NCMI Publication List 2006-2007
Core
- Topf, M., Baker, M. L., Marti-Renom, M. A., Chiu, W. & Sali, A. (2006). Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J Mol Biol 357: 1655-68. pdf
- Hohn, M., Tang, G., Goodyear, G., Baldwin, P.R., Huang, Z., Penczek, P.A., Yang, C., Glaeser, R.M, Adams, P.D., and Ludtke, S.J. (2007). SPARX, a new environment for Cryo-EM image processing. J Struct Biol. 157: 47-55. pdf
- Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., and Ludtke, S. J. (2007). EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol. 157: 38-46. pdf
- Baker, M.L., Z. Yu, W. Chiu, and C. Bajaj. (2006). Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J Struct Biol. 156: 432-41 pdf
- Ju, T., J. Warren, J. Carson, M. Bello, I. Kakadiaris, W. Chiu, C. Thaller, and G. Eichele. (2006). 3D volume reconstruction of a mouse brain from histological sections using warp filtering. J Neurosci Methods 156: 84-100. pdf
- Ju, T., Baker, M.L. and Chiu, W. (2006). Computing a family of skeletons of volumetric models for shape description. Proc Geometric Modeling and Processing. In press.
- Steven J. Ludtke, Dong-Hua Chen, Jiu-Li Song, David T. Chuang and Wah Chiu (2006) Structure of GroEL at 4.5 Å resolution by CryoEM and Single Particle Reconstruction. Biophysical Society Meeting, Feb., Salt Lake City.
- Grant Tang, Liwei Peng , Deepy Mann , Philip R. Baldwin , Wah Chiu , Steven J. Ludtke (2006). EMAN2: A New Software Suite for Image Analysis and Single Particle. Reconstruction, Microscopy & Microanalysis Aug 2006, Chicago.
- Haili Tu, Wah Chiu, Deepy Mann and Steven J. Ludtke (2006). EMEN2: A Flexible and Mineable Data/Metadata Archival System for CryoEM. Microscopy & Microanalysis, Aug 2006, Chicago.
Collaboration
- Baker, M. L., Jiang, W., Rixon, F. J. & Chiu, W. (2005). Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol 79: 14967-70. pdf
- Paredes, A., Weaver, S., Watowich, S. and Chiu, W. (2005). Structural biology of old world and new world alphaviruses. Arch Virol Suppl 19: 179-85.
- Passmore, L. A., Booth, C. R., Venien-Bryan, C., Ludtke, S. J., Fioretto, C., Johnson, L. N., Chiu, W., and Barford, D. (2005). Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation. Mol Cell 20: 855-66. pdf
- Arac, D., Chen, X., Khant, H. A., Ubach, J., Ludtke, S. J., Kikkawa, M., Johnson, A. E., Chiu, W., Sudhof, T. C., and Rizo, J. (2006). Close membrane-membrane proximity induced by Ca(2+)-dependent multivalent binding of synaptotagmin-1 to phospholipids. Nat Struct Mol Biol 13: 209-217. pdf
- Jiang, W., Chang, J., Jakana, J. Weigele, P., King, J. and Chiu, W. (2006). Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature 439: 612-6. pdf
- Chang, J., Weigele, P., King, J., Chiu, W., and Jiang, W. (2006). Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure 14: 1073-1082. pdf
- Schmid, Michael F., Paredes, Angel M., Khant, Htet A., Soyer, Ferda, Chiu, Wah and Shively, Jessup M. (2006). Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J Mol Biol. 364: 526-35 pdf
- Monnier, N., Higo-Moriguchi, K., Sun, Z. Y. J., Prasad, B.V.V., Taniguchi, K., and Dormitzer, P.R. (2006). High-resolution molecular and antigen structure of the VP8* core of a sialic acid-independent human rotavirus strain. J Virol 80: 1513-1523. pdf
- Jiang, X., Kumar, M., Jayaram, H., Ludtke, S. Estes, M.K., and Prasad, B.V.V. (2006). Cryo-EM structures of rotavirus NSP2-NSP5 and NSP2-RNA complexes: Implication fro genome replication. J Virol. 80: 10829-35 pdf
- Michael P. Marsh, Samuel K. Campos, Matthew L. Baker, Christopher Y. Chen, Wah Chiu, and Michael A. Barry (2006) CryoEM of Protein IX-Modified Adenoviruses Suggests a New Position for the C-terminus of Protein IX. J Virol. 80: 11881-6 pdf
Dissemination
- Chiu, W., Baker, M.L. and Almo, S.C. (2006). Structural biology of cellular machines. Trends Cell Biol 16: 144-50.
- Chiu, W., Chen., D., Jakana, J., Chang, J., Jiang, W., Ludtke, S.L. and M.L. Baker. (2006). Visualization of biological nano-machines at subnanometer resolutions. JEOL News 41: 12-17.
- Berman, H.M., S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack, Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, and J.D. Westbrook. 2006. Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14: 1211-7.
- Serysheva, I. I., Chiu, W. and Ludtke, S.J. (2007). Single particle electron cryomicroscopy of the ion channels in the excitation-contraction coupling junction. Methods in Cell Biol, Cellular Electron Microscopy, J. R. McIntosh (ed), Academic Press, San Diego, CA. Vol 79: 407-35.
- Jiang, W. and Chiu, W. (2007). Cryoelectron microscopy of icosahedral virus particles. Methods in Mol Biol, Electron Microscopy, Methods and Protocols. (2nd Ed). J. Kuo (ed), The Humana Press, Totowa, NJ. Vol 369: in press.
