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Program
Electron Crystallography Workshop
at UC Davis, September 7-13, 2008
Organization:
Bryant Gipson (BRGipson@ucdavis.edu)
Scientific Organization:
Ben Hankamer (B.Hankamer@imb.uq.edu.au)
Tom Walz (Thomas_Walz@hms.harvard.edu)
Henning Stahlberg (HStahlberg@ucdavis.edu)
Web Site:
Emergency Phone Numbers:
Henning Stahlberg: +1 (530) 574 0835 (mobile)
Seminars:
1022 Life Sciences, University of California, Davis, CA 95616
Practicals:
WetLab: 15 Briggs Hall, UC Davis (Phone: (530) 754 8285)
TEMs: 29 Briggs Hall, UC Davis (Phone: (530) 754 8338)
Computing: 1131 Meyer Hall, Computer Room, UC Davis
Sponsors:
Program
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Sunday, September 7, 2008 |
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Afternoon |
Arrival Registration 4:00 pm – 6:00 pm Foyer of UCD Conference Housing, Tercero |
Ben Hankamer Thomas Walz Henning Stahlberg Bryant Gipson Po-Lin Chiu Ludovic Renault |
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7:00 pm |
Dinner Buffet. Putah Creek Lodge (at the bottom of the map below) |
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Monday, September 8, 2008 |
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8:00 am |
Breakfast. |
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9:00 am |
Welcome |
Henning Stahlberg |
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9:30 am |
SESSION CHAIR: Daniel Levy
Detergents and their properties |
Ben Hankamer |
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10.10 am |
Lipids and their properties |
Catherine Venien-Bryan |
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10:50 am |
Coffee Break |
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11.15 am |
SESSION CHAIR: Daniel Levy
2D crystallization: Dialysis |
Thomas Walz |
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12:00 pm |
Lunch. Tercero Dining Area |
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1:00 pm |
SESSION CHAIR: Tom Walz
2D crystallization: Monolayer approach & biobeads |
Daniel Levy |
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1.30 pm |
2D crystallization: Detergent chelation and dilution |
Herve Remigy |
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2:00 pm |
Practical: 2D crystallization - Monolayer Trial (Daniel Levy) - Dialysis Trial (Tom Walz, Po-Lin Chiu) - Biobead Trial (Ben Hankamer, Ludovic Renault) - Dilution Demo (Remigy / Engel) |
Practical: Image Processing - Installation of MRC, 2dx, IPLT on the private portable computers - Introduction to the image processing in small sub-groups |
Ben Hankamer Daniel Levy Stahlberg Lab Tom Walz Ansgar Philippsen Andreas Schenk Bryant Gipson Herve Remigy Po-Lin Chiu Ludovic Renault Andreas Engel |
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5:30 pm |
Dinner, Tercero Dining Area. |
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6:30 pm |
Student Posters and Coffee, in 1022 LSA |
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7:30 pm |
SESSION CHAIR: Tom Walz & Daniel Levy
Round table discussion: Improved approaches to 2D crystal production |
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8.15 pm - |
Posters/open hour |
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Tuesday, September 9, 2008 |
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8:00 am |
Breakfast. |
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9:00 am |
SESSION CHAIR: Henning Stahlberg
TEM: Instrumentation for high resolution data collection - Vacuum, Gun (FEG/Thermal, Acc. Voltage), Stage (LN2, Helium), Low-Dose, Spot Scanning |
Ken Downing |
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9:45 am |
Sample Preparation - Methods for enriching crystals from a mixture of crystals and vesicles. - Harvesting crystals: preventing damage to crystals during transfer (monolayer, bilayers). - Benefits of glucose, trehalose etc. - Back injection, Carbon sandwich and other techniques |
Gyobu Nobuhiko |
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10:30 am |
Coffee Break |
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10:45 am |
SESSION CHAIR: Bob Glaeser
Data collection: Imaging - Alignment (Coherence, Beam tilt, stability) - Data collection (Defocus, Astigmatism) - Dose limitation and dose measurement |
Dieter Typke |
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11:20 pm |
Data collection: Diffraction - Principle, Alignment, Operation mode (Exp. Time, etc.), Film/CCD |
Yifan Cheng |
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12:00 pm |
Lunch. Tercero Dining Area |
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1:00 pm |
SESSION CHAIR: Ben Hankamer
TEM and other developments at FEI |
Uwe Luecken |
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1:20 pm |
TEM and other developments at JEOL |
Barbara Armbruster |
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1:40 pm |
CCD camera and other developments at TVIPS |
Matthias Stumpf |
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2:00 pm |
Sample holders and other developments at GATAN |
Chris Booth |
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2:30 pm |
Practical: Sample Preparation / CryoEM data collection - RT & Cryo: Neg. stain (Ludovic Renault) - Cryo: Back injection (H-T Chou, Yifan Cheng) - Cryo: Sandwich (H-T Chou, Gyobu Nobuhiko) - Cryo-EM imaging (Dieter Typke, Po-Lin Chou) - e-Diffraction (Yifan Cheng, James Buban) |
Practical: Image Processing - Installation of MRC, 2dx, IPLT on the private portable computers - Introduction to the image processing in small sub-groups |
Anchi Cheng Andreas Schenk Ansgar Philippsen Bryant Gipson Dieter Typke Gyobu Nobuhiko Hui-Ting Chou James Buban Po-Lin Chiu Yifan Cheng |
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5:30 pm |
Dinner, Tercero Dining Area |
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6:30 pm |
Student Posters and Coffee, in 1022 LSA |
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7:30 pm |
SESSION CHAIR: Henning Stahlberg
Electron detectors: DQE, MTF, Medipix, CMOS detectors, Film vs. CCD |
Bob Glaeser |
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8:15 pm |
Deceleration CCD |
Ken Downing |
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9.00 pm |
Posters/open hour |
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Wednesday, September 10, 2008 |
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8:00 am |
Breakfast. |
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9:00 am |
SESSION CHAIR: Anchi Cheng
Overview of algorithms for 2D crystal image processing - Fourier-space solutions (filtering, unbending) - Real-space solutions |
Henning Stahlberg |
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9:15 am |
Fourier Theory: 2D - Real space / Fourier space - FFT, Correlation, Convolution, Autocorrelation |
Bob Glaeser |
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9.45 am |
Fourier Theory, 3D - Lattice lines, oversampling |
Bob Glaeser |
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10:15 am |
Symmetry - Point groups, Unit cells and lattices, Symmetry operations - Space groups, plane groups, crystallographic notation |
Michael Landsberg |
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10:30 am |
Coffee Break |
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10:45 am |
SESSION CHAIR: Ken Downing
MTF - Determination of the MTF of CCD; Scanner vs. Film |
Dieter Typke |
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11:15 am |
Image Processing in 2D: MRC software for real-space images - Format, Documentation, Work-flow - Programs, Unbending |
Anchi Cheng |
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12:00 pm |
Lunch. Tercero Dining Area |
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1:00 pm |
Practical: Sample Preparation / CryoEM data collection - RT & Cryo: Neg. stain (Ludovic Renault) - Cryo: Back injection (H-T Chou, Gyobu Nobuhiko) - Cryo: Sandwich (H-T Chou, Yifan Cheng) - Cryo-EM imaging (Dieter Typke, Po-Lin Chou) - e-Diffraction (Yifan Cheng, James Buban) |
Practical: Image Processing - Introduction to the image processing in small sub-groups |
Anchi Cheng Andreas Schenk Ansgar Philippsen Bryant Gipson Dieter Typke Gyobu Nobuhiko Hui-Ting Chou James Buban Po-Lin Chiu Yifan Cheng |
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4:00 pm |
SESSION CHAIR: Tom Walz
Beam-induced movement of samples - SpotScanning - Beam-induced drum-head movement vs. charging |
Bob Glaeser
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4:30 pm |
2D crystal screening |
Iban Ubarretxena-Belandia |
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4:45 pm |
Basel System for 2D crystal screening |
Herve Remigy |
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5:00 pm |
Discussion: How do we address the crystallization bottleneck |
Tom Walz |
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5:30 pm |
Dinner, Tercero Dining Area |
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7:00 pm |
SESSION CHAIR: Iban Ubarretxena-Belandia
To Be Announced |
Werner Kühlbrandt |
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7:45 pm |
Membr. assoc. proteins in eicosanoid and glutathione metabolism (MAPEGs) |
Hans Hebert |
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8:30 pm |
Open hour |
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Thursday, September 11, 2008 |
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8:00 am |
Breakfast. |
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9:00 am |
SESSION CHAIR: Andreas Schenk
2dx software |
Bryant Gipson |
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9:45 am |
Tilt geometry |
Henning Stahlberg |
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10:00 am |
A Maximum Likelihood approach to 2D crystals |
Xiangyan Zeng |
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10:20 am |
Coffee Break |
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10:35 am |
SESSION CHAIR: Andreas Engel
IPLT software |
Ansgar Philippsen |
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11:20 am |
Tilted Transfer Function (TTF and TCIF): SpotSplitting and deconvolution |
Ansgar Philippsen |
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11:45 am |
Hybrid Input Output Algorithm |
Bryant Gipson |
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12:15 pm |
Lunch. Tercero Dining Area |
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1:15 pm |
Practical: Image processing of non-tilted 2D crystal data - MRC: Processing of 2D crystal images (Anchi Cheng) - 2dx: Processing of images (Bryant Gipson, Henning Stahlberg) - IPLT: Processing of e-diff pattern (Ansgar Philippsen, Andreas Schenk) - |
Practical: Image processing trouble shooting session - Targeted problem sessions in small groups with requested teachers
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Bryant Gipson Ansgar Philippsen Andreas Schenk Henning Stahlberg Anchi Cheng |
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4:00 pm |
Storer Symposium: Andreas Engel In: 1309 Surge III
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5:30 pm |
Dinner at Tercero Dining Area Also:
Storer Reception for
invited UC Davis guests |
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7:00 pm |
Low-dose STEM |
James Buban |
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7:45 pm |
DTEM |
Nigel Browning |
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8.30 pm |
Open hour |
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Friday, September 12, 2008 |
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8:00 am |
Breakfast. |
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9:00 am |
SESSION CHAIR: Ansgar Philippsen
Merging with the MRC software - Phase origin, Defocus, Beam-tilt, Lattice Lines - ORIGTILT, MAKETRAN |
Anchi Cheng |
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9:30 am |
Merging with the 2dx software - Project management - Iterative merging and re-processing of images |
Henning Stahlberg |
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10:00 am |
Coffee Break |
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10:15 am |
SESSION CHAIR: Tom Walz
3D reconstruction - Lattice line interpolation, 3D volume generation, NCS - 3D Visualization with O / Dino |
Andreas Schenk |
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11:30 am |
Calculation of the variance of a 3D map by the bootstrap method |
Anchi Cheng |
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12:00 pm |
Lunch. |
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1:00 pm |
Practical: Image processing of tilted 2D crystal data - MRC: Processing of 2D crystal images (Anchi Cheng) - 2dx: Processing of non-tilted and tilted images (Bryant Gipson, Henning Stahlberg) - IPLT: Processing of e-diff pattern (Ansgar Philippsen, Andreas Schenk) |
Bryant Gipson Ansgar Philippsen Andreas Schenk Henning Stahlberg Anchi Cheng |
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4:30 pm |
Practical: Image processing trouble shooting session - Targeted problem sessions in small groups with requested teachers |
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5:30 pm |
Closing Remarks |
Ben Hankamer Tom Walz Henning Stahlberg |
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6:00 pm |
Free Time |
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7:00 pm |
Dinner: Hosted by JEOL
Bistro 33 226 F Street Davis, CA 95616 Tel: (530) 756 4556
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Saturday, September 13, 2008 |
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8:00 am |
Breakfast. |
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9:00 am |
Departure |
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Speakers
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Barbara Armbruster Assist. TEM Product Manager, Biology JEOL USA, Inc. 5653 Stoneridge Dr., Suite 110 Pleasanton, CA 94588 +1-925-737 1748 |
James P. Buban Molec. & Cell. Biology UC Davis, Davis, CA 95616 |
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Nigel Browning Lawrence Livermore National Laboratories Chemistry and Materials Science Livermore, CA 94550 +1-530-754 5358 |
Anchi Cheng Department of Cell Biology Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037 +1-858-784 9535 |
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Yifan Cheng Genentech Hall, 600 16th Street, Mission Bay campus of University of California San Francisco |
Ken Downing Lawrence Berkeley National Laboratory Life Sciences Division One Cyclotron Road Mail Stop 941 (Donner) Berkeley, CA 94720 |
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Andreas Engel M.E. Müller Institute for Structural Biology Biozentrum, University of Basel Klingelbergstrasse 50/70 CH-4056 Basel / Switzerland |
Robert M. Glaeser Department of Molecular and Cellular Biology University of California at Berkeley 229 Stanley Hall #3206 Berkeley, CA 94720-3206 +1-510-642 2905 |
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Bryant Gipson Molec. & Cell. Biology UC Davis, Davis, CA 95616 +1-530-754 8285
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Nobuhiko Gyobu Japan Biological Information Res. Center (JBIRC) Japan Biological Information Consortium (JBIC) Aomi 2-41-6, Koto-ku Tokyo 135-0064, Japan +81-3-3599 8092 |
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Ben Hankamer Institute for Molecular Bioscience University of Queensland St. Lucia Campus Brisbane QLD 4072 Australia +61-7-3346 2012 |
Hans Hebert Karolinska Institutet Dept. of Biosciences and Nutrition Novum SE-141 57 Huddinge, Sweden +46-(0)8-608 92 19 |
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Remigy Hervé M.E. Müller Institute for Structural Biology Biozentrum, University of Basel Klingelbergstrasse 50/70 CH-4056 Basel / Switzerland |
Werner Kühlbrandt Department of Structural Biology Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main +49 (0) 69 6303-3001 |
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Michael Landsberg Institute for Molecular Bioscience Queensland Biosciences Precinct Services Rd The University of Queensland St Lucia, QLD, 4072, AUSTRALIA |
Daniel Levy Institut Curie UMR CNRS 168 11 rue P.M.Curie F-75005 Paris France +33-1 42 34 67 81 |
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Ansgar Philippsen Biozentrum Klingelbergstr. 72 CH-4065 Basel Switzerland +41-61-267 2254
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Andreas Schenk Biozentrum Klingelbergstr. 72 CH-4065 Basel Switzerland +41-61-267 2254 |
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Henning Stahlberg Molec. & Cell. Biology Briggs Hall 5 UC Davis, Davis, CA 95616 +1-530-752 8282 |
Dieter Typke Lawrence Berkeley National Laboratory Life Sciences Division One Cyclotron Road Mail Stop 941 (Donner) Berkeley, CA 94720 +1-510-495 2840 |
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Iban Ubarretxena-Belandia Department of Chemistry Marshak Science Building J-1024 The City College of New York, CUNY Convent Avenue & 138th Street New York, New York 10031 +1-212-650 8320 |
Catherine Venien-Bryan Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU |
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Tom Walz Department of Cell Biology Harvard Medical School 240 Longwood Avenue Boston, MA 02115 +1-617-432 4090 |
Xiangyan Zeng Molec. & Cell. Biology Briggs Hall 15 UC Davis, Davis, CA 95616 +1-530-754 8285 |
Workshop Participants
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Adrian Flores Yale University Molecular Biophysics & Biochemistry 333 Cedar Street P.O. Box 208024 New Haven, CT 06520-802 +1-(203)-785 5784 |
Alessia Arduin Chemical Biology Centre Department of Chemistry (R. 841) Imperial College London South Kensington Campus London SW7 2AX UK 0044(0)77 808 28 391 |
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Amanda J. Rice 240 Longwood Avenue Building C, Rm 421 Boston, MA 02115 +1-(617)-432 4097 |
Andrea Maggioni Institute for Glycomics Griffith University Gold Coast Campus PMB 50 Gold Coast Mail Centre QLD 9726 Australia |
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Anna Roujeinikova Manchester Interdisciplinary Biocentre 131 Princess Street University of Manchester M1 7DN UK +44 161 3065155 |
Holger Wille University of California, San Francisco Institute for Neurodegenerative Diseases and Department of Neurology 513 Parnassus Avenue San Francisco, CA 94143-0518 +1-(415)-502 1949 hwille@ind.ucsf.edu |
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John Paul Glaves 3-27 Med Sci Bldg University of Alberta Edmonton, AB, Canada T6G 2H7 780-492-4577 jglaves@ualberta.ca |
Julian Ollesch University of California, San Francisco (UCSF) Institute for Neurodegenerative Diseases (IND) 513 Parnassus Ave, Box0518 San Francisco, CA 94143-0518 +1-(415)-502 1952 jollesch@ind.ucsf.edu |
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Julie Norville Massachusetts Institute of Technology 16-244 77 Massachusetts Ave. Cambridge MA 02139 +1-(626)-235 3751 norville@csail.mit.edu |
Jun-yong Choe Rosalind Franklin University Department of Biochemistry and Molecular Biology 3333 Green Bay Rd North Chicago, IL 60064 +1-(847)-578 8627 junyong.choe@rosalindfranklin.edu |
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Kyung Eun Lee 411, School of life Sciences and Biotechnology Korea University Anam-dong, Suyngbuk-gu, Seoul, Korea kelee7@gmail.com |
Leonardo Rodrigues De Andrade 259 Congressional Lane #413, Rockville, MD, 20852 +1(301)-675 8156 andradeleo@nidcd.nih.gov |
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Matthew Roberts Yale University Dept. Molecular Biophysics and Biochemistry P.O. Box 208024 333 Cedar Street New Haven, CT 06520-8024 +1-(203)-785 5652 |