Listed on this page are publications with contributing work from the NCDIR acknowledging Grant ID: P41 GM109824.
If you are unable to access a full-text copy of any of the following publications, please contact us and we will forward you a copy.

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

Berman HM, Adams PD, Bonvin  AA, Burley SK, Carragher B, Chiu WK, 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.” (submitted)

  1. 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 (LINE-1) in systemic lupus erythematosus.” Arthritis Rheumatol. 2019 Jul 24. doi: 10.1002/art.41054. [Epub ahead of print] PMID: 31342656
  2. Duffy F, Bernabeu M, Babar PH, Kessler A, Wang CW, Vaz M, Chery L, Mandala WL, Rogerson SJ, Taylor TE, Seydel KB, Lavstsen T, Gomes E, Kim K, Lusingu J, Rathod PK, Aitchison JD, Smith JD. “Meta-analysis of Plasmodium falciparum var Signatures Contributing to Severe Malaria in African Children and Indian Adults.” MBio. 2019 Apr 30;10(2). pii: e00217-19. doi: 10.1128/mBio.00217-19. PMC6495371
  3. Duffy FJ, Weiner J 3rd, Hansen S, Tabb DL, Suliman S, Thompson E, Maertzdorf J, Shankar S, Tromp G, Parida S, Dover D, Axthelm MK, Sutherland JS, Dockrell HM, Ottenhoff THM, Scriba TJ, Picker LJ, Walzl G, Kaufmann SHE, Zak DE; GC6-74 Consortium. “Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome.” Front Immunol. 2019 Mar 22;10:527. doi: 10.3389/fimmu.2019.00527. eCollection 2019. PMC6440524
  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
  8. Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling M, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Le Novère N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. “Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics.” Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. PMC6433895
  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. 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)
  13. 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
  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. 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
  1. Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O’Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. “Prediction of enzymatic pathways by integrative pathway mapping.” Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/eLife.31097. PMC5788505
  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
  3. Chase J, Catalano A, Noble AJ, Eng ET, Olinares PDB, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. “Mechanisms of opening and closing of the bacterial replicative helicase.” Elife. 2018 Dec 24;7. pii: e41140. doi: 10.7554/eLife.41140. [Epub ahead of print] PMID: 30582519
  4. Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M. “The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination.” Mol Cell. 2018 Nov 15;72(4):636-649.e8. doi: 10.1016/j.molcel.2018.08.042. Epub 2018 Oct 4. PMC6242708
  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. Viswanath S, Sali A. “Optimizing model representation for integrative structure determination of macromolecular assemblies.”Proc Natl Acad Sci U S A. 2018 Dec 26. pii: 201814649. doi: 10.1073/pnas.1814649116. [Epub ahead of print] PMID: 30587581
  4. 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
  5. 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
  1. 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. 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
  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
  20. 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
  21. 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
  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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  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
  31. 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
  1. Aitchison JD, Rout MP. “The interactome challenge.” J Cell Biol. 2015 Nov 23;211(4):729-32. doi: 10.1083/jcb.201510108. Epub 2015 Nov 16. PMC4657177
  2. Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. “Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.” Biophys J. 2015 Aug 18;109(4):793-805. doi: 10.1016/j.bpj.2015.06.065. PMC4547163
  3. Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS. “Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.” BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15. PMC4407105
  4. Dokudovskaya S, Rout MP. “SEA you later alli-GATOR – a dynamic regulator of the TORC1 stress response pathway.” J Cell Sci. 2015 Jun 15;128(12):2219-2228. Epub 2015 May 1. Review. PMC4487016
  5. Fridy PC, Thompson MK, Ketaren NE, Rout MP. “Engineered high-affinity nanobodies recognizing staphylococcal Protein A and suitable for native isolation of protein complexes.” Anal Biochem. 2015 May 15;477:92-4. doi: 10.1016/j.ab.2015.02.013. Epub 2015 Feb 21. PMC4487016
  6. Hakhverdyan Z, Domanski M. Hough L, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy K, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP and LaCava J. “Rapid, Optimized Interactomic Screening.” Nat Methods. 2015 Jun;12(6):553-60. doi: 10.1038/nmeth.3395 PMC4449307
  7. Heider MR, Gu M, Duffy CM, Mirza AM, Marcotte LL, Walls AC, Farrall N, Hakhverdyan Z, Field MC, Rout MP, Frost A, Munson M. “Subunit connectivity, assembly determinants and architecture of the yeast exocyst complex.” Nat Struct Mol Biol. 2016 Jan;23(1):59-66. doi: 10.1038/nsmb.3146. Epub 2015 Dec 14. PMC4752824
  8. Hubin EA, Tabib-Salazar A, Humphrey LJ, Flack JE, Olinares PD, Darst SA, Campbell EA, Paget MS. “Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA.” Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7171-6. doi: 10.1073/pnas.1504942112. Epub 2015 May 26. PMC4466734
  9. Kleiner RE, Verma P, Molloy KR, Chait BT, Kapoor TM. “Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response.” Nat Chem Biol. 2015 Sep 7. doi: 10.1038/nchembio.1908. [Epub ahead of print] PMC4589150
  10. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. “Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.” Mol Cell. 2015 Sep 3;59(5):794-806. doi: 10.1016/j.molcel.2015.07.016. PMC4560838
  11. Morris DH, Yip CK, Shi Y, Chait BT, Wang QJ. “Beclin 1-VPS34 Complex Architecture: Understanding the Nuts and Bolts of Therapeutic Targets.” Front Biol (Beijing). 2015 Oct;10(5):398-426. Epub 2015 Nov 4. PMC4682202
  12. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. “Molecular architecture of the yeast Mediator complex.” Elife. 2015 Sep 24;4. pii: e08719. doi: 10.7554/eLife.08719. PMC4631838
  13. Sun J, Shi Y, Georgescu RE, Yuan Z, Chait BT, Li H, O’Donnell ME. “The architecture of a eukaryotic replisome.” Nat Struct Mol Biol. 2015 Dec;22(12):976-82. doi: 10.1038/nsmb.3113. Epub 2015 Nov 2. PMID: 26524492