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Timothy Baker

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentMolecular Biology
Address9500 Gilman Drive #0378
La Jolla CA 92093
Phone858-534-5845
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    Collapse Research 
    Collapse Research Activities and Funding
    Parallel Software for Fast, Automated Determination of Virus Structures
    NIH/NIGMS R01GM087708Jun 1, 2010 - May 31, 2014
    Role: Principal Investigator
    Parallel Software for Fast, Automated Determination of Virus Structures
    NIH/NIAID R56AI079095May 15, 2009 - Apr 30, 2010
    Role: Principal Investigator
    Transmission Electron Microscope
    NIH/NCRR S10RR020016Jul 15, 2004 - Jul 14, 2005
    Role: Principal Investigator
    National Resource for Automated Molecular Microscopy
    NIH P41RR017573Sep 30, 2002 - Jul 31, 2012
    Role: Co-Investigator
    Virus Assembly and Transmission
    NIH P01AI045976Sep 1, 1999 - Jul 31, 2010
    Role: Co-Investigator
    STRUCTURAL BASIS FOR VIRAL INFECTION
    NIH P01AI035212Jan 1, 1994 - Dec 31, 1998
    Role: Co-Investigator
    THREE-DIMENSIONAL ELECTRON MICROSCOPY OF MACROMOLECULES
    NIH/NIGMS R13GM049914Jun 25, 1993 - Jun 24, 1994
    Role: Principal Investigator
    Microscopy & Image Analysis of Unstained Macromolecules
    NIH/NIGMS R01GM033050Jun 1, 1983 - May 31, 2018
    Role: Principal Investigator
    Microscopy &Image Analysis of Unstained Macromolecules
    NIH/NIGMS R37GM033050Jun 1, 1983 - Mar 31, 2014
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. McNulty R, Cardone G, Gilcrease EB, Baker T, Casjens SR, Johnson JE. Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release. Biophys J. 2018 Mar 27; 114(6):1295-1301. PMID: 29590587.
      View in: PubMed
    2. Pittman N, Misseldine A, Geilen L, Halder S, Smith JK, Kurian J, Chipman P, Janssen M, Mckenna R, Baker T, D'Abramo A, Cotmore S, Tattersall P, Agbandje-McKenna M. Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction. Viruses. 2017 10 30; 9(11). PMID: 29084163.
      View in: PubMed
    3. Li Z, Wang D, Gu Y, Song S, He M, Shi J, Liu X, Wei S, Li J, Yu H, Zheng Q, Yan X, Baker T, Zhang J, McLellan JS, Li S, Xia N. Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus. MBio. 2017 Sep 26; 8(5). PMID: 28951471.
      View in: PubMed
    4. Xu L, Zheng Q, Li S, He M, Wu Y, Li Y, Zhu R, Yu H, Hong Q, Jiang J, Li Z, Li S, Zhao H, Yang L, Hou W, Wang W, Ye X, Zhang J, Baker T, Cheng T, Zhou ZH, Yan X, Xia N. Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody. Nat Commun. 2017 09 11; 8(1):505. PMID: 28894095.
      View in: PubMed
    5. Mietzsch M, Kailasan S, Garrison J, Ilyas M, Chipman P, Kantola K, Janssen ME, Spear J, Sousa D, McKenna R, Brown K, Söderlund-Venermo M, Baker T, Agbandje-McKenna M. Structural Insights into Human Bocaparvoviruses. J Virol. 2017 06 01; 91(11). PMID: 28331084.
      View in: PubMed
    6. Drouin LM, Lins B, Janssen M, Bennett A, Chipman P, McKenna R, Chen W, Muzyczka N, Cardone G, Baker T, Agbandje-McKenna M. Cryo-electron Microscopy Reconstruction and Stability Studies of the Wild Type and the R432A Variant of Adeno-associated Virus Type 2 Reveal that Capsid Structural Stability Is a Major Factor in Genome Packaging. J Virol. 2016 10 01; 90(19):8542-51. PMID: 27440903; PMCID: PMC5021403 [Available on 03/12/17].
    7. Li Z, Yan X, Yu H, Wang D, Song S, Li Y, He M, Hong Q, Zheng Q, Zhao Q, Gu Y, Zhang J, Janssen ME, Cardone G, Olson NH, Baker T, Li S, Xia N. The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction. Structure. 2016 06 07; 24(6):874-85. PMID: 27276427.
      View in: PubMed
    8. Suzuki Y, Cardone G, Restrepo D, Zavattieri PD, Baker T, Tezcan FA. Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals. Nature. 2016 05 19; 533(7603):369-73. PMID: 27135928; PMCID: PMC4991361 [Available on 11/02/16].
    9. Jose J, Tang J, Taylor AB, Baker T, Kuhn RJ. Fluorescent Protein-Tagged Sindbis Virus E2 Glycoprotein Allows Single Particle Analysis of Virus Budding from Live Cells. Viruses. 2015 Nov 27; 7(12):6182-99. PMID: 26633461; PMCID: PMC4690852.
    10. Chen LS, Hung RJ, Baker T, Horton A, Culverhouse R, Saccone N, Cheng I, Deng B, Han Y, Hansen HM, Horsman J, Kim C, Lutz S, Rosenberger A, Aben KK, Andrew AS, Breslau N, Chang SC, Dieffenbach AK, Dienemann H, Frederiksen B, Han J, Hatsukami DK, Johnson EO, Pande M, Wrensch MR, McLaughlin J, Skaug V, van der Heijden HF, Wampfler J, Wenzlaff A, Woll P, Zienolddiny S, Bickeböller H, Brenner H, Duell EJ, Haugen A, Heinrich J, Hokanson JE, Hunter DJ, Kiemeney LA, Lazarus P, Le Marchand L, Liu G, Mayordomo J, Risch A, Schwartz AG, Teare D, Wu X, Wiencke JK, Yang P, Zhang ZF, Spitz MR, Kraft P, Amos CI, Bierut LJ. CHRNA5 risk variant predicts delayed smoking cessation and earlier lung cancer diagnosis--a meta-analysis. J Natl Cancer Inst. 2015 May; 107(5). PMID: 25873736; PMCID: PMC4822525.
    11. Tseng YS, Gurda BL, Chipman P, McKenna R, Afione S, Chiorini JA, Muzyczka N, Olson NH, Baker T, Kleinschmidt J, Agbandje-McKenna M. Adeno-associated virus serotype 1 (AAV1)- and AAV5-antibody complex structures reveal evolutionary commonalities in parvovirus antigenic reactivity. J Virol. 2015 Feb; 89(3):1794-808. PMID: 25410874; PMCID: PMC4300747.
    12. Janssen ME, Takagi Y, Parent KN, Cardone G, Nibert ML, Baker T. Three-dimensional structure of a protozoal double-stranded RNA virus that infects the enteric pathogen Giardia lamblia. J Virol. 2015 Jan 15; 89(2):1182-94. PMID: 25378500; PMCID: PMC4300635.
    13. Parent KN, Tang J, Cardone G, Gilcrease EB, Janssen ME, Olson NH, Casjens SR, Baker T. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain. Virology. 2014 Sep; 464-465:55-66. PMID: 25043589; PMCID: PMC4157081.
    14. Xiao X, Cheng J, Tang J, Fu Y, Jiang D, Baker T, Ghabrial SA, Xie J. A novel partitivirus that confers hypovirulence on plant pathogenic fungi. J Virol. 2014 Sep 01; 88(17):10120-33. PMID: 24965462; PMCID: PMC4136314.
    15. Tang J, Kearney BM, Wang Q, Doerschuk PC, Baker T, Johnson JE. Dynamic and geometric analyses of Nudaurelia capensis ? virus maturation reveal the energy landscape of particle transitions. J Mol Recognit. 2014 Apr; 27(4):230-7. PMID: 24591180; PMCID: PMC3987702.
    16. Parent KN, Erb ML, Cardone G, Nguyen K, Gilcrease EB, Porcek NB, Pogliano J, Baker T, Casjens SR. OmpA and OmpC are critical host factors for bacteriophage Sf6 entry in Shigella. Mol Microbiol. 2014 Apr; 92(1):47-60. PMID: 24673644; PMCID: PMC4034267.
    17. Yan X, Cardone G, Zhang X, Zhou ZH, Baker T. Single particle analysis integrated with microscopy: a high-throughput approach for reconstructing icosahedral particles. J Struct Biol. 2014 Apr; 186(1):8-18. PMID: 24613762; PMCID: PMC4070310.
    18. Cardone G, Yan X, Sinkovits RS, Baker T. A Real-Time 3D Reconstruction System for Screening Icosahedral Particles Under Different Conditions at the Microscope. Microsc Microanal. 2013 Aug; 19(Suppl 2):764-765. PMID: 25242888.
      View in: PubMed
    19. Cardone G, Yan X, Sinkovits RS, Tang J, Baker T. Three-dimensional reconstruction of icosahedral particles from single micrographs in real time at the microscope. J Struct Biol. 2013 Sep; 183(3):329-341. PMID: 23891839; PMCID: PMC3831522.
    20. Gurda BL, DiMattia MA, Miller EB, Bennett A, McKenna R, Weichert WS, Nelson CD, Chen WJ, Muzyczka N, Olson NH, Sinkovits RS, Chiorini JA, Zolotutkhin S, Kozyreva OG, Samulski RJ, Baker T, Parrish CR, Agbandje-McKenna M. Capsid antibodies to different adeno-associated virus serotypes bind common regions. J Virol. 2013 Aug; 87(16):9111-24. PMID: 23760240; PMCID: PMC3754064.
    21. Parent KN, Takagi Y, Cardone G, Olson NH, Ericsson M, Yang M, Lee Y, Asara JM, Fichorova RN, Baker T, Nibert ML. Structure of a protozoan virus from the human genitourinary parasite Trichomonas vaginalis. MBio. 2013 Apr 02; 4(2). PMID: 23549915; PMCID: PMC3622925.
    22. Dunn SE, Li H, Cardone G, Nibert ML, Ghabrial SA, Baker T. Three-dimensional structure of victorivirus HvV190S suggests coat proteins in most totiviruses share a conserved core. PLoS Pathog. 2013 Mar; 9(3):e1003225. PMID: 23516364; PMCID: PMC3597494.
    23. Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker T, Schulten K, Zheng D, Pang H, Sun F. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. PLoS Pathog. 2013 Jan; 9(1):e1003132. PMID: 23341770; PMCID: PMC3547835.
    24. Nibert ML, Tang J, Xie J, Collier AM, Ghabrial SA, Baker T, Tao YJ. 3D structures of fungal partitiviruses. Adv Virus Res. 2013; 86:59-85. PMID: 23498903.
      View in: PubMed
    25. Ghabrial SA, Dunn SE, Li H, Xie J, Baker T. Viruses of Helminthosporium (Cochlioblus) victoriae. Adv Virus Res. 2013; 86:289-325. PMID: 23498911.
      View in: PubMed
    26. Gurda BL, Raupp C, Popa-Wagner R, Naumer M, Olson NH, Ng R, McKenna R, Baker T, Kleinschmidt JA, Agbandje-McKenna M. Mapping a neutralizing epitope onto the capsid of adeno-associated virus serotype 8. J Virol. 2012 Aug; 86(15):7739-51. PMID: 22593150; PMCID: PMC3421660.
    27. Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker T, Teschke CM. Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials. 2012 Aug; 33(22):5628-37. PMID: 22575828; PMCID: PMC3358469.
    28. DiMattia MA, Nam HJ, Van Vliet K, Mitchell M, Bennett A, Gurda BL, McKenna R, Olson NH, Sinkovits RS, Potter M, Byrne BJ, Aslanidi G, Zolotukhin S, Muzyczka N, Baker T, Agbandje-McKenna M. Structural insight into the unique properties of adeno-associated virus serotype 9. J Virol. 2012 Jun; 86(12):6947-58. PMID: 22496238; PMCID: PMC3393551.
    29. Brodin JD, Ambroggio XI, Tang C, Parent KN, Baker T, Tezcan FA. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat Chem. 2012 Mar 04; 4(5):375-82. PMID: 22522257; PMCID: PMC3335442.
    30. Parent KN, Gilcrease EB, Casjens SR, Baker T. Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures. Virology. 2012 Jun 05; 427(2):177-88. PMID: 22386055; PMCID: PMC3320033.
    31. Tang J, Jose J, Chipman P, Zhang W, Kuhn RJ, Baker T. Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus. J Mol Biol. 2011 Dec 02; 414(3):442-59. PMID: 22001018; PMCID: PMC3407685.
    32. Dunn SE, Li H, Nibert ML, Ghabrial SA, Baker T. Electron Cryo-Microscopy Studies of Helminthosporium victoriae Virus 190S. Microsc Microanal. 2011 Jul; 17(Suppl 2):134-135. PMID: 25132801.
      View in: PubMed
    33. Yan X, Parent KN, Goodman RP, Tang J, Shou J, Nibert ML, Duncan R, Baker T. Virion structure of baboon reovirus, a fusogenic orthoreovirus that lacks an adhesion fiber. J Virol. 2011 Aug; 85(15):7483-95. PMID: 21593159; PMCID: PMC3147939.
    34. Tang J, Lander GC, Olia AS, Olia A, Li R, Casjens S, Prevelige P, Cingolani G, Baker T, Johnson JE. Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22. Structure. 2011 Apr 13; 19(4):496-502. PMID: 21439834; PMCID: PMC3075339.
    35. Ku TH, Chien MP, Thompson MP, Sinkovits RS, Olson NH, Baker T, Gianneschi NC. Controlling and switching the morphology of micellar nanoparticles with enzymes. J Am Chem Soc. 2011 Jun 08; 133(22):8392-5. PMID: 21462979; PMCID: PMC3756928.
    36. Shen PS, Enderlein D, Nelson CD, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker T, Cheng RH, Atwood WJ, Johne R, Belnap DM. The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4. Virology. 2011 Mar 01; 411(1):142-52. PMID: 21239031; PMCID: PMC3057058.
    37. Parent KN, Sinkovits RS, Suhanovsky MM, Teschke CM, Egelman EH, Baker T. Cryo-reconstructions of P22 polyheads suggest that phage assembly is nucleated by trimeric interactions among coat proteins. Phys Biol. 2010 Dec 09; 7(4):045004. PMID: 21149969; PMCID: PMC3202341.
    38. Ng R, Govindasamy L, Gurda BL, McKenna R, Kozyreva OG, Samulski RJ, Parent KN, Baker T, Agbandje-McKenna M. Structural characterization of the dual glycan binding adeno-associated virus serotype 6. J Virol. 2010 Dec; 84(24):12945-57. PMID: 20861247; PMCID: PMC3004313.
    39. Suhanovsky MM, Parent KN, Dunn SE, Baker T, Teschke CM. Determinants of bacteriophage P22 polyhead formation: the role of coat protein flexibility in conformational switching. Mol Microbiol. 2010 Sep; 77(6):1568-82. PMID: 20659287; PMCID: PMC2945288.
    40. Tang J, Pan J, Havens WM, Ochoa WF, Guu TS, Ghabrial SA, Nibert ML, Tao YJ, Baker T. Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophys J. 2010 Jul 21; 99(2):685-94. PMID: 20643089; PMCID: PMC2905076.
    41. Tang J, Ochoa WF, Li H, Havens WM, Nibert ML, Ghabrial SA, Baker T. Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus. J Struct Biol. 2010 Dec; 172(3):363-71. PMID: 20599510; PMCID: PMC3664192.
    42. Gurda BL, Parent KN, Bladek H, Sinkovits RS, DiMattia MA, Rence C, Castro A, McKenna R, Olson N, Brown K, Baker T, Agbandje-McKenna M. Human bocavirus capsid structure: insights into the structural repertoire of the parvoviridae. J Virol. 2010 Jun; 84(12):5880-9. PMID: 20375175; PMCID: PMC2876641.
    43. Parent KN, Khayat R, Tu LH, Suhanovsky MM, Cortines JR, Teschke CM, Johnson JE, Baker T. P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks. Structure. 2010 Mar 10; 18(3):390-401. PMID: 20223221; PMCID: PMC2951021.
    44. Tang J, Sinkovits RS, Baker T. Three-dimensional asymmetric reconstruction of tailed bacteriophage. Methods Enzymol. 2010; 482:185-210. PMID: 20888962; PMCID: PMC3779122.
    45. Sinkovits RS, Baker T. A tale of two symmetrons: rules for construction of icosahedral capsids from trisymmetrons and pentasymmetrons. J Struct Biol. 2010 Apr; 170(1):109-16. PMID: 19963064; PMCID: PMC3834589.
    46. Tang J, Lee KK, Bothner B, Baker T, Yeager M, Johnson JE. Dynamics and stability in maturation of a T=4 virus. J Mol Biol. 2009 Sep 25; 392(3):803-12. PMID: 19627990; PMCID: PMC2766526.
    47. Cherrier MV, Kostyuchenko VA, Xiao C, Bowman VD, Battisti AJ, Yan X, Chipman PR, Baker T, Van Etten JL, Rossmann MG. An icosahedral algal virus has a complex unique vertex decorated by a spike. Proc Natl Acad Sci U S A. 2009 Jul 07; 106(27):11085-9. PMID: 19541619; PMCID: PMC2708736.
    48. Pan J, Dong L, Lin L, Ochoa WF, Sinkovits RS, Havens WM, Nibert ML, Baker T, Ghabrial SA, Tao YJ. Atomic structure reveals the unique capsid organization of a dsRNA virus. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4225-30. PMID: 19246376; PMCID: PMC2657383.
    49. Levy HC, Bowman VD, Govindasamy L, McKenna R, Nash K, Warrington K, Chen W, Muzyczka N, Yan X, Baker T, Agbandje-McKenna M. Heparin binding induces conformational changes in Adeno-associated virus serotype 2. J Struct Biol. 2009 Mar; 165(3):146-56. PMID: 19121398; PMCID: PMC3694330.
    50. Yan X, Yu Z, Zhang P, Battisti AJ, Holdaway HA, Chipman PR, Bajaj C, Bergoin M, Rossmann MG, Baker T. The capsid proteins of a large, icosahedral dsDNA virus. J Mol Biol. 2009 Jan 30; 385(4):1287-99. PMID: 19027752; PMCID: PMC2911444.
    51. Tang J, Ochoa WF, Sinkovits RS, Poulos BT, Ghabrial SA, Lightner DV, Baker T, Nibert ML. Infectious myonecrosis virus has a totivirus-like, 120-subunit capsid, but with fiber complexes at the fivefold axes. Proc Natl Acad Sci U S A. 2008 Nov 11; 105(45):17526-31. PMID: 18981418; PMCID: PMC2582295.
    52. Tang J, Olson N, Jardine PJ, Grimes S, Anderson DL, Baker T. DNA poised for release in bacteriophage phi29. Structure. 2008 Jun; 16(6):935-43. PMID: 18547525; PMCID: PMC2556148.
    53. Ochoa WF, Havens WM, Sinkovits RS, Nibert ML, Ghabrial SA, Baker T. Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. Structure. 2008 May; 16(5):776-86. PMID: 18462682; PMCID: PMC2556151.
    54. Yan X, Sinkovits RS, Baker T. AUTO3DEM--an automated and high throughput program for image reconstruction of icosahedral particles. J Struct Biol. 2007 Jan; 157(1):73-82. PMID: 17029842; PMCID: PMC1847775.
    55. Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker T, Lommel SA. Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol. 2006 Nov; 80(21):10395-406. PMID: 16920821; PMCID: PMC1641784.
    56. Yan X, Dryden KA, Tang J, Baker T. Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J Struct Biol. 2007 Jan; 157(1):211-25. PMID: 16979906; PMCID: PMC1919437.
    57. Mukhopadhyay S, Zhang W, Gabler S, Chipman PR, Strauss EG, Strauss JH, Baker T, Kuhn RJ, Rossmann MG. Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. Structure. 2006 Jan; 14(1):63-73. PMID: 16407066; PMCID: PMC2757649.
    58. Ji Y, Marinescu DC, Zhang W, Zhang X, Yan X, Baker T. A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures. J Struct Biol. 2006 Apr; 154(1):1-19. PMID: 16459100; PMCID: PMC4147871.
    59. Zhang X, Ji Y, Zhang L, Harrison SC, Marinescu DC, Nibert ML, Baker T. Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution. Structure. 2005 Oct; 13(10):1545-57. PMID: 16216585; PMCID: PMC4126556.
    60. Zhang X, Tang J, Walker SB, O'Hara D, Nibert ML, Duncan R, Baker T. Structure of avian orthoreovirus virion by electron cryomicroscopy and image reconstruction. Virology. 2005 Dec 05; 343(1):25-35. PMID: 16153672; PMCID: PMC4152769.
    61. Yan X, Chipman PR, Castberg T, Bratbak G, Baker T. The marine algal virus PpV01 has an icosahedral capsid with T=219 quasisymmetry. J Virol. 2005 Jul; 79(14):9236-43. PMID: 15994818; PMCID: PMC1168743.
    62. Padron E, Bowman V, Kaludov N, Govindasamy L, Levy H, Nick P, McKenna R, Muzyczka N, Chiorini JA, Baker T, Agbandje-McKenna M. Structure of adeno-associated virus type 4. J Virol. 2005 Apr; 79(8):5047-58. PMID: 15795290; PMCID: PMC1069529.
    63. Zhang W, Heil M, Kuhn RJ, Baker T. Heparin binding sites on Ross River virus revealed by electron cryo-microscopy. Virology. 2005 Feb 20; 332(2):511-8. PMID: 15680416; PMCID: PMC4152768.
    64. Zhang Y, Zhang W, Ogata S, Clements D, Strauss JH, Baker T, Kuhn RJ, Rossmann MG. Conformational changes of the flavivirus E glycoprotein. Structure. 2004 Sep; 12(9):1607-18. PMID: 15341726; PMCID: PMC4152830.
    65. Odegard AL, Chandran K, Zhang X, Parker JS, Baker T, Nibert ML. Putative autocleavage of outer capsid protein micro1, allowing release of myristoylated peptide micro1N during particle uncoating, is critical for cell entry by reovirus. J Virol. 2004 Aug; 78(16):8732-45. PMID: 15280481; PMCID: PMC479062.
    66. Kong Y, Zhang X, Baker T, Ma J. A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. J Mol Biol. 2004 May 21; 339(1):117-30. PMID: 15123425; PMCID: PMC4148645.
    67. Walters RW, Agbandje-McKenna M, Bowman VD, Moninger TO, Olson NH, Seiler M, Chiorini JA, Baker T, Zabner J. Structure of adeno-associated virus serotype 5. J Virol. 2004 Apr; 78(7):3361-71. PMID: 15016858; PMCID: PMC371067.
    68. Singh V, Marinescu DC, Baker T. Image segmentation for automatic particle identification in electron micrographs based on hidden Markov random field models and expectation maximization. J Struct Biol. 2004 Jan-Feb; 145(1-2):123-41. PMID: 15065680; PMCID: PMC4167639.
    69. Zhang X, Walker SB, Chipman PR, Nibert ML, Baker T. Reovirus polymerase lambda 3 localized by cryo-electron microscopy of virions at a resolution of 7.6 A. Nat Struct Biol. 2003 Dec; 10(12):1011-8. PMID: 14608373; PMCID: PMC4152824.
    70. Zhang W, Chipman PR, Corver J, Johnson PR, Zhang Y, Mukhopadhyay S, Baker T, Strauss JH, Rossmann MG, Kuhn RJ. Visualization of membrane protein domains by cryo-electron microscopy of dengue virus. Nat Struct Biol. 2003 Nov; 10(11):907-12. PMID: 14528291; PMCID: PMC4148076.
    71. Zhang Y, Corver J, Chipman PR, Zhang W, Pletnev SV, Sedlak D, Baker T, Strauss JH, Kuhn RJ, Rossmann MG. Structures of immature flavivirus particles. EMBO J. 2003 Jun 02; 22(11):2604-13. PMID: 12773377; PMCID: PMC156766.
    72. Nibert ML, Baker T. CPV, a stable and symmetrical machine for mRNA synthesis. Structure. 2003 Jun; 11(6):605-7. PMID: 12791245.
      View in: PubMed
    73. Bernal RA, Hafenstein S, Olson NH, Bowman VD, Chipman PR, Baker T, Fane BA, Rossmann MG. Structural studies of bacteriophage alpha3 assembly. J Mol Biol. 2003 Jan 03; 325(1):11-24. PMID: 12473449; PMCID: PMC4130226.
    74. Bowman VD, Chase ES, Franz AW, Chipman PR, Zhang X, Perry KL, Baker T, Smith TJ. An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons. J Virol. 2002 Dec; 76(23):12250-8. PMID: 12414964; PMCID: PMC136911.
    75. Kim J, Zhang X, Centonze VE, Bowman VD, Noble S, Baker T, Nibert ML. The hydrophilic amino-terminal arm of reovirus core shell protein lambda1 is dispensable for particle assembly. J Virol. 2002 Dec; 76(23):12211-22. PMID: 12414960; PMCID: PMC136864.
    76. Zhang W, Mukhopadhyay S, Pletnev SV, Baker T, Kuhn RJ, Rossmann MG. Placement of the structural proteins in Sindbis virus. J Virol. 2002 Nov; 76(22):11645-58. PMID: 12388725; PMCID: PMC136788.
    77. Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker T, Graves MV, Van Etten JL, Rossmann MG. The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):14758-63. PMID: 12411581; PMCID: PMC137492.
    78. Guasch A, Pous J, Ibarra B, Gomis-Rüth FX, Valpuesta JM, Sousa N, Carrascosa JL, Coll M, Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker T, Rossmann MG. Note to the Paper by Guasch et al. (2002) Detailed Architecture of a DNA Translocating Machine: The High-resolution Structure of the Bacteriophage ?29 Connector Particle. J Mol Biol. 2002 Aug 09; 321(2):379-380. PMID: 25308998.
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    79. He Y, Lin F, Chipman PR, Bator CM, Baker T, Shoham M, Kuhn RJ, Medof ME, Rossmann MG. Structure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex. Proc Natl Acad Sci U S A. 2002 Aug 06; 99(16):10325-9. PMID: 12119400; PMCID: PMC124913.
    80. Zhang W, Fisher BR, Olson NH, Strauss JH, Kuhn RJ, Baker T. Aura virus structure suggests that the T=4 organization is a fundamental property of viral structural proteins. J Virol. 2002 Jul; 76(14):7239-46. PMID: 12072523; PMCID: PMC136343.
    81. Luongo CL, Zhang X, Walker SB, Chen Y, Broering TJ, Farsetta DL, Bowman VD, Baker T, Nibert ML. Loss of activities for mRNA synthesis accompanies loss of lambda2 spikes from reovirus cores: an effect of lambda2 on lambda1 shell structure. Virology. 2002 Apr 25; 296(1):24-38. PMID: 12036315.
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    82. Kuhn RJ, Zhang W, Rossmann MG, Pletnev SV, Corver J, Lenches E, Jones CT, Mukhopadhyay S, Chipman PR, Strauss EG, Baker T, Strauss JH. Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell. 2002 Mar 08; 108(5):717-25. PMID: 11893341; PMCID: PMC4152842.
    83. Liemann S, Chandran K, Baker T, Nibert ML, Harrison SC. Structure of the reovirus membrane-penetration protein, Mu1, in a complex with is protector protein, Sigma3. Cell. 2002 Jan 25; 108(2):283-95. PMID: 11832217; PMCID: PMC4152834.
    84. Pletnev SV, Zhang W, Mukhopadhyay S, Fisher BR, Hernandez R, Brown DT, Baker T, Rossmann MG, Kuhn RJ. Locations of carbohydrate sites on alphavirus glycoproteins show that E1 forms an icosahedral scaffold. Cell. 2001 Apr 06; 105(1):127-136. PMID: 11301008; PMCID: PMC4140091.
    85. Ilang LL, Olson NH, Dokland T, Music CL, Cheng RH, Bowen Z, McKenna R, Rossmann MG, Baker T, Incardona NL. DNA packaging intermediates of bacteriophage phi X174. Structure. 1995 Apr 15; 3(4):353-363. PMID: 7613866; PMCID: PMC4142697.
    86. Rayment I, Baker T, Caspar DL. A Description of the Techniques and Application of Molecular Replacement Used to Determine the Structure of Polyoma Virus Capsid at 22.5 Å Resolution. Acta Crystallogr B. 1983 Aug; 39(4):505-516. PMID: 25242833.
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