P. Penczek

发表

The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles.

J. Frank, P. Penczek, R. Grassucci, 1994, Ultramicroscopy.

A common-lines based method for determining orientations for N > 3 particle projections simultaneously.

J. Frank, P. Penczek, J. Zhu, 1996, Ultramicroscopy.

Resolution measures in molecular electron microscopy.

P. Penczek, 2010, Methods in enzymology.

Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution

J. Frank, P. Penczek, R. Grassucci, 2000, Cell.

Outcome of the First Electron Microscopy Validation Task Force Meeting

M. Baker, W. Chiu, A. Sali, 2012, Structure.

Three-dimensional cryoelectron microscopy of ribosomes.

J. Frank, P. Penczek, R. Grassucci, 2000, Methods in enzymology.

A Primer to Single-Particle Cryo-Electron Microscopy

P. Penczek, N. Grigorieff, Yifan Cheng, 2015, Cell.

A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation.

J. Frank, P. Penczek, C. Spahn, 2006, Journal of structural biology.

Double-tilt electron tomography.

J. Frank, M. Marko, K. Buttle, 1995, Ultramicroscopy.

Automatic particle selection: results of a comparative study.

D. Kriegman, M. Bern, C. Bajaj, 2004, Journal of structural biology.

GTPase activation of elongation factor EF‐Tu by the ribosome during decoding

Wei Zhang, Pawel A Penczek, Justus Loerke, 2009, The EMBO journal.

Structural Snapshots of Actively Translating Human Ribosomes

P. Penczek, T. Mielke, C. Spahn, 2015, Cell.

Structure of the F-actin–tropomyosin complex

William Lehman, Stefan Raunser, Pawel A. Penczek, 2014, Nature.

Three-dimensional reconstruction of single particles embedded in ice.

J Frank, J. Frank, M. Radermacher, 1992, Ultramicroscopy.

Overabundant single-particle electron microscope views induce a three- dimensional reconstruction artifact

Pawel A. Penczek, P. Penczek, N. Boisset, 1998 .

Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms.

Pawel A Penczek, P. Penczek, 2002, Journal of structural biology.

Automated determination of parameters describing power spectra of micrograph images in electron microscopy.

Pawel A Penczek, P. Penczek, P. Baldwin, 2003, Journal of structural biology.

Estimation of variance in single-particle reconstruction using the bootstrap technique.

Chao Yang, J. Frank, P. Penczek, 2006, Journal of Structural Biology.

Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.

Wei Zhang, Marek Kimmel, Pawel A Penczek, 2008, Structure.

Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM.

Pawel A Penczek, Christian M T Spahn, P. Penczek, 2009, Current opinion in structural biology.

Visualization of arrestin recruitment by a G Protein-Coupled Receptor

J. Qian, P. Penczek, G. Skiniotis, 2014, Nature.

Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA

J. Frank, P. Penczek, R. Grassucci, 1991, The Journal of cell biology.

Resolution in Electron Tomography

J. Frank, P. Penczek, 2007 .

Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome.

J. Frank, P. Penczek, J. Zhu, 1997, Journal of structural biology.

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation

J. Ballesta, J. Frank, P. Penczek, 2004, The EMBO journal.

A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome

J. Frank, M. Radermacher, A. Verschoor, 1995, Nature.

Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm.

Chao Yang, Pawel A Penczek, Esmond G Ng, 2005, Journal of structural biology.

Efficiency of 2 D alignment methods

Laurent Joyeux, Pawel A. Penczek, P. Penczek, 2002 .

Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images.

Marek Kimmel, Pawel A Penczek, Christian M T Spahn, 2011, Structure.

Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex.

F. Dimaio, Hao Wu, P. Penczek, 2016, Molecular cell.

Cryo-EMStructureofCaspase-8 TandemDEDFilament Reveals Assembly and RegulationMechanisms of the Death-Inducing Signaling Complex Graphical

F. Dimaio, P. Penczek, E. Egelman, 2016 .

Structure of the 80S Ribosome from Saccharomyces cerevisiae—tRNA-Ribosome and Subunit-Subunit Interactions

Narayanan Eswar, Andrej Sali, Joachim Frank, 2001, Cell.

A 9 Å Resolution X-Ray Crystallographic Map of the Large Ribosomal Subunit

Joachim Frank, Poul Nissen, Thomas A. Steitz, 1998, Cell.

Interaction of the mediator head module with RNA polymerase II.

P. Penczek, F. Asturias, J. Kovacs, 2012, Structure.

Automatic particle picking from electron micrographs.

J Frank, J. Frank, P. Penczek, 1995, Ultramicroscopy.

Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex.

J Frank, J. Frank, A. Verschoor, 1997, Science.

Automatic Particle Picking From Electron Micrographs

J. Frank, P. Penczek, R. Lata, 1995, Microscopy Today.

Utility of Butvar support film and methylamine tungstate stain in three-dimensional electron microscopy: agreement between stain and frozen-hydrated reconstructions.

P. Penczek, J. K. Stoops, S. Kolodziej, 1997, Journal of structural biology.

Membrane insertion of α-xenorhabdolysin in near-atomic detail

P. Penczek, I. Vetter, S. Raunser, 2018, bioRxiv.

Rubisco in complex with Rubisco large subunit methyltransferase

P. Penczek, T. Walz, S. Raunser, 2009, Proceedings of the National Academy of Sciences.

ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane

P. Penczek, T. Becker, R. Beckmann, 2005, Nature Structural &Molecular Biology.

Alternative reconstruction algorithm for NMR imaging

P. Franaszczuk, P. Penczek, K. Leszczynski, 1988, Medical and Biological Engineering and Computing.

MicroED with the Falcon III direct electron detector.

P. Penczek, T. Gonen, J. Hattne, 2019, IUCrJ.

3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound

P. Penczek, F. Asturias, K. Tsai, 2018, eLife.

Membrane insertion of α-xenorhabdolysin in near-atomic detail

P. Penczek, I. Vetter, S. Raunser, 2018, bioRxiv.

Reliable cryo-EM resolution estimation with modified Fourier shell correlation

P. Penczek, 2020, IUCrJ.

EFFECTS OF ANGULAR OVERSAMPLING IN THREE-DIMENSIONAL RECONSTRUCTION

P. Penczek, N. Boisset, J. Taveau, 2003 .

The internal compartmentation of rat‐liver mitochondria: Tomographic study using the high‐voltage transmission electron microscope

J Frank, M Marko, J. Frank, 1994, Microscopy research and technique.

The endosome-associated protein Hrs is hexameric and controls cargo sorting as a "master molecule".

M. Waxham, J. Lee, P. Penczek, 2006, Structure.

Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy

P. Penczek, N. Coudray, D. Stokes, 2012, Proceedings of the National Academy of Sciences.

Hepatitis C Virus IRES RNA-Induced Changes in the Conformation of the 40S Ribosomal Subunit

J Frank, P A Penczek, K. Zhou, 2001, Science.

Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proton-spin contrast-variation).

J. Frank, P. Penczek, K. Nierhaus, 1997, Journal of molecular biology.

Gridding-based direct Fourier inversion of the three-dimensional ray transform.

Pawel A Penczek, Hermann Schomberg, Robert Renka, 2004, Journal of the Optical Society of America. A, Optics, image science, and vision.

Variance in three-dimensional reconstructions from projections

P. A. Penczek, P. Penczek, 2002, Proceedings IEEE International Symposium on Biomedical Imaging.

Numerical representation of the structural pattern as a way to predict HPLC retention

P. Penczek, B. Radwanski, A. Bylina, 1983 .

Structure of the Rigor Actin-Tropomyosin-Myosin Complex

Stefan Raunser, Pawel A. Penczek, Dietmar J. Manstein, 2012, Cell.

Three‐dimensional cryo‐electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 Å resolution

J. Ballesta, J. Frank, P. Penczek, 2000, The EMBO journal.

SPARX, a new environment for Cryo-EM image processing.

Chao Yang, Robert M Glaeser, Steven J Ludtke, 2007, Journal of structural biology.

SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.

A Leith, J Frank, P Penczek, 1996, Journal of structural biology.

Quaternary structure of Octopus vulgaris hemocyanin. Three-dimensional reconstruction from frozen-hydrated specimens and intramolecular location of functional units Ove and Ovb.

J. Frank, P. Penczek, N. Boisset, 1994, Journal of molecular biology.

Iterative stable alignment and clustering of 2D transmission electron microscope images.

Pawel A Penczek, Jia Fang, Francisco J Asturias, 2012, Structure.

Lumbricus terrestris hemoglobin--the architecture of linker chains and structural variation of the central toroid.

N Boisset, P A Penczek, P. Penczek, 2001, Journal of structural biology.

Image restoration in cryo-electron microscopy.

Pawel A Penczek, P. Penczek, 2010, Methods in enzymology.

Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation.

J Frank, J. Frank, P. Penczek, 1998, Proceedings of the National Academy of Sciences of the United States of America.

A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome.

J. Frank, M. Radermacher, A. Verschoor, 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy

David Baker, Frank DiMaio, Pawel A Penczek, 2015, Proceedings of the National Academy of Sciences.

Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.

P. Penczek, T. Walz, E. Egelman, 2014, Molecular cell.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

Markus Stabrin, Stefan Raunser, Felipe Merino, 2017, Journal of visualized experiments : JoVE.

Fundamentals of three-dimensional reconstruction from projections.

Pawel A Penczek, P. Penczek, 2010, Methods in enzymology.

Ab initio cryo-EM structure determination as a validation problem

Pawel A. Penczek, Francisco J. Asturias, P. Penczek, 2014, 2014 IEEE International Conference on Image Processing (ICIP).

Architecture of the Protein-Conducting Channel Associated with the Translating 80S Ribosome

A. Sali, J. Frank, P. Penczek, 2001, Cell.

1 Supplemental Information

Paul C. Whitford, Karissa Y. Sanbonmatsu, Pawel A. Penczek, 2008 .

CTER-rapid estimation of CTF parameters with error assessment.

Pawel A Penczek, Jia Fang, Xueming Li, 2014, Ultramicroscopy.

Structural organization of the anaphase-promoting complex bound to the mitotic activator Slp1.

Pawel A Penczek, Thomas Walz, Yifan Cheng, 2007, Molecular cell.

Application of template matching technique to particle detection in electron micrographs.

Pawel A Penczek, Zhong Huang, P. Penczek, 2004, Journal of structural biology.

A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.

J. Frank, P. Penczek, A. Leith, 2000, Structure.

Real-space processing of helical filaments in SPARX.

Guozhi Tao, Stefan Raunser, Pawel A Penczek, 2012, Journal of structural biology.

The Transform Class in SPARX and EMAN2.

Pawel A Penczek, P R Baldwin, P. Penczek, 2007, Journal of structural biology.

Escherichia coli 70 S ribosome at 15 A resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein.

J Frank, J. Frank, P. Penczek, 1998, Journal of molecular biology.

Hepatitis C Virus IRES RNA—Induced Changes in the Conformation of the 40S

Jennifer A. Doudna, Joachim Frank, Pawel A. Penczek, 2001 .

Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome

J. Frank, P. Penczek, R. Grassucci, 1996, Science.

Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.

Pawel A Penczek, Robert Tjian, Carla Inouye, 2006, Structure.

EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome

Joachim Frank, Amy B. Heagle, Rajendra K. Agrawal, 1999, Nature Structural Biology.

MyD88 Death-Domain Oligomerization Determines Myddosome Architecture: Implications for Toll-like Receptor Signaling

D. Klenerman, P. Penczek, N. Gay, 2020, Structure.

Visualization of Trna Movements on the Escherichia coli 70s Ribosome during the Elongation Cycle

Joachim Frank, Rajendra K. Agrawal, J. Frank, 2000, The Journal of cell biology.

Cryoelectron Microscopy and Image Analysis of the Cardiac Ryanodine Receptor*

T. Wagenknecht, P. Penczek, S. Fleischer, 1998, The Journal of Biological Chemistry.

Effect of Buffer Conditions on the Position of tRNA on the 70 S Ribosome As Visualized by Cryoelectron Microscopy*

J. Frank, P. Penczek, R. Grassucci, 1999, The Journal of Biological Chemistry.

Arrangement of the Respiratory Chain Complexes in Saccharomyces cerevisiae Supercomplex III2IV2 Revealed by Single Particle Cryo-Electron Microscopy*

P. Penczek, W. Dowhan, E. Mileykovskaya, 2012, The Journal of Biological Chemistry.

Structure of the ribosome-bound cricket paralysis virus IRES RNA

Eric Westhof, E. Westhof, P. Penczek, 2006, Nature Structural &Molecular Biology.

Three-dimensional reconstruction of Androctonus australis hemocyanin labeled with a monoclonal Fab fragment.

J. Frank, P. Penczek, N. Boisset, 1995, Journal of structural biology.

Three-dimensional Architecture of Human α2-Macroglobulin Transformed with Methylamine

Joachim Frank, Pawel A. Penczek, J. Frank, 1993 .

Efficiency of 2D alignment methods.

Laurent Joyeux, Pawel A Penczek, P. Penczek, 2002, Ultramicroscopy.

Estimating alignment errors in sets of 2-D images.

Pawel A Penczek, P R Baldwin, P. Penczek, 2005, Journal of structural biology.

Estimating alignment errors in sets of images

Philip Baldwin, Pawel Penczek, P. Penczek, 2004, 2004 2nd IEEE International Symposium on Biomedical Imaging: Nano to Macro (IEEE Cat No. 04EX821).

Automatic Particle Picking From Electron Micrographs

Joachim Frank, Pawel A. Penczek, J. Frank, 1995, Microscopy Today.

Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice.

J Frank, J. Frank, P. Penczek, 1996, Journal of molecular biology.

A marker-free alignment method for electron tomography.

J Frank, Y Liu, P A Penczek, 1995, Ultramicroscopy.

Haloarcula marismortui 50S subunit-complementarity of electron microscopy and X-Ray crystallographic information.

J Frank, J. Frank, P. Penczek, 1999, Journal of structural biology.

The Ribosome - Three-Dimensional Structure and Ligand-Binding Studies

P. Penczek, R. Grassucci, I. Gabashvili, 1998, Microscopy and Microanalysis.

Cryo-Electron Microscopy of the Translational Apparatus: Experimental Evidence for the Paths of mRNA, tRNA, and the Polypeptide Chain

J. Frank, P. Penczek, R. Grassucci, 2000 .

Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy.

J. Frank, P. Penczek, R. Grassucci, 1999, Structure.

Rearrangement of the 16S precursor subunits is essential for the formation of the active 20S proteasome.

P. Kloetzel, P. Penczek, E. Krüger, 2004, Biophysical journal.

Alignment, classification, and three-dimensional reconstruction of single particles embedded in ice.

J Frank, P Penczek, W Liu, 1992, Scanning microscopy. Supplement.

Functional Interpretation of the Cryo-Electron Microscopy Map of the 30S Ribosomal Subunit from Escherichia coli

D. Case, S. Harvey, J. Frank, 2000 .

Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.

J. Frank, P. Penczek, R. Grassucci, 2001, Molecular cell.

Conformational Heterogeneity of Macromolecules Analyzed by Cryo-Electron Microscopy

J. Frank, P. Penczek, C. Spahn, 2006, Microscopy and Microanalysis.

On the correction of the contrast transfer function in biological electron microscopy

Joachim Frank, Pawel A. Penczek, J. Frank, 1995 .

Three-dimensional reconstruction of a complex of human alpha 2-macroglobulin with monomaleimido Nanogold (Au1.4nm) embedded in ice.

J. Frank, P. Penczek, R. Grassucci, 1992, Journal of structural biology.

The parallelization of SPIDER on distributed-memory computers using MPI.

Chao Yang, Robert M Glaeser, Joachim Frank, 2007, Journal of structural biology.

Three-dimensional architecture of human alpha 2-macroglobulin transformed with methylamine.

J. Frank, P. Penczek, N. Boisset, 1993, Journal of molecular biology.

The Structure of The 70S E. Coli Rtoosome In Ice

J. Frank, P. Penczek, S. Srivastava, 1990 .

EMAN2: Software for Image Analysis and Single Particle Reconstruction

Steven J. Ludtke, Chao Yang, Wen Jiang, 2006, Microscopy and Microanalysis.

Structure-Function Relationships of the Saccharomyces cerevisiae Fatty Acid Synthase

P. Penczek, J. K. Stoops, J. P. Schroeter, 1996, The Journal of Biological Chemistry.

A Primer to Single-Particle Cryo-Electron Microscopy

P. Penczek, N. Grigorieff, Yifan Cheng, 2015, Cell.

MicroED with the Falcon III direct electron detector

P. Penczek, T. Gonen, J. Hattne, 2019, bioRxiv.

Iterative stable alignment and clustering of 2D transmission electron microscope images.

P. Penczek, F. Asturias, J. Chittuluru, 2012, Structure.

Real-space processing of helical filaments in SPARX.

P. Penczek, E. Egelman, D. Stokes, 2012, Journal of structural biology.