Daniel Castaño-Diez

Summary

Affiliation: University of Basel
Country: Switzerland

Publications

  1. doi request reprint Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms
    Daniel Castaño-Diez
    BioEM Lab at C CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH 4058 Basel, Switzerland Center for Cellular Imaging and NanoAnalytics C CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH 4058 Basel, Switzerland Electronic address
    J Struct Biol 197:135-144. 2017
  2. doi request reprint Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments
    Daniel Castaño-Diez
    Center for Cellular Imaging and Nano Analytics C CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH 4058 Basel, Switzerland
    J Struct Biol 178:139-51. 2012
  3. doi request reprint Automation of image processing in electron crystallography
    Marcel Arheit
    C CINA, Biozentrum, University Basel, Basel, Switzerland
    Methods Mol Biol 955:313-30. 2013
  4. doi request reprint Merging of image data in electron crystallography
    Marcel Arheit
    C CINA, Biozentrum, University Basel, Basel, Switzerland
    Methods Mol Biol 955:195-209. 2013
  5. doi request reprint Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core
    Julia Kowal
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University Basel, Mattenstrasse 26, 4058 Basel, Switzerland
    Structure 21:2152-61. 2013
  6. doi request reprint Image processing of 2D crystal images
    Marcel Arheit
    C CINA, Biozentrum, University Basel, Basel, Switzerland
    Methods Mol Biol 955:171-94. 2013
  7. doi request reprint The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles
    Mikhail Kudryashev
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland Electronic address
    Structure 24:165-70. 2016
  8. doi request reprint Assessing the benefits of focal pair cryo-electron tomography
    Mikhail Kudryashev
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University Basel, WRO 1058, Mattenstrasse 26, CH 4058 Basel, Switzerland
    J Struct Biol 178:88-97. 2012
  9. pmc In situ structural analysis of the Yersinia enterocolitica injectisome
    Mikhail Kudryashev
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University of Basel, Basel, Switzerland
    elife 2:e00792. 2013

Collaborators

  • Bryant R Gipson
  • Matteo Dal Peraro
  • Mikhail Kudryashev
  • Henning Stahlberg
  • Marcel Arheit
  • Julia Kowal
  • Raphaël Thierry
  • Marlise Amstutz
  • Guy R Cornelis
  • Xiangyan Zeng
  • Alexandra Graf-Meyer
  • Luigino Grasso
  • Gherici Hassaine
  • Cédric Deluz
  • Horst Vogel
  • Matteo T Degiacomi
  • Stefan Schmelz
  • Christopher Ke Bleck
  • Andreas Diepold
  • Dirk W Heinz
  • Andreas Engel
  • Priyanka Abeyrathne
  • Mohamed Chami
  • Stefan Münnich
  • Philippe Ringler
  • Ulrich Wiesand
  • Marco Stenta
  • Shirley A Müller

Detail Information

Publications9

  1. doi request reprint Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms
    Daniel Castaño-Diez
    BioEM Lab at C CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH 4058 Basel, Switzerland Center for Cellular Imaging and NanoAnalytics C CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH 4058 Basel, Switzerland Electronic address
    J Struct Biol 197:135-144. 2017
    ..Dynamo Catalogue is part of the open source package Dynamo and includes tools to ensure format compatibility with the subtomogram averaging functionalities of other packages, such as Jsubtomo, PyTom, PEET, EMAN2, XMIPP and Relion...
  2. doi request reprint Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments
    Daniel Castaño-Diez
    Center for Cellular Imaging and Nano Analytics C CINA, Biozentrum, University of Basel, Mattenstrasse 26, CH 4058 Basel, Switzerland
    J Struct Biol 178:139-51. 2012
    ..Dynamo executables do not require licenses for third party commercial software. Sources, executables and documentation are freely distributed on http://www.dynamo-em.org...
  3. doi request reprint Automation of image processing in electron crystallography
    Marcel Arheit
    C CINA, Biozentrum, University Basel, Basel, Switzerland
    Methods Mol Biol 955:313-30. 2013
    ..While the processing of 2D crystal images has been fully automated, the merging process is still semi-manual...
  4. doi request reprint Merging of image data in electron crystallography
    Marcel Arheit
    C CINA, Biozentrum, University Basel, Basel, Switzerland
    Methods Mol Biol 955:195-209. 2013
    ..Processed image data from non-tilted and tilted 2D crystals then need to be merged into a 3D reconstruction of the membrane protein structure. We here describe the process of the 3D merging, using the 2dx software system...
  5. doi request reprint Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core
    Julia Kowal
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University Basel, Mattenstrasse 26, 4058 Basel, Switzerland
    Structure 21:2152-61. 2013
    ..These petals harbor the binding site of YscD, a component of the inner membrane ring. A change in their orientation adapts the length of the YscC secretin and facilitates its interaction with YscD. ..
  6. doi request reprint Image processing of 2D crystal images
    Marcel Arheit
    C CINA, Biozentrum, University Basel, Basel, Switzerland
    Methods Mol Biol 955:171-94. 2013
    ..However, image imperfections require a crystal unbending procedure to be applied to the image before evaluation in Fourier space. We here describe the process of 2D crystal image unbending, using the 2dx software system...
  7. doi request reprint The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles
    Mikhail Kudryashev
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland Electronic address
    Structure 24:165-70. 2016
    ..In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating...
  8. doi request reprint Assessing the benefits of focal pair cryo-electron tomography
    Mikhail Kudryashev
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University Basel, WRO 1058, Mattenstrasse 26, CH 4058 Basel, Switzerland
    J Struct Biol 178:88-97. 2012
    ..Further, in computational simulations on synthetic datasets we show the applicability of the method to sub-tomogram averaging, demonstrating its potential for achieving higher resolution...
  9. pmc In situ structural analysis of the Yersinia enterocolitica injectisome
    Mikhail Kudryashev
    Center for Cellular Imaging and Nanoanalytics C CINA, Biozentrum, University of Basel, Basel, Switzerland
    elife 2:e00792. 2013
    ..We suggest that elasticity is critical for some two-membrane spanning protein complexes to cope with variations in the intermembrane distance. DOI:http://dx.doi.org/10.7554/eLife.00792.001. ..