About me
About me …
I currently live in Seattle and have been for the past 4 years. I am a PostDoc at the University of Washington in the laboratory of David Baker. I have been working for many years now on the problem of Protein Structure Prediction. I write code for Rosetta, our simulation software and have been heavily involved in writing for our large distributed computing project Rosetta@HOME and the massive Bluegene machine at the Argonne National Lab.
In my spare time I help run a maker space in Seattle called ALTSpace and I’m interested in installation art and sculpture. Currently I’m involved in installing the Groovik’s Cube at the Pacific Science Center in September 2011.
Contact ..
Blogs:
http://beautifulproteins.blogspot.com/
http://www.airlighttimespace.org/
Or drop me an email here: mike DOT tyka AT gmail DOT com
GPG key information:
pub 4096R/3643DAC9 2010-12-30 Key fingerprint = A00E AD6C A9A1 CB02 C07A E2C4 1BA1 9825 3643 DAC9 uid Mike Tyka sub 4096R/CA38E347 2010-12-30 [expires: 2011-12-30]
Full CV
| Dr. Michael Tyka Henry Wellcome Research Fellow Baker Group Department of Biochemistry Languages: Fluent written & spoken, English & German. Good knowledge of Polish & French. |
University of Washington J Wing, HSB, Room J-555 1959 NE Pacific Street Seattle, WA 98195 |
Research / Developer experience
- Henry Wellcome Postdoctoral Research Fellow with Prof. D. Baker, University of Washington, Seattle (2007-2011)
- Graduate research with Prof. D. Baker, University of Washington, Seattle, Participation in the CASP7 experiment as part of the Baker Group (2006)
- Graduate research with Prof. A. R. Clarke and Dr. R. B. Sessions, University of Bristol: “Development of novel methods for free-energy calculations” (2002-2006)
- Main Developer of the ROSETTA Molecular modelling software (50+ developers, 400k lines of code, C++) (2005-2011)
- Lead developer of a powerful, highly flexible molecular mechanics suite implementing many classic and novel simulation algorithms and force fields (40k+lines C++&Python) (2003-2007)
- Extensive programming experience in C/C++, Python, Java Script, Assembler, and Fortran. I have been developing software for massively parallel computer systems including Rosetta@Home/BOINC, Bluegene (64k+ processors), SIMD Architectures (Clearspeed) and commodity x86 clusters.
- Graduate research with Prof. D. Baker, University of Washington, Seattle, sponsored by the Worldwide University Network (WUM): “Development of parallel, genetic algorithms for protein structure prediction” (2005)
- With Prof. A. R. Clarke and Dr. R. B. Sessions, University of Bristol, sponsored by the Nuffield Foundation: “Development of computer programs for ab initio protein structure prediction using Monte Carlo based methods” (2002)
- With Prof. W. Martin, Heinrich Heine Universität, Düsseldorf “Phylogenetic analysis of mitochondrial genes in Arabidopsis thaliana” (2001)
Recent talks:
- SciFoo, O’Reilley Media & Google Inc., Mountain View 2011, Invited speaker for Ignite Session “Art & Science: Building the world’s largest functional Rubik’s cube”
- FooCamp, O’Reilley Media, Sebastapol 2010. Invited speaker for Ignite FooCamp “The invention of the wheel – nature’s hidden creativity”
- Invited speaker at Bioinformatics 2008 Conference “High Resolution Structure Prediction with Rosetta”
- CCPB Biomolecular Simulation. 2007 Talk: “A Molecular Mechanics Engine for Python”
Education:
- PhD, Biochemistry, University of Bristol, with Prof. A. R. Clarke, “Absolute Free Energy Calculations for Biomolecular Systems” (2003-2007)
- BSc with First Class Honours, Biochemistry with Biotechnology and Microbiology, University of Bristol (2000 – 2003)
- A-Levels (6 ‘A’ grades) in Physics, Chemistry, Biology, Mathematics, General Studies and German; English at GCSE (A), Culford School, Bury St. Edmunds, Suffolk (1998 – 2000)
Honours and Awards:
- Sir Henry Wellcome Postdoctoral Fellowship Grant (2007-2011)
- Worldwide University Network Exchange Grant (2005)
- Denton Prize for best final year PhD talk (2005)
- William Garner Prize for best overall mark in the final degree assessment (BSc) (2003)
- Herman Watson Prize for best Practical Project (BSc) (2003)
- Fellowship from “Studienstiftung des Deutschen Volkes” (National German Scholarship) (2000-2004)
- German National Science Competition, 2nd Prize (2001)
Publications:
- Tyka, M., Keedy, D.A., André, I., DiMaio, F., Song, Y., Richardson, D.C., Richardson, J.S., Baker, D. (2011) Alternate states of proteins revealed by detailed energy landscape mapping Journal of Molecular Biology 405, 607-618
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Wang, R.Y., Han, Y., Krassovsky, K., Sheffler, W., Tyka, M., Baker, D. (2011) Modeling Disordered Regions in Proteins Using Rosetta PloS one, 2011
- Khatib, F., Cooper, S., Tyka, M., Makedon, I., Vertex, Grom, Popović, Z., Baker, D. (2011) Game-based Algorithm Discovery for Protein Folding Proc. Natl. Acad. Sci. USA
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Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufmann, K. W. , Renfrew, P.D., Smith, C.A, Sheffler, W., Davis, I.W., Cooper S., Treuille, A., Mandell, D. J., Richter, F., Ban Y.A., Fleishman, S. J., Corn, J. E., Kim, D.E., Lyskov S., Berrondo M., Mentzer, S. , Popovic, Z., Havranek, J. J., Karanicolas, J., Das, R., Meiler, J., Kortemme, T., Gray, J.J., Kuhlman, B., Baker D., Bradley, P. (2011) Rosetta3: an object oriented suite for the simulation and design of macromolecules. Methods in Enzymology. 487 545-574.
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Song, Y., Tyka, M., Leaver-Fay, A., Thompson, J., David Baker (2011) Structure-guided forcefield optimization Proteins. 79 1898-1909.
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Wang, C., Vernon, R., Lange, O., Tyka, M., D. Baker (2010) Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry Protein Science 19 (3), 494 – 506
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Raman, S., Lange, O.L., Ross, P., Tyka, M.,Wang, X. ,Aramin, J., Liu, G., Ramelot, R.A., Eletsky, A., Szyperski, T., Kennedy, M.A., Prestegard, J., Montelione, G.T., Baker, D. (2010) NMR Structure Determination for Larger Proteins Using Backbone-Only Data. Science 19 327 1014 – 1018
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Krieger, E., Joo, K., Lee, .J, Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., Karplus, K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8 (2009). Proteins 77 Suppl 9:114-22.
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DiMaio, F., Tyka, M.D., Baker, M.L., Chiu, W., Baker, D. (2009) Refinement of protein structures into low-resolution density maps using rosetta. J. Mol. Biol. 392(1) 181-90
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Raman, S., Vernon, R., Thompson J., Tyka, M., Sadreyev, R., Pei, J., Kim, D., Kellogg, E., DiMaio, F., Lange, O., Kinch, L., Sheffler, W., Kim, B.H., Das, R., Grishin, N.V., Baker D. (2009) Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 2009; 77 Suppl 9 89-99.
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Das, R., Qian, B., Raman, S., Vernon, R. Thompson, J., Bradley, P., Khare, S., Tyka, M. D., Bhat, D.C. Chivian, Kim, D., Sheffler, W., Malmström, L., Wollacott, A.M., Wang, C., Andre, I., Baker, D. (2007) CASP7 Structure Prediction with Rosetta@home, Proteins. 69 Suppl 8:118-28
- Tyka, M. D., Rea, J., Sessions, R. B., Clarke, A. R. (2007). A highly modular, object-oriented molecular mechanics library for Python.
- Tyka, M. D., Clarke, A.R., Sessions, R.B. (2007). Absolute free energy calculations of liquids using a harmonic reference state. J. Phys. Chem. B. 111(32) 9571-80
- Tyka, M. D.; Clarke, A. R.; Sessions, R. B. (2006) An Efficient, Path-Independent Method for Free-Energy Calculations. J. Phys. Chem. B. 110 (34) 17212-17220
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