Resource De Novo Structural Patter n Mining in Cellular Electron Cryotomograms Graphical

[1]  Frank Alber,et al.  Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell , 2018, Cell.

[2]  Frank Alber,et al.  TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis. , 2017, Structure.

[3]  Eric P. Xing,et al.  Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms , 2017, Bioinform..

[4]  Wei Dai,et al.  Convolutional Neural Networks for Automated Annotation of Cellular Cryo-Electron Tomograms , 2017, Nature Methods.

[5]  Min Xu,et al.  Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking , 2016, BMC Bioinformatics.

[6]  A. Hyman,et al.  Visualizing the molecular sociology at the HeLa cell nuclear periphery , 2016, Science.

[7]  Nassir Navab,et al.  Automatic particle picking and multi-class classification in cryo-electron tomograms , 2014, 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI).

[8]  Achilleas S Frangakis,et al.  M-free: scoring the reference bias in sub-tomogram averaging and template matching. , 2014, Journal of structural biology.

[9]  Grant J. Jensen,et al.  Correlated cryogenic photoactivated localization microscopy and electron cryotomography , 2014, Nature Methods.

[10]  J. Leadbetter,et al.  Structure and Expression of Propanediol Utilization Microcompartments in Acetonema longum , 2014, Journal of bacteriology.

[11]  V. Lučić,et al.  Cryo-electron tomography: The challenge of doing structural biology in situ , 2013, The Journal of cell biology.

[12]  Min Xu,et al.  Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms , 2013, Bioinform..

[13]  Yuxiang Chen,et al.  Fast and accurate reference-free alignment of subtomograms. , 2013, Journal of structural biology.

[14]  R. Snapp,et al.  Projection-based volume alignment. , 2013, Journal of structural biology.

[15]  J. Briggs.  Structural biology in situ--the potential of subtomogram averaging. , 2013, Current opinion in structural biology.

[16]  G. Sapiro,et al.  A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography. , 2013, Journal of structural biology.

[17]  Min Xu,et al.  High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization , 2012, BMC Systems Biology.

[18]  Frank Alber,et al.  High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. , 2012, Journal of structural biology.

[19]  Felix J. B. Bäuerlein,et al.  Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography , 2012, Proceedings of the National Academy of Sciences.

[20]  Ben M. Webb,et al.  Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies , 2012, PLoS biology.

[21]  John M Heumann,et al.  Clustering and variance maps for cryo-electron tomography using wedge-masked differences. , 2011, Journal of structural biology.

[22]  Min Xu,et al.  Template-free detection of macromolecular complexes in cryo electron tomograms , 2011, Bioinform..

[23]  A. Frangakis,et al.  Classification of electron sub-tomograms with neural networks and its application to template-matching. , 2011, Journal of structural biology.

[24]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[25]  Wah Chiu,et al.  Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. , 2010, Structure.

[26]  Hstau Y Liao,et al.  Definition and estimation of resolution in single-particle reconstructions. , 2010, Structure.

[27]  Lingbo Yu,et al.  Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data. , 2010, Journal of structural biology.

[28]  Harold W. Kuhn,et al.  The Hungarian method for the assignment problem , 1955, 50 Years of Integer Programming.

[29]  M. Valle,et al.  Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. , 2009, Structure.

[30]  Min Xu,et al.  3D Rotation Invariant Features for the Characterization of Molecular Density Maps , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine.

[31]  R. Aebersold,et al.  Visual proteomics of the human pathogen Leptospira interrogans , 2009, Nature Methods.

[32]  M Radermacher,et al.  DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. , 2009, Journal of structural biology.

[33]  M. Wistrand,et al.  Proteome Organization in a Genome-Reduced Bacterium , 2009 .

[34]  M. Groll,et al.  Structural analysis of spiro beta-lactone proteasome inhibitors. , 2008, Journal of the American Chemical Society.

[35]  G Sapiro,et al.  Classification and 3D averaging with missing wedge correction in biological electron tomography. , 2008, Journal of structural biology.

[36]  R. Sockett,et al.  Laboratory Maintenance of Bdellovibrio , 2008, Current protocols in microbiology.

[37]  Friedrich Förster,et al.  Classification of cryo-electron sub-tomograms using constrained correlation. , 2008, Journal of structural biology.

[38]  Mark Ellisman,et al.  Applications of direct detection device in transmission electron microscopy. , 2008, Journal of structural biology.

[39]  Christopher R Booth,et al.  Methods for aligning and for averaging 3D volumes with missing data. , 2008, Journal of structural biology.

[40]  Gernot Guigas,et al.  The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved , 2007, FEBS letters.

[41]  Sergei Vassilvitskii,et al.  k-means++: the advantages of careful seeding , 2007, SODA '07.

[42]  John W Sedat,et al.  UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. , 2007, Journal of structural biology.

[43]  C. Starks,et al.  Structure of a NADH-insensitive hexameric citrate synthase that resists acid inactivation. , 2006, Biochemistry.

[44]  Frederico J. Gueiros-Filho,et al.  GroES/GroEL and DnaK/DnaJ Have Distinct Roles in Stress Responses and during Cell Cycle Progression in Caulobacter crescentus , 2006, Journal of bacteriology.

[45]  V. Lamour,et al.  Recombinant Thermus aquaticus RNA polymerase for structural studies. , 2006, Journal of molecular biology.

[46]  Wolfgang Baumeister,et al.  A visual approach to proteomics , 2006, Nature Reviews Molecular Cell Biology.

[47]  M. Bewley,et al.  The asymmetry in the mature amino-terminus of ClpP facilitates a local symmetry match in ClpAP and ClpXP complexes. , 2006, Journal of structural biology.

[48]  J. Holton,et al.  Structures of the Bacterial Ribosome at 3.5 Å Resolution , 2005, Science.

[49]  E. Orlova,et al.  Dodecameric Structure of the Small Heat Shock Protein Acr1 from Mycobacterium tuberculosis* , 2005, Journal of Biological Chemistry.

[50]  F. Avilés,et al.  Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Friedrich Förster,et al.  TOM software toolbox: acquisition and analysis for electron tomography. , 2005, Journal of structural biology.

[52]  E. Canale-Parola,et al.  Morphological and physiological characteristics ofSpirillum gracile sp.n. , 2005, Antonie van Leeuwenhoek.

[53]  Wolf-Dieter Schubert,et al.  Plasmin(ogen)-binding alpha-enolase from Streptococcus pneumoniae: crystal structure and evaluation of plasmin(ogen)-binding sites. , 2004, Journal of molecular biology.

[54]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[55]  J. Wang,et al.  STRUCTURAL BASIS FOR GROEL-ASSISTED PROTEIN FOLDING FROM THE CRYSTAL STRUCTURE OF (GROEL-KMGATP) 14 AT 2.0 ANGSTROM RESOLUTION , 2003 .

[56]  F. Förster,et al.  Identification of macromolecular complexes in cryoelectron tomograms of phantom cells , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  W. Wriggers,et al.  Fast rotational matching. , 2002, Acta crystallographica. Section D, Biological crystallography.

[58]  Niels Volkmann,et al.  A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. , 2002, Journal of structural biology.

[59]  Kalyanmoy Deb,et al.  A fast and elitist multiobjective genetic algorithm: NSGA-II , 2002, IEEE Trans. Evol. Comput..

[60]  Pawel A Penczek,et al.  Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms. , 2002, Journal of structural biology.

[61]  B. Gallois,et al.  Structural description of the active sites of mouse L-chain ferritin at 1.2 Å resolution , 2002, JBIC Journal of Biological Inorganic Chemistry.

[62]  Tony F. Chan,et al.  Active contours without edges , 2001, IEEE Trans. Image Process..

[63]  A S Frangakis,et al.  Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[64]  C. Hill,et al.  Structural basis for the activation of 20S proteasomes by 11S regulators , 2000, Nature.

[65]  Boguslaw Stec,et al.  A cis-proline to alanine mutant of E. coli aspartate transcarbamoylase: kinetic studies and three-dimensional crystal structures. , 2000, Biochemistry.

[66]  M. Delarue,et al.  Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates. , 2000, Journal of molecular biology.

[67]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[68]  A G Leslie,et al.  Molecular architecture of the rotary motor in ATP synthase. , 1999, Science.

[69]  D. Sherratt,et al.  X‐ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site‐specific recombination , 1999, The EMBO journal.

[70]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[71]  H M Holden,et al.  Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding. , 1999, Biochemistry.

[72]  N. Glansdorff,et al.  The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Sam T. Roweis,et al.  EM Algorithms for PCA and SPCA , 1997, NIPS.

[74]  Edward H. Egelman,et al.  The RecA hexamer is a structural homologue of ring helicases , 1997, Nature Structural Biology.

[75]  Jared R. Leadbetter,et al.  Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes , 1996, Applied and environmental microbiology.

[76]  J R Kremer,et al.  Computer visualization of three-dimensional image data using IMOD. , 1996, Journal of structural biology.

[77]  S. Farestam.  Sub-pixel Distance Maps and Weighted Distance Transforms , 1994 .

[78]  D. Eisenberg,et al.  Refined atomic model of glutamine synthetase at 3.5 A resolution. , 1989, The Journal of biological chemistry.

[79]  M. Unser,et al.  A new resolution criterion based on spectral signal-to-noise ratios. , 1987, Ultramicroscopy.

[80]  W. O. Saxton,et al.  The correlation averaging of a regularly arranged bacterial cell envelope protein , 1982, Journal of microscopy.

[81]  J. Frank,et al.  Signal-to-noise ratio of electron micrographs obtained by cross correlation , 1975, Nature.

[82]  Bernice W. Polemis.  Nonparametric Statistics for the Behavioral Sciences , 1959 .