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.

  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. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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 2 PMC9623979
  15. 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
  16. 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
  17. 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/ Epub 2022 Aug 24. PMID: 36028415. Review
  18. 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
  19. 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
  20. 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
  7. Herricks T, Donczew M, Sherman DR, Aitchison JD. “ODELAM: Rapid Sequence-independent Detection of Drug Resistance in Mycobacterium tuberculosis Isolates.” Bio Protoc. 2021 May 20;11(10):e4027. doi: 10.21769/BioProtoc.4027. eCollection 2021 May 20. PMC8187124
  8. Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA. “Structural basis for transcription complex disruption by the Mfd translocase.” Elife. 2021 Jan 22;10:e62117. doi: 10.7554/eLife.62117. PMC7864632
  9. Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA. “Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.” Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2102516118. doi: 10.1073/pnas.2102516118. PMC8126829
  10. Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. “Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape.” Elife. 2021 Dec 7;10:e73027. doi: 10.7554/eLife.73027. PMC8651292
  11. Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. “Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.” bioRxiv. 2021 Apr 10:2021.04.08.438911. doi: 10.1101/2021.04.08.438911. Preprint. PMC8043454
  12. Neal ML, Wei L, Peterson E, Arrieta-Ortiz ML, Danziger SA, Baliga NS, Kaushansky A, Aitchison JD. “A systems-level gene regulatory network model for Plasmodium falciparum.” 2021 May 21;49(9):4891-4906.doi: 10.1093/nar/gkaa1245. PMC8136813
  13. Niu Y, Tao X, Vaisey G, Olinares PDB, Alwaseem H, Chait BT, MacKinnon R. “Analysis of the mechanosensor channel functionality of TACAN.” Elife. 2021 Aug 10;10:e71188. doi: 10.7554/eLife.71188. PMC8376246
  14. Nivedita N, Aitchison JD, Baliga NS. “Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance.” Front Microbiol. 2021 Sep 10;12:712631. doi: 10.3389/fmicb.2021.712631. eCollection 2021. PMC8461305
  15. Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT. ‘Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM.” Structure. 2021 Feb 4;29(2):186-195.e6. doi: 10.1016/j.str.2020.11.001. Epub 2020 Nov 19. PMC7867593
  1. Plumlee CR, Duffy FJ, Gern BH, Delahaye JL, Cohen SB, Stoltzfus CR, Rustad TR, Hansen SG, Axthelm MK, Picker LJ, Aitchison JD, Sherman DR, Ganusov VV, Gerner MY, Zak DE, Urdahl KB. “Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis.” Cell Host Microbe. 2021 Jan 13;29(1):68-82.e5. doi: 10.1016/j.chom.2020.10.003. Epub 2020 Nov 2. PMC7854984
  2. Ptak C, Saik NO, Premashankar A, Lapetina DL, Aitchison JD, Montpetit B, Wozniak RW. “Phosphorylation-dependent mitotic SUMOylation drives nuclear envelope-chromatin interactions.” J Cell Biol. 2021 Dec 6;220(12):e202103036. doi: 10.1083/jcb.202103036. Epub 2021 Nov 17. PMC8641411
  3. Porubsky V, Smith L, Sauro HM. “Publishing reproducible dynamic kinetic models.” Brief Bioinform. 2021 May 20;22(3):bbaa152. doi: 10.1093/bib/bbaa152. PMC8138891
  4. Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharath K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A. “Bayesian metamodeling of complex biological systems across varying representations.” Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2104559118. doi: 10.1073/pnas.2104559118. PMC8536362
  5. Ricardo-Lax I, Luna JM, Thao TTN, Le Pen J, Yu Y, Hoffmann HH, Schneider WM, Razooky BS, Fernandez-Martinez J, Schmidt F, Weisblum Y, Trüeb BS, Berenguer Veiga I, Schmied K, Ebert N, Michailidis E, Peace A, Sánchez-Rivera FJ, Lowe SW, Rout MP, Hatziioannou T, Bieniasz PD, Poirier JT, MacDonald MR, Thiel V, Rice CM. “Replication and single-cycle delivery of SARS-CoV-2 replicons.” Science. 2021 Nov 26;374(6571):1099-1106. doi: 10.1126/science.abj8430. Epub 2021 Oct 14. PMID: 34648371
  6. Sahu PK, Duffy FJ, Dankwa S, Vishnyakova M, Majhi M, Pirpamer L, Vigdorovich V, Bage J, Maharana S, Mandala W, Rogerson SJ, Seydel KB, Taylor TE, Kim K, Sather DN, Mohanty A, Mohanty RR, Mohanty A, Pattnaik R, Aitchison JD, Hoffman A, Mohanty S, Smith JD, Bernabeu M, Wassmer SC. “Determinants of brain swelling in pediatric and adult cerebral malaria.” JCI Insight. 2021 Sep 22;6(18):e145823. doi: 10.1172/jci.insight.145823. PMC8492338
  7. Sali A. “From integrative structural biology to cell biology.”J Biol Chem. 2021 Jan-Jun;296:100743. doi: 10.1016/j.jbc.2021.100743. Epub 2021 May 4. PMC8203844
  8. Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A. “Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.” Protein Sci. 2021 Jan;30(1):250-261. doi: 10.1002/pro.3995. Epub 2020 Dec 3. PMC7737781
  9. Schureck MA, Darling JE, Merk A, Shao J, Daggupati G, Srinivasan P, Olinares PDB, Rout MP, Chait BT, Wollenberg K, Subramaniam S, Desai SA. “Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake.” Elife. 2021 Jan 4;10:e65282. doi: 10.7554/eLife.65282. doi: 10.7554/eLife.65282. PMC7840181
  10. Vallat B, Webb B, Fayazi M, Voinea S, Tangmunarunkit H, Ganesan SJ, Lawson CL, Westbrook JD, Kesselman C, Sali A, Berman HM. “New system for archiving integrative structures.” Acta Crystallogr D Struct Biol. 2021 Dec 1;77(Pt 12):1486-1496. doi: 10.1107/S2059798321010871. Epub 2021 Nov 29. PMC8647179
  11. Welsh C, Nickerson DP, Rampadarath A, Neal ML, Sauro HM, Gennari JH. “libOmexMeta: Enabling semantic annotation of models to support FAIR principles.” Bioinformatics. 2021 Jun 16;37(24):4898-900. doi: 10.1093/bioinformatics/btab445. Online ahead of print. PMC8665746
  12. Wieczorek M, Ti SC, Urnavicius L, Molloy KR, Aher A, Chait BT, Kapoor TM. “Biochemical reconstitutions reveal principles of human γ-TuRC assembly and function.” J Cell Biol. 2021 Mar 1;220(3):e202009146. doi: 10.1083/jcb.202009146. PMC7844428
  13. Yu Y, Li S, Ser Z, Sanyal T, Choi K, Wan B, Kuang H, Sali A, Kentsis A, Patel DJ, Zhao X. “Integrative analysis reveals unique structural and functional features of the Smc5/6 complex.” Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2026844118. doi: 10.1073/pnas.2026844118. PMC8126833
  14. Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. “IMProv: A Resource for Crosslink-Driven Structure Modeling that Accommodates Protein Dynamics.” Mol Cell Proteomics. 2021 Aug 18:100139. doi: 10.1016/j.mcpro.2021.100139. Online ahead of print. PMC8452774
  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
  2. Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. “Genetic interaction mapping informs integrative structure determination of protein complexes.” Science. 2020 Dec 11;370(6522):eaaz4910. doi: 10.1126/science.aaz4910. PMID: 33303586
  3. Carter V, LaCava J, Taylor MS, Liang SY, Mustelin C, Ukadike KC, Bengtsson A, Lood C, Mustelin T. “High Prevalence and Disease Correlation of Autoantibodies Against p40 Encoded by Long Interspersed Nuclear Elements in Systemic Lupus Erythematosus.” Arthritis Rheumatol. 2020 Jan;72(1):89-99. doi: 10.1002/art.41054. PMC6935427
  4. Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA. “Stepwise Promoter Melting by Bacterial RNA Polymerase.” Mol Cell. 2020 Apr 16;78(2):275-288.e6. doi: 10.1016/j.molcel.2020.02.017. Epub 2020 Mar 10. PMC7166197
  5. Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait B, Kapoor T, Darst SA, Campbell EA. “Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.” 2020 Sep 17;182(6):1560-1573.e13. doi: 10.1016/j.cell.2020.07.033. Epub 2020 Jul 28. PMC7386476
  6. Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. “NCBP3 positively impacts mRNA biogenesis.” Nucleic Acids Res. 2020 Oct 9;48(18):10413-10427. doi: 10.1093/nar/gkaa744. PMC7544205
  7. Dou Y, Kalmykova S, Pashkova M, Oghbaie M, Jiang H, Molloy KR, Chait BT, Rout MP, Fenyö D, Jensen TH, Altukhov I, LaCava J. “Affinity proteomic dissection of the human nuclear cap-binding complex interactome.” Nucleic Acids Res. 2020 Oct 9;48(18):10456-10469. doi: 10.1093/nar/gkaa743. PMC7544204
  8. Ganesan SJ, Feyder MJ, Chemmama IE, Fang F, Rout MP, Chait BT, Shi Y, Munson M, Sali A. “Integrative Structure and Function of the Yeast Exocyst Complex”. Protein Sci. 2020 Jun;29(6):1486-1501.  doi: 10.1002/pro.3863.  Epub 2020 May 1. PMC7255525
  9. Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L. “Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.” Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4088-4098. doi: 10.1073/pnas.1915542117. Epub 2020 Feb 7. PMID: 32034103
  10. 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. 2020 Dec 30:S0969-2126(20)30473-1. doi: 10.1016/j.str.2020.12.006. Online ahead of print. PMID: 33412091
  11. Herricks T, Donczew M, Mast FD, Rustad T, Morrison R, Sterling TR, Sherman DR, Aitchison JD. “ODELAM, rapid sequence-independent detection of drug resistance in isolates of Mycobacterium tuberculosis.” Elife. 2020 May 13;9:e56613. doi: 10.7554/eLife.56613. PMC7263823
  12. Kieuvongngam V, Olinares PDB, Palillo A, Oldham ML, Chait BT, Chen J. “Structural basis of substrate recognition by a polypeptide processing and secretion transporter.” Elife. 2020 Jan 14;9. pii: e51492. doi: 10.7554/eLife.51492. PMC6959990
  13. Korvatska O, Kiianitsa K, Ratushny A, Matsushita M, Beeman N, Chien WM, Satoh JI, Dorschner MO, Keene CD, Bammler TK, Bird TD, Raskind WH. Triggering Receptor Expressed on Myeloid Cell 2 R47H Exacerbates Immune Response in Alzheimer’s Disease Brain. Front Immunol. 2020 Sep 25;11:559342. doi: 10.3389/fimmu.2020.559342. eCollection 2020. PMID: 33101276 
  14. Kwon Y, Kaake R, Echeverria I, Suarez M, Shamsabadi MK, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. “Structural Basis of CD4 Downregulation by HIV-1 Nef”. Nat Struct Mol Biol. 2020 Sep;27(9):822-828. doi: 10.1038/s41594-020-0463-z. Epub 2020 Jul 27. PMC7483821
  15. Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. “Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality.” J Cell Biol. 2020 Oct 5;219(10):e202006159. doi: 10.1083/jcb.202006159. PMID: 32785687
  16. Mast FD, Rachubinski RA, Aitchison JD. “Peroxisome Prognostications: Exploring the birth, life, and death of an organelle.” 2020. J Cell Biol. 2020 Mar 2;219(3):e201912100. doi: 10.1083/jcb.201912100. PMC7054992
  17. Mickolajczyk KJ, Olinares PDB, Niu Y, Chen N, Warrington SE, Sasaki Y, Walz T, Chait BT, Kapoor TM. “Long-range intramolecular allostery and regulation in the dynein-like AAA protein Mdn1.” Proc Natl Acad Sci U S A. 2020 Aug 4;117(31):18459-18469. doi: 10.1073/pnas.2002792117. Epub 2020 Jul 21. PMC7414173
  18. Navare AT, Mast FD, Olivier JP, Bertomeu T, Neal M, Carpp LN, Kaushansky A, Coulombe-Huntington J, Tyers M, Aitchison JD. “Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality.” bioRxiv. 2020 Nov 6:2020.10.12.336487. doi: 10.1101/2020.10.12.336487. PMC7654857
  19. Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT. “Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM.” Structure. 2020 Nov 17:S0969-2126(20)30413-5. doi: 10.1016/j.str.2020.11.001. PMID: 33217329
  20. Olinares PDB, Chait B, “Native mass spectrometry analysis of affinity-captured endogenous yeast exosome complexes”, Methods Mol Biol. 2020;2062:357-382. doi: 10.1007/978-1-4939-9822-7_17. PMID: 31768985 (Book chapter).
  21. Saik NO, Park N, Ptak C, Adames N, Aitchison JD, WozniakR. “Recruitment of an Activated Gene to the Nuclear Pore Complex Requires Sumoylation.” Front Genet. 2020 Mar 6;11:174. doi: 10.3389/fgene.2020.00174. PMC7067905
  22. Saeed M, Kapell S, Hertz NT, Wu X, Bell K, Ashbrook AW, Mark MT, Zebroski HA, Neal ML, Flodström-Tullberg M, MacDonald MR, Aitchison JD, Molina H, Rice CM. “Defining the proteolytic landscape during enterovirus infection.” PLoS Pathog. 2020 Sep 30;16(9):e1008927. doi: 10.1371/journal.ppat.1008927. eCollection 2020 Sep. PMC7549765
  23. Sparks S, Hayama R, Rout MP, Cowburn D. “Analysis of Multivalent IDP Interactions: Stoichiometry, Affinity, and Local Concentration Effect Measurements.” Methods Mol Biol. 2020;2141:463-475. doi: 10.1007/978-1-0716-0524-0_23. (Book chapter) PMID: 32696372
  24. White KL, Singla J, Loconte V, Chen JH, Ekman A, Sun L, Zhang X, Francis JP, Li A, Lin W, Tseng K, McDermott G, Alber F, Sali A, Larabell C, Stevens RC. “Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography.” Sci Adv. 2020 Dec 9;6(50):eabc8262. doi: 10.1126/sciadv.abc8262. PMC7725475
  25. Wieczorek M, Urnavicius L, Ti SC, Molloy KR, Chait BT, Kapoor TM. “Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex.” 2020 Jan 9;180(1):165-175.e16. doi: 10.1016/j.cell.2019.12.007. Epub 2019 Dec 17. PMC7027161
  26. Winczura K, Domanski M, LaCava J.  “Affinity Proteomic Analysis of the Human Exosome and Its Cofactor Complexes.” Methods Mol Biol. 2020;2062:291-325. doi: 10.1007/978-1-4939-9822-7_15. PMID: 31768983
  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
  7. Jiang H, Taylor MS, Molloy KR, Altukhov I, LaCava J. “Identification of RNase-sensitive LINE-1 Ribonucleoprotein Interactions by Differential Affinity Immobilization.” Bio Protoc. 2019 Apr 5;9(7). pii: e3200. doi: 10.21769/BioProtoc.3200. PMC6519465
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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
  10. Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D’Arcy S, Chook YM. “Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone.” Elife. 2019 Mar 11;8. pii: e43630. doi: 10.7554/eLife.43630. PMC6453568
  11. Regier MC, Olszewski E, Carter CC, Aitchison JD, Kaushansky A, Davis J, Berthier E, Beebe DJ, Stevens KR. “Spatial presentation of biological molecules to cells by localized diffusive transfer.” Lab Chip. 2019 Jun 11;19(12):2114-2126. doi: 10.1039/c9lc00122k. PMC6755031
  12. Rout MP, Sali A. “Principles for Integrative Structural Biology Studies.” Cell. 2019 May 30;177(6):1384-1403. doi: 10.1016/j.cell.2019.05.016. Review. PMID: 31150619
  13. Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. “Modeling biological complexes using Integrative Modeling Platform.” Methods Mol Biol. 2019;2022:353-377. doi: 10.1007/978-1-4939-9608-7_15. PMID: 31396911 (Book chapter)
  14. Vallat B, Webb B, Westbrook J, Sali A, Berman HM. “Archiving and disseminating integrative structure models.” J Biomol NMR. 2019 Jul;73(6-7):385-398. doi: 10.1007/s10858-019-00264-2. Epub 2019 Jul 5. PMC6692293
  15. Vijayan K, Cestari I, Mast FD, Glennon EKK, McDermott SM, Kain HS, Brokaw AM, Aitchison JD, Stuart K, Kaushansky A. “Plasmodium secretion induces hepatocyte lysosome exocytosis and promotes parasite entry.” iScience. 2019 Nov 22;21:603-611. doi: 10.1016/j.isci.2019.10.054. Epub 2019 Oct 31.PMC6889558
  16. Viswanath S, Sali A. “Optimizing model representation for integrative structure determination of macromolecular assemblies.” Proc Natl Acad Sci USA. 2019 Jan 8;116(2):540-545. PMC6329962
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  2. Chan HL, Beckedorff F, Zhang Y, Garcia-Huidobro J, Jiang H, Colaprico A, Bilbao D, Figueroa ME, LaCava J, Shiekhattar R, Morey L. “Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms.” Nat Commun. 2018 Aug 23;9(1):3377. doi: 10.1038/s41467-018-05728-x. PMC6107513
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  19. 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
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  22. 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
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  30. 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
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  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