Laboratory of Neural Injury and Repair, the Wadsworth Center, Albany, NY

William T. Baxter

Laboratory of Neural Injury and Repair, The Wadsworth Center, Albany, NY [email protected]

Education

1992-99 PhD. Pharmacology, SUNY Health Science Center 1983-85 M.S. Computer Science, University at Buffalo, NY 1975-79 B.A. Psychology, University at Albany, NY

Work Experience

7/11 - present Programmer/Analyst, Laboratory of Neural Injury and Repair The Wadsworth Center, Albany ,NY

Assisted in analysis of EEG data for P300 speller for ALS patients. Created a database of electro- corticography studies for generation of an ECoG functional atlas. Maintenance of computer systems monitoring recovery in spinal and peripheral nerve damage studies.

5/00 – 7/11 Computer Scientist, Department of Translational Medicine The Wadsworth Center, Albany ,NY

Wrote a graphical user interface to the SPIDER software used in single-particle reconstruction of macromolecules from electron micrographs. Moderated programmer meetings to facilitate communication between various projects, including a laboratory automation system. Tested and analyzed algorithms for the classification of heterogeneous data in single-particle reconstruction, including a maximum likelihood approach, which was tested on both the RPI BlueGene cluster as well as the NCSA Teragrid.

6/99 - 5/00 Programmer/Analyst, Health Research, Inc. Division of Epidemiology, NYS Dept. Health, Albany, NY

Programmer/administrator during development of a system to allow laboratories and other health providers to report communicable disease test results via the internet. In addition to incorporating standard internet technologies (HTML, Javascript), this project also involved testing software using the HL7 standard for transmission of patient data.

11/90 – 6/99 Scientific Programmer, Department of Pharmacology, SUNY Health Science Center, Syracuse, NY

Developed software for acquisition, image processing and analysis of movies of electrical activity in heart tissue (written in C and C++). Computers were interfaced with lab equipment, including frame grabbers, stimulators, and data acquisition boards. This system was the cornerstone of research in the optical mapping laboratories, resulting in over 40 publications in peer-reviewed journals. Other duties included the maintenance and administration of the optical mapping laboratories. Unix projects included numerical simulations of cardiac activity. 6/89 - 8/90 Scientific Programmer, New Methods Research, Inc., Syracuse, NY

Maintained and developed image processing software for magnetic resonance imaging. Tested and debugged a large heterogeneous software system written in C and Fortran running under Unix and X windows on a variety of platforms. Specified, designed, and implemented routines for image processing and statistical analysis of MR images. Improved the user interface to include mouse-driven real-time tools and a graphical system for analyzing 3D data.

9/84 - 6/89 Programmer in computer vision laboratory, Computer Science Dept., SUNY Buffalo

Wrote software implementing edge detection algorithms in a Unix environment using the C language. In a related project in the Department of Physiology, image processing operations were applied to digitized pictures of brain tissue in order to visualize an injected dye. A model and its computer simulation were developed of the organization of orientation-sensitive cells in the visual cortex.

Publications and manuscripts

Leith, A., Baxter, W.T., Frank, J. Use of SPIDER and SPIRE in Image Reconstruction. Interna- tional Tables for Crystallography, Volume F, Crystallography of Biological Macro- molecules, eds. Michael Rossmann, Eddy Arnold, and Daniel Himmel, Wiley; 2012.

Baxter, W.T., Grassucci, R.A., Gao, H., Frank, J. Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules. J. Struct. Biol. 166:126-132, 2009.

Villa, E., Sengupta, J., Trabuco, L., LeBarron, J., Baxter, W.T., Shaikh, T., Grasucci, R., Nissen, P., Ehrenberg, M., Schulten, K., Frank, J. Ribosome-induced changes in EF-Tu conformation control GTP Hydrolysis. PNAS. 106:1063-1068, 2009.

Shaikh, T.R., Gao, H., Baxter, W.T., Asturias, F., Boisset, N., Leith, A., Frank, J. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols. DOI: 10.1038/nprot2008.156. 2008.

Shaikh, T.R., Trujillo, R., LeBarron, J.S., Baxter, W.T., Frank, J. Particle-verification for single- particle, reference-based reconstruction using multivariate data analysis and classification. J. Struct. Biol. 164(1): 41-48, 2008.

LeBarron, J., Grassucci, R.A., Shaikh, T.R., Baxter, W.T., Sengupta, J., Frank, J. Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. J. Struct. Biol. 164(1):24-32, May 2008.

Baxter, W.T., Leith, A., Frank, J. SPIRE: The SPIDER Reconstruction Engine. J. Struct. Biol. 157:56-63, 2007.

Adiga, U., Baxter, W.T., Hall, R.J., Frank, J. and Glaeser, R.M. Particle picking by segmentation: A comparative study with SPIDER-based manual particle picking. J. Struct. Biol. 152:211-220, 2005.

2 Adiga U., Malladi R., Baxter W. Glaser R. A binary segmentation approach for boxing ribosome particles in cryo EM micrographs. J. Struct. Biol. 145:142-151, 2004.

Baxter, W.T., Leith, A., and Frank, J. A scripting language approach to control software for cryo- electron microscopy. Proc IEEE Intl. Symp. Biomed. Imag., 301-304, 2002.

Baxter, W.T. Transillumination and optical properties of cardiac tissue. In: Optical Mapping of Cardiac Excitation and Arrhythmias. Rosenbaum, D.S., Jalife, J., eds. Armonk, NY: Futura; 2001.

Baxter, W.T. and Davidenko, J.M. Video mapping of spiral waves in the heart. In: Optical Mapping of Cardiac Excitation and Arrhythmias. Rosenbaum, D.S., Jalife, J., eds. Armonk, NY: Futura; 2001.

Baxter, W.T., Mironov, S.F., Zaitsev, A.V., Pertsov, A.M. and Jalife, J. Visualizing excitation waves inside cardiac muscle using transillumination. Biophysical Journal 80:516-530, 2001.

Baxter, W. T. Intramural optical recordings of cardiac electrical activity via transillumination. PhD dissertation, October 1999.

Baxter, W.T., Davidenko, J.M., Loew, L.M., Wuskell, J.P. and Jalife, J. Technical features of a CCD video camera system to record cardiac fluorescence data. Annals of Biomedical Engineering 25:713-725, 1997.

Mandapati, R., Baxter, W.T., Gray, R., Davidenko, J., Jalife, J. Quantification of effects of global ischemia on dynamics of ventricular fibrillation in isolated rabbit heart. Circulation 98:1688-1696, 1998.

Asano, Y., Davidenko, J.M., Baxter, W.T., Gray, R.A. and Jalife, J. Optical mapping of drug- induced polymorphic arrhythmias and torsade de pointes in the isolated rabbit heart. Journal of the American College of Cardiology 29:831-842, 1997.

Gray, R.A., Baxter, W.T., Cabo, C., Davidenko, J.M., Pertsov, A.M. and Jalife, J. Video imaging of re-entry on the epicardial surface of the isolated rabbit heart. In: Computational Biology of the Heart, edited by Panfilov, A.V. and Holden, A.V. New York: John Wiley & Sons, 1997, p. 277-294.

Cabo, C., Pertsov, A.M., Davidenko, J.M., Baxter, W.T., Gray, R.A. and Jalife, J. Vortex shedding as a precursor of turbulent electrical activity in cardiac muscle. Biophysical Journal 70:1105-1111, 1996.

Cabo, C., Pertsov, A.M., Baxter, W.T., Davidenko, J.M. and Jalife, J. Measurements of curvature in an ionic model of cardiac tissue. Chaos, Solitons & Fractals 5:481-489, 1995.

Davidenko, J.M., Salomonsz, R., Pertsov, A.M., Baxter, W.T. and Jalife, J. Effects of pacing on stationary reentrant activity. Theoretical and experimental study. Circulation Research 77:1166-1179, 1995.

Gray, R.A., Jalife, J., Panfilov, A.V., Baxter,W.T., Cabo,C., Davidenko,J.M. and Pertsov,A.M.

3 Mechanisms of cardiac fibrillation. Science 270:1222-1223, 1995.

Gray, R.A., Jalife, J., Panfilov, A., Baxter,W.T., Cabo,C., Davidenko,J.M. and Pertsov,A.M. Nonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart. Circulation 91:2454-2469, 1995.

Baxter, W.T., Davidenko, J.M., Cabo, C. and Jalife, J. Video Imaging of cardiac transmembrane activity. Clinical Applications of Modern Imaging Technology II SPIE:357-366, 1994.

Cabo, C., Pertsov, A.M., Baxter, W.T., Davidenko, J.M., Gray, R.A. and Jalife, J. Wave-front curvature as a cause of slow conduction and block in isolated cardiac muscle. Circulation Research 75:1014-1028, 1994.

Pertsov, A.M., Davidenko, J.M., Salomonsz, R., Baxter, W.T. and Jalife, J. Spiral waves of excitation underlie reentrant activity in isolated cardiac muscle. Circulation Research 72:631-650, 1993.

Davidenko, J.M., Pertsov, A.M., Salomonsz, R., Baxter, W.T. and Jalife, J. Spatiotemporal irregularities of spiral wave activity in isolated ventricular muscle. Journal of Electrocardiology 24 Suppl:113-122, 1992.

Davidenko, J.M., Pertsov, A.V., Salomonsz, R., Baxter, W. and Jalife, J. Stationary and drifting spiral waves of excitation in isolated cardiac muscle. Nature 355:349-351, 1992.

Baxter, W.T. and Dow, B.M. Horizontal organization of orientation-sensitive cells in primate visual cortex. Biological Cybernetics 61:171-182, 1989.