Publications: 2007 - NCMI - Baylor College of Medicine

NCMI Publication List 2007-2008

Core

Booth, C. R., J. Jakana, and W. Chiu (2006). Assessing the capabilities of a 4kx4k CCD camera for electron cryo-microscopy at 300kV. J Struct Biol 156:556-563.
Tang, G., L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees, and S.J. Ludtke (2007). EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 157(1): p. 38-46.
Baker, M. L., Jiang, W., Wedemeyer, W. J., Rixon, F. J., Baker, D. and Chiu, W. (2006). Ab initio modeling of the Herpesvirus VP26 core domain assessed by cryoEM density. PLoS Comput Biol 2(11): e146.
Hohn, M., G. Tang, G. Goodyear, P.R. Baldwin, Z. Huang, P.A. Penczek, C. Yang, R.M. Glaeser, P.D. Adams, and S.J. Ludtke (2007). SPARX, a new environment for Cryo-EM image processing. J Struct Biol 157(1): p. 47-55.
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: 432-441.
Baker, M.L., Ju, T. and Chiu, W. (2007). Identification of secondary structure elements in intermediate resolution density maps. Structure, 15:7-19.
Ju, T., Baker, M.L. and Chiu, W. (2007). Computing a family of skeletons of volumetric models for shape description. Computer-AIDED Design, 39:352-360.
Liu, X., Jiang, W., Jakana, J. and Chiu, W. (2007). Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-path Simulated Annealing optimization algorithm. J Struct Biol, in press.
Michael P. Marsh, Juan T. Chang, Christopher R. Booth, Nathan L. Liang, Michael F. Schmid, Wah Chiu (2007). Modular software platform for low-dose electron microscopy and tomography. J Mirosc in press.
Chen, D.H., Jakana, J. and Chiu, W. (2007). Cryo-EM Data Collected on a 300-kV Liquid Helium-Cooled Electron Cryomicroscope. J Chinese Elect Microsc, in press.
Abeysinghe, S., Ju, T., Baker, M.L., Chiu, W. (2007) Shape modeling and matching in identifying protein structure from low-resolution images. ACM Symposium on Solid and Physical Modeling. in press

Collaboration

Chen, D. H., Song, J. L., Chuang, D. T., Chiu, W. & Ludtke, S. J. (2006). An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate. Structure 14: 1711-22.
Schmid, M. F., Paredes, A. M., Khant, H. A., Soyer, F., Aldrich, H. C., Chiu, W. & Shively, J. M. (2006). Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J Mol Biol 364: 526-535.
Marsh, M. P., Campos, S. K., Baker, M. L., Chen, C. Y., Chiu, W. & Barry, M. A. (2006). Cryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX. J Virol 80: 11881-6.
Jiang, X., H. Jayaram, M. Kumar, S.J. Ludtke, M.K. Estes, and B.V. Prasad (2006). Cryoelectron microscopy structures of rotavirus NSP2-NSP5 and NSP2-RNA complexes: implications for genome replication. J Virol 80(21): p. 10829-35.
Chang, J., M. F. Schmid, F. Rixon, and Chiu, W. (2007). Electron cryo-tomography reveals the portal in the herpesvirus capsid. J Virol, 81: 2065-2068.
Pope, W. H., Weigele, P. R., Chang, J., Pedulla, M. L., Ford, M. E., Houtz, J. M., Jiang, W., Chiu, W., Hatfull, G. F., Hendrix, R. W. & King, J. (2007). Genome sequence, structural proteins, and capsid organization of the cyanophage syn5: A "horned" bacteriophage of marine Synechococcus. J Mol Biol, 368: 966-81.
Bello, M., Ju, T., Carson, J., Warren, J., Chiu, W. and Kakadiaris, I.A. (2007). Learning-based segmentation framework for tissue images containing gene expression data. IEEE Trans on Med Imaging, 26: 728-44.
Reissmann, S., C. Parnot, C.R. Booth, W. Chiu, and J. Frydman (2007). Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins. Nat Struct Mol Biol 14: 432-40.

Dissemination

Jiang, W. and Chiu, W. (2006). Cryoelectron microscopy of icosahedral virus particles. In: Methods in Mol Biol. Ed. J. Kuo, The Humana Press, Totowa, NJ, 369, 345-363.
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, 79: 407-35.
Johnson, J.E. and Chiu, W. (2007). DNA packaging and delivery machines in tailed bacteriophages. Curr Opin Struct Biol, 17: 237-43.
Glaeser, R.M., Downing, K., DeRosier, D., Chiu, W. and Frank, J. (2007). Electron crystallography of biological macromolecules. Oxford University Press, N.Y., N.Y.
Chiu, W, Chang, J and Rixon, F (2008). Cryoelectron Microscopy. Encyclopedia of Virology, Elsevier Ltd., in press.
Baker, M.L., Zhou, Z.H., Chiu, W. (2007) Structure of Phytoreoviruses. Ed. M.L. Nibert, Horizon Scientific Press, UK in press