Daniel Castano-Diez | C-CINA

Daniel Castano-Diez

Current Project

Iterative refinement strategies for low and medium resolution electron density maps

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Short Biography

I studied my BSc in Physics in Bilbao (Spain), my MSc in Applied Mathematics in Madrid and completed my PhD in Applied Mathematics and Numeric Simulation in Bonn.

In 2005, I joined the Unit for Structural Biology at the European Molecular Biology Laboratory in Heidelberg as a postdoc, and C-CINA in 2009 as software developer. Then I moved to Frankfurt in 2014 to be a joint manager of the Scientific Computing Unit in the Max Planck Institute for Brain Research. Since 2015 I am a senior scientist in the BioEM lab in the Biozentrum of the University of Basel.

Publications
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Lewy pathology in Parkinson's disease consists of crowded organelles and lipid membranes

Shahmoradian, S., Lewis, A., Genoud, C., Graff, A., Pérez Navarro, P., Goldie, K., Sütterlin, R., Castano-Diez, D., Ingrassia, A., Rozemuller, A.J.M., Paepe, A.D., Erny, J.Staempfli, A., Hoernschemeyer, J., Niedieker, D., El-Mashtoly, S.F., Gerwert, K., Bohrmann, B., Britschgi, M., Stahlberg, H., van de Berg, W.D.J., Lauer, M.E.

Nature Neuroscience 22, 1099-1109 (2019)

DOI: Nature Neurosc.

20

‘Differential visual proteomics’: Enabling the proteome-wide comparison of protein structures of single-cells

Syntychaki, A., Rima, L., Schmidli, C., Stohler, T., Bieri, A., Sütterlin, R., Stahlberg, H., Castano-Diez, D., Braun, T.

J. of Proteome Research 18(9), 3521-3531 (2019)

19

Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Pérez Navarro, P., Genoud, C., Castano-Diez, D., Graff-Meyer, A., Lewis, A., de Gier, Y., Lauer, M.E., Britschgi, M., Bohrmann, B., Frank, S., Hench, J., Schweighauser, G., Rozemuller, A.J.M., van de Berg, W.D.J., Stahlberg, H., Shahmoradian, S.

Scientific Reports 8(18046), (2018)

18

Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package

Pérez Navarro, P., Stahlberg, H., Castano-Diez, D.

Frontiers in Molecular Biosciences 5(82), 1-18 (2018)

17

Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals

Opara, N., Mohacsi, I., Makita, M., Castano-Diez, D., Diaz, A., Jurani, P., Marsh, M., Meents, A., Milne, C.J., Mozzanica, A., Padeste, C., Panneels, V., Sikorski, M., Song, S., Stahlberg, H., Vartiainen, I., Vera, L., Wang, M., Willmott, P.R., David, C.

Structural Dynamics 5(5), 054303 (2018)

16

CryoEM structure of the extended type VI secretion system sheath–tube complex

Wang, J., Brackmann, M., Castano-Diez, D., Kudryashev, M., Goldie, K., Maier, T., Stahlberg, H., Basler, M.

Nature Microbiology 2(11), 1507-1512 (2017)

15

Focus: The interface between data collection and data processing in cryo-EM

Biyani, N., Righetto, R., McLeod, R., Caujolle-Bert, D., Castano-Diez, D., Goldie, K., Stahlberg, H.

J. Struct. Biol. 198(2), 124-133 (2017)

14

Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms

Castano-Diez, D., Kudryashev, M., Stahlberg, H.

J. Struct. Biol. 197(2), 135-144 (2017)

DOI: 10.1016/j.jsb.2016.06.005

13

The structure of the mouse serotonin 5-HT3 receptor in lipid vesicles

Kudryashev, M., Castano-Diez, D., Deluz, C., Hassaine, G., Grasso, L., Graff, A., Vogel, H., Stahlberg, H.

Structure 24(1), 165-170 (2016)

DOI: 10.1016/j.str.2015.11.004

12

Automation of image processing in electron crystallography

Arheit, M., Castano-Diez, D., Thierry, R., Gipson, B. R., Zeng, X., Stahlberg, H.

Methods Mol Biol 955, 313-30 (2013)

11

Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core

Kowal, J., Chami, M., Ringler, P., Müller, S., Kudryashev, M., Castano-Diez, D., Amstutz, M., Cornelis, G. R., Stahlberg, H., Engel, A.

Structure 21(12), 2152-61 (2013)

10

Image processing of 2D crystal images

Arheit, M., Castano-Diez, D., Thierry, R., Gipson, B. R., Zeng, X., Stahlberg, H.

Methods Mol Biol 955, 171-94 (2013)

9

In situ structural analysis of the Yersinia enterocolitica injectisome

Kudryashev, M., Stenta, M., Schmelz, S., Amstutz, M., Wiesand, U., Castano-Diez, D., Degiacomi, M. T., Munnich, S., Bleck, C. K., Kowal, J., Diepold, A., Heinz, D. W., Dal Peraro, M., Cornelis, G. R., Stahlberg, H.

Elife 2, e00792 (2013)

8

Merging of image data in electron crystallography

Arheit, M., Castano-Diez, D., Thierry, R., Abeyrathne, P., Gipson, B. R., Stahlberg, H.

Methods Mol Biol 955, 195-209 (2013)

7

Electron microscopy analysis of 2D crystals of membrane proteins

Abeyrathne, P.D., Arheit, M., Kebbel, F., Castano-Diez, D., Goldie, K., Chami, M., Renault, L., Kühlbrandt, W., Stahlberg, H.

Comprehensive Biophysics 1, 277-310 (2012)

DOI: 10.1016/B978-0-12-374920-8.00119-3

6

Assessing the benefits of focal pair cryo-electron tomography

Kudryashev, M., Stahlberg, H., Castano-Diez, D.

J Struct Biol 178(2), 88-97 (2012)

5

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments

Castano-Diez, D., Kudryashev, M., Arheit, M., Stahlberg, H.

J Struct Biol 178(2), 139-51 (2012)

4

Limiting factors in single particle cryo electron tomography

Kudryashev, M., Castano-Diez, D., Stahlberg, H.

Comput Struct Biotechnol J 1, e201207002 (2012)

3

Alignment of cryo-electron tomography datasets

Amat, F., Castano-Diez, D., Lawrence, A., Moussavi, F., Winkler, H., Horowitz, M.

Method Enzymol 482, 343-367 (2010)

DOI: 10.1016/S0076-6879(10)82014-2

2

3D reconstruction from 2D crystal image and diffraction data

Schenk, A. D., Castano-Diez, D., Gipson, B., Arheit, M., Zeng, X., Stahlberg, H.

Methods Enzymol 482, 101-29 (2010)

1

Senior Scientist (Software)

+41 61 387 32 14

C-CINA, Biozentrum, Uni Basel, Room P.20, Mattenstrasse 26, CH-4058 Basel, Switzerland

daniel.castano@unibas.ch