| Hohn, M., Tang, G., Goodyear, G., Baldwin, P.R., Huang, Z., Penczek, P.A., Yang, Ch., Glaeser, R.M., Adams, P., Ludtke, S.J.: SPARX, a new environment for cryo-EM image processing. J. Struct. Biol., 157:47-55, 2007.
Pullan, L., Mullapudi, S., Huang, Z., Baldwin, P.R., Chin, Ch., Sun, W., Tsujimoto, S., Kolodziej, S., Stoops, J.K., Lee, J.C., Waxham, M.N., Bean, A.J., Penczek, P.A.: The endosome-associated protein Hrs is hexameric and controls cargo sorting as a "master molecule". Structure, 14:661-671, 2006.
Penczek, P.A., Frank, J., Spahn, Ch.M.T.: A method of focused classification, based on the bootstrap 3-D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol., 154: 184-194, 2006.
Penczek, P.A., Chao, Y., Frank, J., Spahn, Ch.M.T.: Estimation of variance in single particle reconstruction using the bootstrap technique. J. Struct. Biol., 154:168-183, 2006.
Schüler, M., Connell, S. R., Lescoute, A., Giesebrecht, J., Dabrowski, M., Schroeer, B., Mielke, T., Penczek, P. A., Westhof, E., Spahn, C. M. T.: Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat. Struct. Mol. Biol., 13:1092-1096, 2006.
Blau, M., Mullapudi, S., Becker, T., Dudek, J., Zimmermann, R., Penczek, P.A. and Beckmann, R.: ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane. Nature Structural and Molecular Biology, 12:1015-1016, 2005.
Grob, P., Cruse, M. J., Inouye, C., Peris, M., Penczek, P. A., Tjian, R., and Nogales, E.: Conformational flexibility of human TFIID revealed by cryo electron microscopy studies. Structure, 14:511-520, 2006.
Baldwin, P.R. and Penczek P.A.: Estimating alignment errors in sets of 2-D images. J. Struct. Biol., 150:211-225, 2005.
Yang, C., Ng, E.G. and Penczek P.A.: Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm. J. Struct. Biol., 149:53-64, 2005
Mullapudi, S., Pullan, L., Bishop, O. T., Khalil, H., Stoops, J. K., Beckmann, R., Kloetzel, P. M., Kruger, E. and Penczek, P. A.: Rearrangement of the 16S precursor subunits is essential for the formation of the active 20S proteasome. Biophysical J., 87:4098-4105, 2004.
Penczek, P.A., Renka, R. and Schomberg, H.: Gridding-based direct Fourier inversion of the three-dimensional ray transform. J. Opt. Soc. Am. A. 21:499-509, 2004.
Huang, Z. and Penczek, P.A.: Application of template matching technique to particle detection in electron micrographs. J. Struct. Biol. 145:29-40, 2004.
Joyeux, L. and Penczek, P.A.: Efficiency of 2D alignment methods. Ultramicroscopy 92:33-46, 2002.
Huang, Z., Baldwin, P.R., Mullapudi, S.R. and Penczek, P.A.: Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biol. 144:79-94, 2003.
Penczek, P.A.: Three-dimensional Spectral Signal-to-Noise Ratio for a class of reconstruction algorithms. J. Struct. Biol. 138:34-46, 2002.
Beckmann, R., Spahn, C. M. T., Eswar, N., Helmers, J., Penczek, P.A., Sali, A., Frank, J. and Blobel, G.: Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107:361-372, 2001.
Mouche, F., Boisset, N. and Penczek, P.A.: Lumbricus terrestris hemoglobin - the architecture of linker chains and structural variation of the central toroid. J. Struct. Biol. 133:176-192, 2001.
Spahn, Ch.M.T., Kieft, J.S., Grassucci, R.A., Penczek, P.A., Zhou, K., Doudna, J.A. and Frank, J.: Hepatitis C virus IRES RNA induced changes in the conformation of the 40S subunit. Science 291:1959-1962, 2001.
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