Computer Scientist
While I have always primarily been a programmer in various research laboratories, I have also been an active participant in research, demonstrated by co-authoring numerous publications. I have extensive programming experience, in numerous languages including C, C++, Java, Perl, Python, Fortran, and Unix shell scripting. I have also used a variety of web technologies including Javascript, HTML, XML and XML schema. In particular, I wrote several large programs in C/C++ in the Department of Pharmacology at the SUNY Health Science Center in Syracuse NY. These included a program for displaying and analyzing movies of cardiac electrical activity. My most recent large scale project was a user interface written in Python, called SPIRE, for image analysis in Joachim Frank’s laboratory at the Wadsworth Center, which is described at http://www.wadsworth.org/spider_doc/spire/doc/index.html
2012
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Use of SPIDER and SPIRE in Image Reconstruction.. Use of SPIDER and SPIRE in Image Reconstruction. International Tables for Crystallography. 2012;F(Crystallography of Biological Macromolecules). Available at: http://xrpp.iucr.org/cgi-bin/itr?url_ver=Z39.88-2003&rft_dat=what%3Dchapter%26volid%3DFb%26chnumo%3D19o8%26chvers%3Dv0001.
Use of SPIDER and SPIRE in image reconstruction.pdf (330.11 KB)
2009
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Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.. Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules. J Struct Biol. 2009;166(2):126-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19269332. Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.pdf (636.01 KB)
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Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci U S A. 2009;106(4):1063-8. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19122150. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.pdf (1.71 MB)
2008
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SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc. 2008;3(12):1941-74. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19180078. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.pdf (2.04 MB)
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Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification.. Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification. J Struct Biol. 2008;164(1):41-8. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18619547. Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification.pdf (2.75 MB)
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Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. J Struct Biol. 2008;164(1):24-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18606549. Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.pdf (1.69 MB)
2007
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SPIRE: the SPIDER reconstruction engine.. SPIRE: the SPIDER reconstruction engine. J Struct Biol. 2007;157(1):56-63. Available at: http://www.ncbi.nlm.nih.gov/pubmed/17055743. SPIRE the SPIDER reconstruction engine.pdf (875.94 KB)
2005
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Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking.Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking. J Struct Biol. 2005;152(3):211-20. Available at: http://www.ncbi.nlm.nih.gov/pubmed/16330229. Particle picking by segmentation a comparative study with SPIDER-based manual particle picking.pdf (727.35 KB)
2004
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A binary segmentation approach for boxing ribosome particles in cryo EM micrographs.. A binary segmentation approach for boxing ribosome particles in cryo EM micrographs. J Struct Biol. 2004;145(1-2):142-51. Available at: http://www.ncbi.nlm.nih.gov/pubmed/15065681. adiga2004.pdf (577.76 KB)
2002
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A scripting language approach to control software for cryo-electron microscopy.. A scripting language approach to control software for cryo-electron microscopy. Proc IEEE Int. Symp. Biomed. Imag. 2002. Available at: http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1029253&abstractAccess=no&userType=inst. baxter2002.pdf (275.08 KB)
2001
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Visualizing excitation waves inside cardiac muscle using transillumination.. Visualizing excitation waves inside cardiac muscle using transillumination. Biophys J. 2001;80(1):516-30. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11159422. Visualizing excitation waves inside cardiac muscle using transillumination.pdf (639.82 KB)
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Transillumination and optical properties of cardiac tissue.. Transillumination and optical properties of cardiac tissue. Optical Mapping of Cardiac Excitation and Arrhythmias. 2001.
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Video mapping of spiral waves in the heart.. Video mapping of spiral waves in the heart. Optical Mapping of Cardiac Excitation and Arrhythmias. 2001.
1998
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Quantification of effects of global ischemia on dynamics of ventricular fibrillation in isolated rabbit heart.Quantification of effects of global ischemia on dynamics of ventricular fibrillation in isolated rabbit heart. Circulation. 1998;98(16):1688-96. Available at: http://www.ncbi.nlm.nih.gov/pubmed/9778336. Quantification of effects of global ischemia on dynamics of ventricular fibrillation in isolated rabbit heart.pdf (544.04 KB)
1997
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Technical features of a CCD video camera system to record cardiac fluorescence data.. Technical features of a CCD video camera system to record cardiac fluorescence data. Ann Biomed Eng. 1997;25(4):713-25. Available at: http://www.ncbi.nlm.nih.gov/pubmed/9236983. Technical features of a CCD video camera system to record cardiac fluorescence data.pdf (1.86 MB)
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Optical mapping of drug-induced polymorphic arrhythmias and torsade de pointes in the isolated rabbit heart.. Optical mapping of drug-induced polymorphic arrhythmias and torsade de pointes in the isolated rabbit heart. J Am Coll Cardiol. 1997;29(4):831-42. Available at: http://www.ncbi.nlm.nih.gov/pubmed/9091531. Optical mapping of drug-induced polymorphic arrhythmias and torsade de pointes in the isolated rabbit heart.pdf (915.29 KB)
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Video imaging of re-entry on the epicardial surface of the isolated rabbit heart.Video imaging of re-entry on the epicardial surface of the isolated rabbit heart. Computational Biology of the Heart. 1997. Available at: http://www.researchgate.net/publication/266334442_Video_imaging_of_re-entry_on_the_epicardial_surface_of_the_isolated_rabbit_heart.
1996
1995
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Effects of pacing on stationary reentrant activity. Theoretical and experimental study.. Effects of pacing on stationary reentrant activity. Theoretical and experimental study. Circ Res. 1995;77(6):1166-79. Available at: http://www.ncbi.nlm.nih.gov/pubmed/7586230.
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Mechanisms of cardiac fibrillation.Mechanisms of cardiac fibrillation. Science. 1995;270(5239):1222-3; author reply 1224-5. Available at: http://www.ncbi.nlm.nih.gov/pubmed/7502055.
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Nonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart.Nonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart. Circulation. 1995;91(9):2454-69. Available at: http://www.ncbi.nlm.nih.gov/pubmed/7729033.
1994
1993
1992
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Spatiotemporal irregularities of spiral wave activity in isolated ventricular muscle.. Spatiotemporal irregularities of spiral wave activity in isolated ventricular muscle. J Electrocardiol. 1992;24 Suppl:113-22. Available at: http://www.ncbi.nlm.nih.gov/pubmed/1552240.
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Stationary and drifting spiral waves of excitation in isolated cardiac muscle.. Stationary and drifting spiral waves of excitation in isolated cardiac muscle. Nature. 1992;355(6358):349-51. Available at: http://www.ncbi.nlm.nih.gov/pubmed/1731248.
1989
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Horizontal organization of orientation-sensitive cells in primate visual cortex.. Horizontal organization of orientation-sensitive cells in primate visual cortex. Biol Cybern. 1989;61(3):171-82. Available at: http://www.ncbi.nlm.nih.gov/pubmed/2548628.