Biomachina Sponsored Contributions

Listed are independent contibutions from our members that were sponsored in part by grants to Willy Wriggers.

• Publications
• Talks and Seminars
• Poster Presentations
• Other Meetings Attended

Publications (for publications co-authored by Willy Wriggers click here)

1. Manuel Wahle and Stefan Birmanns. GPU-Accelerated Visualization of Protein Dynamics in Ribbon Mode. SPIE Proceedings Vol. 7868, Visualization and Data Analysis (2011), Pak Chung Wong; Jinah Park; Ming C. Hao; Chaomei Chen; Katy Börner; David L. Kao; Jonathan C. Roberts, Editors. [Article-PDF]
2. Mirabela Rusu and Stefan Birmanns. Evolutionary Tabu Search Strategies for the Simultaneous Registration of Multiple Atomic Structures in Cryo-EM Reconstructions. J. Struct. Biol., Vol. 170, pp. 164-171, 2010. [Article-PDF]
3. Jochen Heyd and Stefan Birmanns. Immersive Structural Biology: A New Approach to Hybrid Modeling of Macromolecular Assemblies. Virtual Reality, Vol: 13, pp. 245 - 255, July 2009. [Article-PDF]
4. Jochen Heyd and Stefan Birmanns. Beyond the Black Box: Interactive Global Docking of Protein Complexes. Microscopy Today, Vol: 16 # 4, July 2008. [Article-PDF]

Talks and Seminars (for talks by Willy Wriggers click here)

• GPU-Accelerated Visualization of Protein Dynamics in Ribbon Mode. Manuel Wahle. Visualization and Data Analysis 2011, San Francisco, California, 24 January 2011.

• New Approaches for Docking of Atomic Structures into 3D Cryo-Electron Microscopy. Jochen Heyd.
  1. Reconstructions NLM Informatics Training Conference, National Institutes of Health, Bethesda, MD, June 2008.
  2. Keck Seminar (Keck Annual Research Conference Poster Winners) Rice University, Houston, Texas, March 13, 2008.

• Biomolecular Mechanisms Revealed by Integrative Modeling of Multi-Resolution Structural Data. Mirabela Rusu. School of Biomedical Informatics Seminar Series, Houston, Texas, November 2010. 

• Parallel Genetic Algorithm with Biased Initial Population for the Simultaneous Hybrid Modeling of Molecular Assemblies. Mirabela Rusu. Microscopy and Microanalysis 2010, Portland, Oregon, August 1, 2010.

• Structural Characterization of Biomolecular Assemblies using Small Angle Scattering Techniques. Mirabela Rusu. School of Health Information Sciences Seminar Series, Houston, Texas, March 2009.

• Sculptor: A Software Package for Interactive and Algorithmic Multi-Resolution Modeling. Stefan Birmanns.
  1. Basel Computational Biology Center, Switzerland, August 30, 2010 (host V. Mariani).
  2. Short course "3D Electron Microscopy of Macromolecular Assemblies" at Microscopy and Microanalysis 2010, Portland, Oregon, August 1, 2010.
  3. 4th International UVM Practical Course on Three-dimensional Cryo Electron Microscopy of Single Particles
     University of Vermont, Burlington, VT, August 2 - 9, 2009.
  4. University of Vermont, Burlington. December 8, 2008 (hosts: Teresa Ruiz and Michael Radermacher).
  5. Microscopy and Microanalysis 2008, Albuquerque, New Mexico, August 3-7, 2008. 
  6. 52nd Annual Meeting, Biophysical Society, Long Beach, California. February 2-6, 2008.
  7. Symposium on Visualization Tools for Cellular Complexity - VTCC06, Max Planck Institute of Biochemistry, Martinsried, Germany, December 15, 2006.

• Workshop: Innovations in Nanoscale Modeling and Imaging of Biological Systems. April 17-23, 2006, Houston. Biomachina Lab Members, 21 Invited Speakers.

• Local Dynamic Domain Analysis of Protein Dynamics. Zhiyong Zhang.
  1. 62nd Southwest Regional American Chemical Society Meeting, October 19-22, 2006.
  2. Center for Biophysical Modeling and Simulation, University of Utah. May 23, 2006 (host Gregory A. Voth).
  
  
• Visuo-Haptic Rendering and Anchor-Point Matching for Hybrid Modeling of Macromolecular Assemblies. Stefan Birmanns.
  1. Annual American Crystallographic Association Meeting. Salt Lake City, Utah. July 24, 2007.
  2. 51st Annual Meeting, Biophysical Society. Baltimore, MD. March 4, 2007.
  3. 62nd Southwest Regional American Chemical Society Meeting, October 19-22, 2006.
  4. Biological Small Angle Scattering Group, EMBL Hamburg, Germany. November 21th, 2005 (host D. Svergun).
  5. Geometrica Group, INRIA Sophia, France. November 10th, 2005.
  6. Visualization of Large Biomolecular Complexes, San Diego Supercomputer Center, La Jolla, CA. September 11 - 13, 2005.
  7. Visual Computing Lab, Dept. of Computer Science, June 14, 2005 (host I. Kakadiaris).
  8. Mechatronics and Robotics, Aachen, Germany, September 15, 2004.
  9. The 21st Annual Houston Conference on Biomedical Engineering Research, Houston Society for Engineering for Medicine and Biology, February 12, 2004.
  
  
• Tau paired helical filament assembly in Alzheimer's Diseases. Michael DeTure. IMM Seminar Series, University of Texas Health Science Center at Houston, December 15, 2004.

• Scientific Applications of High Performance Computing. Stefan Birmanns.
  1. Biostatistics Seminar, UT School of Public Health, March 1, 2004.
  2. Supercomputer Open House, School of Health Information Sciences, University of Texas Health Science Center at Houston, December 16, 2003.
  
  
• Situs User and Modeling Workshop. February 3-5, 2003, San Diego. Julio Kovacs, Pablo Chacón, Yao Cong, Florence Tama, Stefan Birmanns, Willy Wriggers.

Poster Presentations (for posters co-authored by Willy Wriggers click here)

• Yeast Phosphofructokinase: Modeling Four Bacterial Tetramers to Act in Concert. Carsten Peters, Mirabela Rusu, Stefan Birmanns and Teresa Ruiz. Microscopy and Microanalysis 2010, Portland, Oregon, August 1, 2010.

• Integrative Structural Bioinformatics: The Sculptor Modeling Software. Stefan Birmanns. 54th Annual Meeting, Biophysical Society, San Francisco, California, February 20 - 24, 2010.

• New Local Variance Based Adaptive Filtering Method for Cryo-Electron Microscopy Data. Zbigniew Starosolski and Stefan Birmanns.   20th Keck Center Annual Research Conference, Houston, Texas, October 15-16, 2010.

• Learning Mixture Networks Reveal Functional Dynamics of Molecular Assemblies. Stefan Birmanns. 53rd Annual Meeting, Biophysical Society, Boston, Massachusetts, February 28 - March 4, 2009.

• Efficient Rendering of Time-Varying Proteins. Manuel Wahle and Stefan Birmanns.
  
  1. 18th Keck Center Annual Research Conference, Houston, Texas, October 3-4, 2008.
  2. 19th Keck Center Annual Research Conference, Houston, Texas, October 29-30, 2009.
  3. 53rd Annual Meeting, Biophysical Society, Boston, Massachusetts, February 28 - March 4, 2009.

• Real-Time Ambient Occlusion for Molecular Visualization. Manuel Wahle and Stefan Birmanns. 15th Sealy Structural Biology Symposium, Galveston, Texas, March 19, 2010.

• Simultaneous Multicomponent Registration of High-Resolution X-Ray Structures into Electron Microscopy Maps. Mirabela Rusu and Stefan Birmanns.
  1. 54th Annual Meeting, Biophysical Society, San Francisco, California, February 20 - 24, 2010.
  2. 19th Keck Center Annual Research Conference, Houston, Texas, October 29-30, 2009.

• Integrative Multi-Resolution Modeling of Pleiomorphic Biomolecular Systems. Mirabela Rusu and Stefan Birmanns.
  1. 52nd Annual Meeting, Biophysical Society, Long Beach, California. February 2-6, 2008.
  2. 53rd Annual Meeting, Biophysical Society, Boston, Massachusetts, February 28 - March 4, 2009.
  3. 14th Sealy Structural Biology Symposium, Galveston, Texas, March 27th, 2009.

• Interactive Docking of Atomic Structures into 3D Cryo-Electron Microscopy Reconstructions Guided by Global Optimization. Jochen Heyd and Stefan Birmanns.
  1. 52nd Annual Meeting, Biophysical Society, Long Beach, California. February 2-6, 2008.
  2. 13th Sealy Structural Biology Symposium, Galveston, Texas, May 16-17, 2008 (Poster Session Winner).
  3. 18th Keck Center Annual Research Conference, Houston, Texas, October 3-4, 2008 (First Prize Poster Award).
  4. 53rd Annual Meeting, Biophysical Society, Boston, Massachusetts, February 28 - March 4, 2009.

• Virtual and Augmented Reality. Stefan Birmanns. GI-Fachgruppe VR/AR at the University of Aachen, Virtual Reality Center, Germany. 26 - 27 September 2005.

Other Meetings Attended

• The Eleventh Annual Structural Biology Symposium. Galveston, Texas, May 19-20, 2006 (John Robinson, Jun Wan, Tanmay Sachan).
• Frontiers in Macromolecular Simulations, Birmingham, AL, April 7-8, 2006 (John Robinson).
  
• 50th Annual Meeting, Biophysical Society. Salt Lake City, Utah. February 18-22, 2006 (John Robinson, Jun Wan).
• Texas Life Science Conference, Houston November 15-17, 2004 (Paul Boyle).
  
• Tutorial of Cryo Specimen Preparation, Baylor College of Medicine, Houston, Texas. November 16, 2004 (Hilary Wriggers, Michael DeTure).
• Texas Branch Meeting of The American Society for Microbiology. Houston, Texas, November 4-6, 2004 (Hilary Wriggers).
• Tutorial of TEM for Biological Cryo-Specimens, Baylor College of Medicine, Houston, Texas. October 11, 2004 (Michael DeTure).
• Presenting Data and Information: A One-Day Course Taught by Edward Tufte, Houston, Texas, October 5, 2004 (Paul Boyle, Zhiyong Zhang, Char Hu, Valerio Mariani, Chance Coble).
  
• The Ninth Annual Structural Biology Symposium. Galveston, Texas, April 30 - May 1, 2004 (Stefan Birmanns).
• Workshop Signal Transduction II: Muscles and Synapse, Mathematical Biosciences Institute, Columbus, Ohio, March 8-12, 2004 (Paul Boyle).
• Theoretical and Computational Biophysics Summer School, University of Illinois at Urbana-Champaign. June 2-13, 2003 (Surendra Negi).
• Automatic Particle Selection for Cryo-electron Microscopy, The Scripps Research Institute, La Jolla, California. April 24-25, 2003 (Yao Cong).

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