j.chembiol.2017.10.001. [Epub ahead of print] PMC5775914
  14. Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F. “The three-dimensional genome organization of Drosophila melanogaster through data integration.” Genome Biol. 2017 Jul 31;18(1):145. doi: 10.1186/s13059-017-1264-5. PMC5576134
  15. López García de Lomana A, Kaur A, Turkarslan S, Beer KD, Mast FD, Smith JJ, Aitchison JD, Baliga NS. “Adaptive Prediction Emerges Over Short Evolutionary Time Scales.” Genome Biol Evol. 2017 Jun 1;9(6):1616-1623. doi: 10.1093/gbe/evx116. PMC5570091
  16. 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. PMC5681675
  17. 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. PMC5399782
  18. Niepel M, Farr JC, Rout MP, Strambio-De-Castillia C. “Rapid isolation of functionally intact nuclei from the yeast Saccharomyces” bioRxiv. July 12, 2017. doi: https://doi.org/10.1101/162388
  19. Obado SO, Field MC, Rout MP. “Comparative interactomics provides evidence for functional specialization of the nuclear pore complex.” Nucleus. 2017 May 2:1-13. doi: 10.1080/19491034.2017.1313936. [Epub ahead of print] PMC5597298
  20. Rout MP, Field MC. “The Evolution of Organellar Coat Complexes and Organization of the Eukaryotic Cell.” Annu Rev Biochem. 2017 Jun 20;86:637-657. doi: 10.1146/annurev-biochem-061516-044643. Epub 2017 May 3. Review. PMID: 28471691
  21. 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. PMC5333908
  22. Santanach A, Blanco E, Jiang H, Molloy KR, Sansó M, LaCava J, Morey L, Di Croce 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. PMC5663739
  23. 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. PMID: 28661652
  24. 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 Feb 2. pii: S0969-2126(17)30006-0. doi: 10.1016/j.str.2017.01.006. [Epub ahead of print] PMC5342941
  25. 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. PMC5768525
  26. Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG. “The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling.”Mol Biol Cell. 2017 Nov 7;28(23):3298-3314. doi: 10.1091/mbc.E17-06-0397. Epub 2017 Aug 16. PMC5687031
  27. 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 Epub 2017 Aug 15. PMC5625060
  28. 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. PMC5417825
  29. Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND. Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PLoS Comput Biol. 2017 May 17;13(5):e1005489. doi: 10.1371/journal.pcbi.1005489. eCollection 2017 May. PMC5453602
  30. Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. “Integrative structure modeling with IMP.” Protein Sci. 2017 Sep 28. doi: 10.1002/pro.3311. [Epub ahead of print] PMC5734277
  31. Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O’Donoghue AJ, Craik CS. “Immunoproteasome functions explained by divergence in cleavage specificity and regulation.” Elife. 2017 Nov 28;6. pii: e27364. doi: 10.7554/eLife.27364. PMC5705213
  32. 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. PMC5696578
  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
  2. Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. “Revealing Higher Order Protein Structure Using Mass Spectrometry.” J Am Soc Mass Spectrom. 2016 Jun;27(6):952-65. doi: 10.1007/s13361-016-1385-1. PMC5125627
  3. Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J. “Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling.” Mol Cell Proteomics. 2016 Aug;15(8):2730-43. doi: 10.1074/mcp.M115.056473. Epub 2016 Jun 1. PMC4974347
  4. Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. “CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.” J Mol Biol. 2016 Feb 22;428(4):709-19. doi: 10.1016/j.jmb.2016.01.029. PMC4794384
  5. 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
  6. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. “Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform.” Cell. 2016 Nov 17;167(5):1215-1228.e25. doi: 10.1016/j.cell.2016.10.028. [Epub ahead of print] PMC5130164
  7. 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
  8. 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.  PMC4752824
  9. 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
  10. Kellner N, Schwarz J, Sturm M, Fernandez-Martinez J, Griesel S, Zhang W, Chait BT, Rout MP, Kück U, Hurt E. “Developing genetic tools to exploit Chaetomium thermophilum for biochemical analyses of eukaryotic macromolecular assemblies”, Sci Rep. 2016 Feb 11. PMC4750058
  11. Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL. “Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.” Cell. 2016 Jul 28;166(3):766-78. doi: 10.1016/j.cell.2016.06.041. PMID: 27453469
  12. LaCava J, Jiang H, Rout MP. “Protein Complex Affinity Capture from Cryomilled Mammalian Cells.” J Vis Exp. 2016 Dec 9;(118). doi: 10.3791/54518. PMID: 28060343 . Full text link
  13. 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
  14. 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
  15. 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
  16. Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. “Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.” Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1. PMC5030136
  17. 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
  18. 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
  19. 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 Dec 15;44(22):10554-10570. PMC5159534
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. “A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions.” J Phys Chem B. 2016 Nov 3. [Epub ahead of print] PMID: 27807976
  27. 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
  28. 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. PMC5084692
  29. 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
  30. Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. “Simple rules for passive diffusion through the nuclear pore complex.” J Cell Biol. 2016 Oct 10;215(1):57-76. PMC5057280
  31. Volpon L, Culjkovic-Kraljacic B, Osborne MJ, Ramteke A, Sun Q, Niesman A, Chook YM, Borden KL. “Importin 8 mediates m7G cap-sensitive nuclear import of the eukaryotic translation initiation factor eIF4E.” Proc Natl Acad Sci U S A. 2016 May 10;113(19):5263-8. doi: 10.1073/pnas.1524291113. Epub 2016 Apr 25. PMC4868427