DCB Publications
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- Berezhkovskii AM, Murphy RD, Buchete NV "Network random walk model of two-state protein folding: Test of the theory" J. Chem. Phys. 138(3):036101, 2pp.
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM, Bezrukov SM "Particle lifetime in cylindrical cavity with absorbing spot on the wall: Going beyond the narrow escape problem" J. Chem. Phys. 137(23), 234108, 6 pp.
[Abstract] [Full Article] - Berezhkovskii AM "Aris-Taylor dispersion from single-particle point of view" J. Chem. Phys. 137(6) 066101, 2 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Sample C, Shvartsman SY "Formation of morphogen gradients: Local accumulation time" Phys. Rev. E 83(5) 051906, 7 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV "Extended narrow escape problem. Boundary homogenization based analysis" Phys. Rev. E 82(1) 011114, 5 pp.
[Abstract] [Full Article] - Nestorovich EM, Karginov VA, Berezhkovskii AM, Parsegian VA, Bezrukov SM "Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative" Proc. Natl. Acad. Sci. USA 109(45):18453-58
[Abstract] [Full Article] - Banerjee A, Berezhkovskii A, Nossal R "Distribution of lifetime and maximum size of abortive clathrin-coated pits." Phys. Rev. E 86, 031907, 8 pp.
[Abstract] [Full Article] - Berezhkovskii AM "Aris-Taylor dispersion from single-particle point of veiw." J. Chem. Phys. 137(6), 066101, 2 pp.
[Abstract] [Full Article] - In Silico Approaches to Structure and Function of Cell Components and Their Assemblies; in Comprehensive Biophysics; S. A. Hassan and E. L. Mehler, Vol. 9, pp 190-228, Academic Press (2011) [Full Article]
- Microscopic Mechanism of Nanocrystal Formation from Solution by Cluster Aggregation and Coalescence S A Hassan; J. Chem. Phys. 134, 114508 (2011)
[Abstract] [Full Article] - Banerjee A, Berezhkovskii A, Nossal R "Stochastic Model of Clathrin-Coated Pit Assembly." Biophys. J. 102(12):2725-30
[Abstract] [Full Article] [Supplementary] - Dagdug L, Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu, Bezrukov SM "Force-dependent mobility and entropic rectification in tubes of periodically varying geometry" J. Chem. Phys. 136(21) 214110, 6 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Lizunov VA, Zimmerberg J, Bezrukov SM "Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles" J. Chem. Phys. 136(21) 211102, 4 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Lizuniv VA, Zimmerberg J, Bezrukov SM "Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles" J. Chem. Phys. 136(21), 211102, 4 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Lizunov VA, Zimmerberg J, Bezrukov SM "Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles" J. Chem. Phys. 136(21): 211102, 4 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Lizunov VA, Zimmerberg J, Bezrukov SM "Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles" J. Chem. Phys. 136(21): 211102, 4 pp.
[Abstract] [Full Article] - Dagdug L, Vazquez M-V, Berezhkovskii AM, Zitserman VY, Bezrukov SM "Diffusion in the presence of cylindrical obstacles arranged in a square lattice analyzed with generalized Fick-Jacobs equation." J. Chem.Phys. 136(20): 204106, 5 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L "Effect of binding on escape from cavity through narrow tunnel" J. Chem. Phys. 136(12) 124110
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV "Search for a small hole in a cavity wall by intermittent bulk and surface diffusion." J. Chem. Phys. 136(5): 054115, 6 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Surface area of the domain visited by a spherical Brownian particle" Chaos 21(4) 047519, 3 pp.
[Abstract] [Full Article] - Pineda I, Vazquez M-V, Berezhkovskii AM, Dagdug L "Diffusion in periodic two-dimensional channels formed by overlapping circles: Comparison of analytical and numerical results." J. Chem. Phys. 135(22):224101, 5 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Shvartsman SY "Physical interpretation of mean local accumulation time of morphogen gradient formation" J. Chem. Phys. 135(15): 154115, 6 pp.
[Abstract] [Full Article] - Zitserman VYu, Berezhkovskii AM, Antipov AE, Makhnovskii YuA "Drift velocity of Brownian particle in a periodically tapered tube induced by a time-periodic force with zero mean: Dependence on the force period" J. Chem. Phys. 135(12):121102-1-4
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Effective drift and diffusion of a particle jumping between mobile and immobile states." J. Electroanal. Chem. 660:352-355
[Abstract] [Full Article] - Berezhkovskii AM, Szabo A, Zhou H-X "Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels." J. Chem. Phys. 135(7):075103-1-5
[Abstract] [Full Article] - Berezhkovakii AM, Szabo A "Time scale separation leads to position-dependent diffusion along the slow coordinate." J. Chem. Phys. 135(7):074108-1-5
[Abstract] [Full Article] - Berezhkovskii AM "Ordinary differential equation for local accumulation time." J. Chem. Phys. 135(7):074112-1-5
[Abstract] [Full Article] - Berezhkovskii AM, Lizunov VA, Zimmerberg J, Bezrukov SM "Functional Role for Transporter Isoforms in Optimizing Membrane Transport" Biophys. J.101(2):L14-L16
[Abstract] [Full Article] - Berezhkovskii AM, Sample C, Shvartsman SY "Formation of morphogen gradients: Local accumulation time." Phys. Rev. E 83(5):051906, 7pp.
[Abstract] [Full Article] - Gordon PV,Sample C, Berezhkovskii AM, Muratov CB, Svartsman SY "Local kinetics of morphogen gradients." PNAS 108(15):6157-62
[Abstract] [Full Article] [Supplementary] - Berezhkovskii AM, Dagdug L "Analytical treatment of biased diffusion in tubes with periodic dead ends." J. Chem. Phys. 134(12):124109, 8 pp.
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu, Bezrukov SM "Turnover behavior of effective mobility in a tube with periodic entropy potential." J. Chem. Phys. 134(10): 101102-1-3
[Abstract] [Full Article] - Berezhkovskii AM "Renewal theory for single-molecule systems with multiple reaction channels." J. Chem. Phys. 134(7), 8 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Sample C, Shvartsman SY "How long does it take to establish a morphogen gradient" Biophys. J. 99(8):L59-61
[Abstract] [Full Article] - Berezhkovskii AM, Pustovoit MA, Bezrukov SM "Fluxes of non-interacting and strongly repelling particles through a single conical channel: Analytical results and their numerical tests." Chem. Phys. 375(2-3): 523-28
[Abstract] [Full Article] - C.A. Johnson, W.W. Lau, G. Wang, K. Collie, J.F. Jones, Jr., M. Vos, L. Krueger An Ensemble Classification System for Research Categorization and Decision Support in Portfolio Analysis
[Abstract] [Full Article] [Supplementary] - Berezhkovskii AM, Dagdug L "Bised diffusion in tubes formed by spherical compartments." J. Chem. Phys. 133(13):134102 (6 pp.)
[Abstract] [Full Article] - Berezhkovskii AM, Pustovoit MA, Bezrukov SM "Entropic effects in channel-facilitated transport: Inter-particle interactions break the flux symmetry." Phys. Rev. E 80(2): 020904(R), 4 pp.
[Abstract] [Full Article] - Dagdug L, Vazquez M-V, Berezhkovskii AM, Bezrukov SM "Unbiased diffusion in tubes with corrugated walls" J. Chem. Phys. 133(3): 034707, 3 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV "Extended narrow escape problem: Boundary homogenization-based analysis." Phys. Rev. E82(1): 011114, 5pp.
[Abstract] [Full Article] - Nestorovich EM, Karginov VA, Berezhkovskii AM, Bezrukov SM "Blockage of Anthrax PA63 Pore by a Multicharged High-Affinity Toxin Inhibitor" Biophys. J. 99(1):134-143
[Abstract] [Full Article] - Berezhkovskii AM, Dagdug L, Makhnovskii YuA, Zitserman VYu "Communications: Drift and diffusion in a tube of periodically varying diameter. Driving force induced intermittency." J. Chem. Phys. 132(22): 221104-1-4
[Abstract] [Full Article] - Makhnovskii YuA, Berezhkovskii AM, Zitserman VYu, "Diffusion in a tube of alternating diameter." Chem. Phys. 370(1-3):238-43
[Abstract] [Full Article] - Berezhkovskii AM "Variance of residence time spent by diffusing particle in a sub-domain: Path integral based approach" Chem. Phys. 370(1-3):253-57
[Abstract] [Full Article] - Modeling Aqueous Solvent Effects through Local Properties of Water; in Modeling Solvent Environments: Applications to Simulations of Biomolecules, Ed M. Feig, Wiley-VCH [Full Article]
- Makhnovskii YuA, Berezhkovskii AM, Zitserman VYu "Diffusion in a tube of alternating diameter." Chem. Phys. 367(1):110-14
[Abstract] [Full Article] - Yonqing Zhang, Supriyo De, John R. Garner, Kirstin Smith, S. Alex Wang, and Kevin G. Becker "Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information." BMC Medical Genomics, 2010 Jan 21;3:1. doi:10.1186/1755-8794-3-1
[Abstract] [Full Article] - Supriyo De, Yongqing Zhang, John R Garner, S. Alex Wang, and Kevin G. Becker Physiol. Genomics (August 3, 2010). doi:10.1152/physiolgenomics.00008.2010
[Abstract] [Full Article] - Steele ME, Narva AS, Mahooty S, Romancito G, Kempner KM "Using Telehealth to Improve Kidney Disease Care for the Zuni Indian Population" 15th Annual International Meeting of the American Telemedicine Association, vol. 16, pp. S-111, May 2010. [Full Article]
- Berezhkovskii AM, Barzykin AV, Zitserman VYu "One-dimensional description of diffusion in a tube of abruptly changing diameter: Boundary homogenization based approach." J. Chem. Phys. 131(22): 224110-1-8
[Abstract] [Full Article] - RZ Freidlin, Y Assaf, PJ Basser "Multivariate hypothesis testing for tissue clustering and classification: a DTI study of Excised Rat Spinal Cord" - Joint Annual Meeting ISMRM-ESBM, 2007
[Abstract] Full Article - RZ Freidlin, Y Assaf, PJ Basser "Multivariate hypothesis testing of DTI data for tissue clustering" -B IEEE Int. Symp. Biomed Imag, 2007
[Abstract] Full Article - Komlosh ME, Lizak MJ, Horkay F, Freidlin RZ, Basser PJ. "Observation of microscopic diffusion anisotropy in the spinal cord using double-pulsed gradient spin echo MRI." Magn Reson Med. 2008 Apr;59(4):803-9.
[Abstract] [PubMed] Detection of microscopic anisotropy in gray matter and in a novel tissue phantom using double Pulsed Gradient Spin Echo MR.Komlosh ME, Horkay F, Freidlin RZ, Nevo U, Assaf Y, Basser PJ.J Magn Reson. 2007 Nov;189(1):38-45. Epub 2007 Jul 18.
[Abstract] [Full Article]Observation of microscopic diffusion anisotropy in the spinal cord using double-pulsed gradient spin echo MRI.Komlosh ME, Lizak MJ, Horkay F, Freidlin RZ, Basser PJ. Magn Reson Med. 2008 Apr;59(4):803-9
[Abstract] [PubMed]Parsimonious model selection for tissue segmentation and classification applications: a study using simulated and experimental DTI data.Freidlin RZ, Ozarslan E, Komlosh ME, Chang LC, Koay CG, Jones DK, Basser PJ.IEEE Trans Med Imaging. 2007 Nov;26(11):1576-84.
[Abstract] [PubMed]A multivariate hypothesis testing framework for tissue clustering and classification of DTI data. Freidlin RZ, Ozarslan E, Assaf Y, Komlosh ME, Basser PJ.NMR Biomed. 2009 Aug;22(7):716-29.
[Abstract] [PubMed]- C. Johnson, H. Cheung, R Martino, S. Bailey, D. Russ, A. Fletcher, B. Trus, "IRPgrid: A Feasibility Study of Grid Technologies for the NIH Intramural Research Program"
[Abstract] Presentation (2009) - Daniel E. Russ, Faye C. Austin, Carl A. Roth, Calvin A. Johnson, "Primary Assessment of High-Risk High-Reward Research at NIH Using Context-Sensitive Text Mining" NIH Research Festival 2009. Presentation (2009)
- H. Cheung, T. Caruso, A. Frazin, A. Ravindran, T. Doan, A. Wang, C. Johnson," A Protocol Lifeycycle Tracking Tool for Clinical Research." NIH Research Festival 2009.
[Abstract] Presentation (2009) [Supplementary] - Makhnovskii YuA, Berezhkovskii AM, Zitserman VYu "Time-dependent diffusion in tubes with periodic partitions." J. Che. Phys. 131(10): 104705-1-5
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM "Drift and diffusion in periodic potentials: Upstream and downstream step times are distributed identically" J. Chem. Phys. 131(5): 056101, 3 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Barzykin AV, Zitserman VYu "Escape from cavity through narrow tunnel." J. Chem. Phys. 130(24) 245104-1 - 245104-6
[Abstract] [Full Article] - Berezhkovskii A, Hummer G, Szabo A "Reactive flux and folding pathways in network models of coarse-grained protein dynamics." J. Chem. Phys. 130(20):205102, 5pp.
[Abstract] [Full Article] - Intramolecular Disulfide Bridges of the Prolactin Receptor Short Form are required for its Inhibitory Action on the Function of the Long Form of the Receptor Y. L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau; Mol. Cell. Biol. 29, 2546 (2009)
[Abstract] [Full Article] - Lau W, Shum L, Johnson C "Salivary Proteome Wiki: A Collaborative Environment to Share and Annotate Proteomics Data." Clinical Proteomics (Proc. of 8th Human Proteome Organisation Congress). 5(Suppl. 1): 13, Sept, 2009 [Full Article] [Supplementary]
- Shvartsman SY, Coppey M, Berezhkovskii AM "MAPK signaling in equations and embryos." Fly 3(1):62-67
[Abstract] [PubMed] - Bailey MJ, Coon SL, Carter DA, Humphries A, Kim JS, Shi Q, Gaildrat P, Morin F, Ganguly S, Hogenesch JB, Weller JL, Rath MF, Mller M, Baler R, Sugden D, Rangel ZG, Munson PJ, Klein DC. Night/Day Changes in Pineal Expression of >600 Genes: CENTRAL ROLE OF ADRENERGIC/cAMP SIGNALING." J Biol Chem. 2009 Mar 20;284(12):7606-22. Epub 2008 Dec 22.
[Abstract] [PubMed] - Berezhkovskii AM, Coppey M, Shvartsman SY "Signaling gradients in cascades of two-state reaction-diffusion systems" Proc. Natl. Acad. Sci. USA. 106(4):1087-92
[Abstract] [Full Article] - Nancy S. Longo, Patricia L. Lugar, Sule Yavuz, Wen Zhang, Peter H. L. Krijger, Daniel E. Russ, Dereje D. Jima, Sandeep S. Dave, Amrie C. Grammer and Peter E. Lipsky "Analysis of somatic hypermutation in X-HIgM syndrome reveals specific deficiencies in mutational targeting " Blood, preprint, doi:10.1182/blood-2008-10-183632
[Abstract] [Full Article] - Christopher D Dharmaraj, Anthony R Fletcher, Phuc N Doan, Nallathamby Devasahayam, Shingo Matsumato, Calvin Johnson, John A. Cook, James B. Mitchell, Sankaran Subramanian, Murali C Krishna "Reconstruction for Time-Domain In-Vivo EPR 3-D Multi-Gradient Oximetric Imaging - A Parallel Processing Perspective, " International Journal of Biomedical Imaging, vol. 2009, Article ID 528639, 2009. doi:10.1155/2009/528639
[Abstract] [Full Article] - Berezhkovskii AM, Coppey M, Sealfon SC, Shvartsman S "Cell-to-cell communication: Time and length scales of ligand internalization in cultures of suspended cells." J. Chem. Phys. 128 (22): 225102-1 - 6
[Abstract] [Full Article] - Vazquez MV, Berezhkovskii AM, Dagdug L "Diffusion in linear porous media with periodic entropy barriers: A tube formed by contacting spheres." J. Chem. Phys. 129:046101.
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM, Makhnovskii YA, Zitserman VY "Transient diffusion in a tube with dead ends" J Chem. Phys. 127(22): 224712-1 - 224712-9
[Abstract] [Full Article] - Coppey M, Berezhkovskii AM, Kin Y, Boettiger AN, Shvartsma SY "Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein." Dev. Biol. 312: 623-30
[Abstract] [Full Article] - Johnson C., Lau W., Bhandari A., and Hays T. , A Best-Fit Model for Concept Vectors in Biomedical Research Grants, Proc. AMIA Symp. 2008: 993.
[Abstract] [Full Article] [Supplementary] - Dagdug L, Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu "Particle size effect on diffusion in tubes with dead ends: Nonmonotonic size dependence of effective diffusion constant" J. Chem. Phys. 129(18): 184706-1 -5
[Abstract] [Full Article] - Shvartsman SY,Mathieu Coppey M, and Berezhkovskii AM "Dynamics of maternal morphogen gradients in Drosophila" Current Opinion in Genetics and Development 18(4): 342-47 (2008)
[Abstract] [Full Article] - D. E. Russ, F. C. Austin, G. Sun, W. Lau, C. A. Johnson "Context-Dependent Text Mining for the Retrospective Identification of High-Risk, High-Reward Research", Poster 2008 NIH Research Festival DCB Technical Report (2008) [Supplementary]
- Zitserman VYu, Berezhkovskii AM, Pustovoit MA, Bezrukov SM "Relaxation and fluctuations of the number of particles in a membrane channel at arbitrary particle-channel interaction." J. Chem. Phys. 129(9): 5 pp.
[Abstract] [Full Article] - "Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions" S. A. Hassan; J. Phys. Chem. B 112, 10573 (2008)
[Abstract] [Full Article] - Ajay, Zavaleta A, Frazin A, Chintala S, and Cheung H. "Semantic Wiki for Collaborative Annotation of Chemical Biology Data."NIH Research Festival 2008. [Full Article]
- Vazquez MV, Berezhkovskii AM, Dagdug L "Diffusion in linear porous media with periodic entropy barriers: A tube formed by contacting spheres." J Chem. Phys. 129(4):046101-1-2
[Abstract] [Full Article] - Coppey M, Boettiger AN, Berezhkovskii AM, Shvartsman SY "Nuclear Trapping Shapes the Terminal Gradient in the Drosophila Ebryo." Current Biology 18(12): 915-19
[Abstract] [Full Article] - J. Pavlicek, S. L. Coon, S. Ganguly, J. L. Weller, S. A. Hassan, D. L. Sackett, and D. C. Klein "Evidence that Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase" J. Biol. Chem. 283, 14552 (2008)
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Fluctuation theorem for channel-facilitated membrane transport of interacting and non-interacting solutes" J Phys. Chem. B 112(19): 6228-32
[Abstract] [Full Article] - Berezhkovskii AM, Weiss GH "Propagators and related descriptors for non-Markovian asymmetric random walks with and without boundaries" J Chem. Phys. 128(4) 044914, 5 pp.
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Counting translocations of strongly repelling particles through single channels: Fluctuation theorem for membrane transport" Phys. Rev. Lett. 100(3): 038104, 4pp.
[Abstract] [Full Article] - S. A. Hassan Morphology of Ion Clusters in Aqueous Electrolytes; Phy. Rev. E 77, 031501 (2008)
[Abstract] [Full Article] - Berezhkovskii AM, Bezrukov SM "Counting Translocations of Strongly Repelling Particles through Single Channels: Fluctuation Theorem for Membrane Transport." Phys. Rev. Lett. 100(3): 038104, 4pp.
[Abstract] [Full Article] - Berezhkovskii AM, Weiss GH "Propagators and related descriptors for non-Markovian asymmetric random walks with and without boundaries." J. Chem. Phys. 128(1): 044914, 5 pp.
[Abstract] [Full Article] - Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, and Hirschman L. " Overview of BioCreative II Gene Normalization." Genome Biology. 9(S2):S3, 2008.
[Abstract] [Full Article] - Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tasi RTH , Hung HC, Lau WW, Johnson CA, Stre R, Yoshida K, Kim S, Shin SY, Zhang BT, Baumgartner WA, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozguro A, Erkan G, Radev DR, Krauthammer M, Luong TB, Hoffmann R, Sander C, and Valencia A "Introducing Meta-Services for Biomedical Information Extraction." Genome Biology. 9(S2):S6, 2008
[Abstract] [Full Article] - Kakareka JW, Smith PD, Pohida TJ, Hendler RW,"Simultaneous measurements of fast optical and proton current kinetics in the bacteriorhodopsin photocycle using an enhanced spectrophotometer". J. Biochem. Biophys. Methods 70 (2008) 11161123
[Abstract] [PubMed] - Coppey M, Berezhkovskii AM, Kin Y, Boettinger AN, Shvartsman SY "Modeling the Bicoid gradient: Diffusion and reversible nuclear trapping of stable protein" Developmental Biology 312(2):623-30
[Abstract] [Full Article] - Dagdug L, Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu "Transient diffusion in a tube with dead ends." J Chem. Phys. 127(22) 224712, 9pp.
[Abstract] [Full Article] - Cheung H., Wang A., Fann Y., Upender B., Chinatala S., Frazin A., Nie W., Martino R.L., and Johnson C. "A Web-Based, Meta-Data Driven, Clinical Research Platform for Managing Multiple Clinical Research Studies," Proceedings of the American Medical Informatics Association (AMIA) 2007 Annual Symposium, November, 2007, Chicago, IL, M-054
[Abstract] [Full Article] [Supplementary] - Coppey M, Berezhkovskii AM, Kim Y, Boettiger AN, Shvartsman SY "Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein" Dev. Biol.
[Abstract] [Full Article] - Vogel A, Chernomordik V, Riley J, Hassan M, Amyot, F, Dasgeb B, Demos S, Pursley R, Little R, Yarchoan R, Tao Y, Gandjbakhche A "Using noninvasive multispectral imaging to quantitatively assess tissue vasculature" Journal of Biomedical Optics. 2007 12(5): 051604(1-13).
[Abstract] [Full Article] - Berezhkovskii AM,Barzykin AV "Simple formulas for the trapping rate by nonshperical absorber and capacitance of nonspherical conductor." J Chem. Phys. 126(10): 106102-1-3
[Abstract] [Full Article] Berezhkovskii AM, Bezrukov SM
"Site model for channel-facilitated membrane transport: Invariance of translocation-time distribution with respect to direction of passage." J Phys. Cond. Matter 19(6): 065148-1-10
Berezhkovskii AM, Pustovoit MA, Bezrukov SM
"Diffusion in a tube of varying cross section: Numerical study of reduction to effective one-dimensional description." J Chem. Phys. 126(13): 134706-1-5
J. Chem. Phys. 126, 134706, 5 pp. (2007).
[Abstract] [Full Article]- Bezrukov SM, Berezhkovskii AM, Szabo A "The diffusion model of the solute dynamics in the membrane channel: mapping onto two-site model and optimizing the flux."J Chem. Phys. 127(11):115101-1-8
[Abstract] [Full Article] - Becker KG, Zhang Y, Shenoy N, Smith KE, Karolchik D, Hsu F, Wang SA "GAD and GADview: a genomic view of common human disease" HUGOs 12th Human Genome Meeting, B.128 [Full Article]
- Hassan M, Riley J, Chernomordik V, Smith P, Pursley R, Lee SB, Capala J, Gandjbakhche A; Fluorescence Lifetime Imaging System for in vivo Studies. Molecular Imaging 6(4):229-236.
[Abstract] [Full Article] - Hiebel AC, Lee YS, Bilsky E, Giuvelis D, Deschamps JR, Parrish DA, Aceto MD, May EL, Harris LS, Coop A, Dersch CM, Partilla JS, Rothman RB, Cheng, K, Jacobson AE, Rice KC "Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent m-Agonist d-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series" J. Med. Chem. 2007, 50, 3765-3776
[Abstract] - S. A. Hassan, "Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution", J. Phys. Chem. B 111 , 227 (2007)
[Abstract] [Full Article] - Trus, BL, Newcomb, WW, Cheng, N, Cardone, G, Marekov, L, Homa, FL, Brown, JC, Steven, AC, "Allosteric Signalling and a Nuclear Exit Strategy: Binding of UL25/UL17 Heterodimers to DNA-filled HSV-1 Capsids" Mol. Cell (2007)
[Abstract] [Full Article] - M. Rodriguez, J.-S. Liow, S. Thada, M. Sibomana, S. Chelikani, T. Mulnix, C.A. Johnson, C. Michel, W.C. Barker, and R.E. Carson, "Count-Rate Dependent Component-Based Normalization for the HRRT", IEEE Transaction on Nuclear Science, vol. 54, no. 3, pp. 486-495 (2007).
[Abstract] [Full Article] - Subramanian S, Koscielniak JW, Devasahayam N, Pursley RH, Pohida TJ, Krishna MC; A new strategy for fast radiofrequency CW EPR imaging: Direct detection with rapid scan and rotating gradients. J Magn Reson. 186:212-219. (2007)
[Abstract] [PubMed] - Lau, William W., Becker, Kevin G., and Johnson, Calvin A., "Rule-based Human Gene Normalization in Biomedical Text with Confidence Estimation", LSS Computational Systems Bioinformatics, San Diego, August, 2007, pp. 371-379.
[Abstract] [PubMed] - Lau WW, Johnson CA, "Rule-based Gene Normalization with Statistical and Heuristic Confidence Measure", Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, 2007, pp. 165 - 167.
[Abstract] [Full Article] Berezhkovskii AM, Szabo A
"Perturbation theory of Phy-value analysis." J Chem. Phys. 125(10): 104902-1-5
Berezhkovskii AM, Makhnovskii YuA, Zitserman VYu
"Escape from a cavity through a small window: Turnover of the rate as a function of friction constant." J Chem. Phys. 125(19): 194501-1-7
Pustovoit MA, Berezhkovskii AM, Bezrukov SM
"Analytical theory of hysteresis in ion channel: Two-state model." J Chem. Phys. 125(19): 194907-1-8
Dagdug L, Berezhkovskii AM
"Diffusion-limited binding to a site on the wall of a membrane channel." J Chem. Phys. 125(24): 244705-1-7
Berezhkovskii AM, Hummer G, Bezrukov SM
"Uphill and downhill direct translocation times through membrane channels." Phys. Rev. Lett. 97(2): 020601-1-4
Berezhkovskii AM
"Lateral diffusion near the interface of two immiscible liquids." Acta Physica Polonica B 37(5): 1397-407
Berezhkovskii AM, Weiss GH
"Diffusion in Multilayer Media: Transient Behavior of the Lateral Diffusion Coefficient." J Chem. Phys. 124(15): 154710-1-10
Berezhkovskii AM, Monine MI, Muratov CB, Shvartsman SY
"Homogenization of the boundary conditions on surfaces with regular arrays of traps." J Chem. Phys. 124 (3) 036103-1-3
- Nishizuka1,S., Washburn,N.R., and Munson, P.J. "Evaluation method of ordinary flatbed scanners for quantitative density analysis" BioTechniques. 40:442-448 (2006)
[Abstract] [Full Article] - Wang,S., Zhang, J., Theel,S., Barb, J.J, Munson, P.J. and Danner,R.L. "Nitric oxide activation of Erk1/2 regulates thestability and translation of mRNA transcriptscontaining CU-rich elements" Nucleic Acids Research, Vol. 34, No. 10 30443056 (2006)
[Abstract] [Full Article] - Talwar,S.,Munson,P.J., Barb,J.,Fiuza, C., Cintron,A.P., Logun,C., Tropea,M., Khan,S., Reda,D., Shelhamer,J.H., Danner,R.L. and Suffredini,A.F. "Gene expression profiles of peripheral blood leukocytes after endotoxin challenge in humans" Physiol Genomics 25:203-215, (2006)
[Abstract] [Full Article] - Sam,V., Tai,C.H., Garnier1,J., Gibrat,J.F., Lee,B. and Munson, P.J. "ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification" BMC Bioinformatics. 7:206 (2006)
[Abstract] [Full Article] - HUYNH,T.T., PACAK,K., WONG,D.L., LINEHAN,W.M., GOLDSTEIN,D.S., ELKAHLOUN,A.G., MUNSON,P.J. and Eisenhofer,G."Transcriptional Regulation ofPhenylethanolamineN-Methyltransferase in Pheochromocytomas from Patients with von HippelLindau Syndrome and Multiple Endocrine Neoplasia Type 2" Ann. N.Y. Acad. Sci. 1073: 241252 (2006)
[Abstract] [Full Article] - Hoover,S.E., Cohrs,R.J., Rangel,Z.G., Gilden,D.H., Munson, P. and Cohen, J.I. "Downregulation of Varicella-Zoster Virus (VZV) Immediate-EarlyORF62 Transcription by VZV ORF63 Correlates withVirus Replication In Vitro and with Latency" JOURNAL OF VIROLOGY. 80.7.34593468 (2006)
[Abstract] [Full Article] - Torre,C., Ying,S., Munson, P.J.,Meduri,G.U., and Suffredini, A.F."Proteomic analysis of inflammatory biomarkers inbronchoalveolar lavage" Proteomics 6: 39493957 (2006)
[Abstract] [Full Article] - Cassiani-Ingoni,R.,Cabral, E.S.,Lunemann,J.D,Garza,Z.,Magnus,T.,Gelderblom,H.,Munson,P.J.,Marques,M. and Roland Martin, "Borrelia burgdorferi Induces TLR1 and TLR2 in Human Microgliaand Peripheral Blood Monocytes but Differentially RegulatesHLA-Class II Expression" J Neuropathol Exp Neurol Volume 65, Number 6, (2006)
[Abstract] [Full Article] - Cabral,E.S.,Gelderblom,H.,Hornung,R.L.,Munson,P.J.,Martin,R.and Marques,A.R "Borrelia burgdorferi LipoproteinMediated TLR2Stimulation Causes the Down-Regulation of TLR5in Human Monocytes" The Journal of Infectious Diseases: 193:84959 (2006)
[Abstract] [Full Article] - BROUWERS,F.M.,ELKAHLOUN,A.G.,Munson,P.J.,EISENHOFER, G.,BARB,J.LINEHAN,W.M.,LENDERS,J.W.M,KRIJGER,R.D., MANNELLI,M.,UDELSMAN,R., OCAL,I.T.,SHULKIN,B.L.,BORNSTEIN,S.R.,BREZA,J., KSINANTOVA,L.AND PACAK,K. "Gene Expression Profiling of Benignand Malignant Pheochromocytoma" Ann. N.Y. Acad. Sci. 1073: 541556 (2006)
[Abstract] [Full Article] - Z.Xiang, "Advances in homology protein structure modeling", Curr. Prot. Pept. Sci. 7:217, (2006)
[Abstract] [PubMed] - E L Mehler, S A Hassan, S Kortagere and H Weinstein "Ab Initio Computer Modeling of loops in G-Protein Coupled Receptors: Lessons from the Crystal Structure of Rhodopsin" Proteins 64, 673 (2006)
[Abstract] [Full Article] - SA Hassan, G Hummer, and YS Lee "Effects of Electric Fields on Proton Transport through Water Chains" J. Chem. Phys. 124, 204510 (2006)
[Abstract] [Full Article] - Freidlin R.Z, Ohazama C.J., Arai A.E., McGarry D.P., Panza J.A., Trus B.L. "NIHmagic: 3D Visualization, Registration and Segmentation Tool" [Full Article]
- Dudko O.K., Weiss G.H. and Chernomordik V. "Mean-time-of flight of photons in transillumination measurements of optically anisotropic tissue with an inclusion", Phys. Med. Biol. 51: 4719-4733 (2006)
[Abstract] [Full Article]
[Abstract] [PubMed]- Husain, FT., Fromm, SJ., Pursley, RH., Hosey, LA., Braun, AR., Horwitz, B. Neural Bases of Categorization of Simple Speech and Nonspeech Sounds. Human Brain Mapping, 2006, 27:636-651
[Abstract] [PubMed] - Pursley R, Salem G, Devasahayam N, Subramanian S, Koscielniak J, Krishna M, Pohida T; Integration of Digital Signal Processing Technologies with Pulse Electron Paramagnetic Resonance. Journal of Magnetic Resonance, 178 (2): 220-227
[Abstract] [PubMed] - Sun G, Lau W, Wang A, Shenoy N, Becker K, Cheung H "Ranking and Presenting Gene-Disease Associations from Biomedical Literature." Poster. 2006 Summer Research Program Student Poster Day. [Full Article]
- McQueen PG, McKenzie FE "Competition for red blood cells can enhance Plasmodium vivax parasitemia in mixed-speces malaria infections," American Journal of Tropical Medicine and Hygiene, Vol. 75, pp. 112-125 (2006).
[PubMed] - Williams R., Azuara V., Perry P., Sauer S., Dvorkina M., Jorgensen H., Jeffery Roix, McQueen P., Misteli T., Merkenschlager M. and Fisher A.
"Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus" Journal of Cell Science 119, 132-140 (2006) [PubMed] - Dudko O.K., Hummer G., and Szabo A., "Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments", Phys. Rev. Lett. 96 (10), 108101 (2006)
- Dudko OK, Szabo A, Ketter J, and R.M.Wightman.Analytic theory of the current at inlaid planar ultramicroelectrodes: Comparison with experiments on elliptic disks"J ELECTROANAL CHEM 586 (1): 18-22
- Gupta V., Parisi M., Sturgill D., Nuttall R., Doctolero M., Dudko O.K., Malley J.D., Eastman P.S., and Oliver B.
"Global analysis of X-chromosome dosage compensation", Journal of Biology 5:3 - Lau WW "Survey of Clinical Knowledge Management and Analysis of Unstructured Text " Technical Report, 2006 Full Article
- Sankaran Subramanian, Calvin A. Johnson, Nallathamby Devasahayam, Ken-ichiro Matsumoto1, Fuminori Hyodo, John Cook, and Murali C. Krishna.
"In Vivo Spectal-Spatial Imaging for Ocygen Mapping Using Single-Point, Time-Domain Electron Paramagnetic Resonance," Proceedings, the 2006 IEEE International Symposium on Biomedical Imaging, Crystal City, VA, 2006. - Li X, Hassan SA, Mehler EL "Long Dynamics Simulations of Proteins using Atomistic Forcefields and Continuum Representation of Solvent Effects: Calculation of Structural and Dynamics Properties" Proteins 60:464-484 (2006) Full Article
- Martino, R.L., Russ, D.E., and Johnson, C.A., "Parallel Computing in the Analysis of Gene Expression Relationships." Chapter 11 in: A.Y. Zomaya, editor, Parallel Computing Bioinformatics, New York, N.Y.: Wiley, pp. 265-284.
[Abstract] - Petricoin III, E.F., Bichsel,V.E., Calvert,V.S., Espina,V., Winters,W., Young, L., Belluco,C., Trock, B.J., Lippman, M., Fishman, D.A., Sgroi, D.C.,Munson, P.J., Esserman, L.J., and Liotta, L.A. "Mapping Molecular Networks Using Proteomics:A Vision for Patient-Tailored Combination Therapy" Journal of Clinical Oncology. 23:3614-3621.
[Abstract] [Full Article] - Kovanen, P.E.,Young, L., Al-Shami1, A., Rovella,V., Pise-Masison,C.A, Radonovich, M.F., Powell, J., Fu, J., Brady, J.N., Munson, P.J., and Leonard,W.J. "Global analysis of IL-2 target genes: identificationof chromosomal clusters of expressed genes" International Immunology, Vol. 17, No. 8, pp. 10091021
[Abstract] [Full Article] - Cui,X., Zhang,J., Ma,P.,Myers, D.E, Goldberg,I.G., Sittler, K.J.,Barb,J.J., Munson,P.J.,Cintron,A.P.,McCoy,J.P.,Wang, S. and Danner, R.L. "cGMP-independent nitric oxide signaling and regulation of the cell cycle" BMC Genomics.6:151 doi:10.1186/1471-2164-6-151 (2005)
[Abstract] [Full Article] - Komlosh M.E., Lizak M.J., Horkay F., Friedlin R.Z. and Basser P.J. "Detection of local anisotropy using double-PGSE filter imaging" Presentation (2005)
- Pursley R, Salem G, Devasahayam N, Subramanian S, Krishna M, Pohida T; Direct Detection and Time-locked Subsampling Applied to Pulsed Electron Paramagnetic Resonance Imaging. Review of Scientific Instruments, 76(5): 53709-53715.
[Abstract] [PubMed] - Dudko OK, Berezhkovskii AM, Weiss GH
"Time-dependent diffusion coefficients in periodic porous materials" J PHYS CHEM B 109 (45): 21296-21299 - Sergio A. Hassan "Amino Acid Side Chain Interactions in the Presence of Salts" J. Phys. Chem. B 109:21989 (2005) Full Article
- Baggett D, McAuliffe M, Lockett S. "Whole Cell Segmentation in Solid Tissue Sections." Cytology
- Muanza TM, Cotrim A, McAuliffe MJ, Sowers AL, Baum BJ, Cook JA, Feldchtein F, Amazeen PG, Colman CN, Mitchell JB.
"Evaluation of Radiation-Induced Oral Mucositis by Optical Coherence Tomography." Clinical Cancer Research Vol. 11 pp 5221-5127. July 2005 - McCreedy ES, Cheng R, Hemler P, Viswanathan A, Wood B, McAuliffe MJ.
"Radio Frequency Ablation Registration, Segmentation, and Fusion Tool." IEEE Computer-Based Medical Systems (CBMS) pp. 259-264. June 2005. - Jia, G, Baudendistel KT, von Tengg-Kobligk H, Heverhagen JT, Polzer H, Henry H, McAuliffe MJ, Levine AL, Rosol TJ, Knopp MV.
"Assessing Prostate Volume by Magnetic Resoance Imaging, A Comparison of Different Measurement Approaches for Organ Volume Analysis." Investigative Radiology. Volume 40, pp. 243-248. April 2005. - Bazin PL, Gandler W, McAuliffe, MJ, Pham DL.
"A Software Tool for Atlas-based Volumetric Neuroimage Analysis." International Symposium on Medical Imaging, SPIE. Volume 5747. pp 1824-1833. April 2005 - Steven AC, Heymann JB, Cheng N, Trus BL, Conway JF
"Virus maturation: dynamics and mechanism of a stabilizing structural transition that leads to infectivity" Curr Opin Struct Biol. 15(2):227-36
[PubMed] - Olga K. Dudko and Attila Szabo
"Time-dependent rate coefficients for diffusion-influenced reactions with centrosymmetric potentials" J PHYS CHEM B 109 (12): 5891-5894 - Olga K. Dudko and George H. Weiss
"Estimation of Anisotropic Optical Parameters of Tissue in a Slab Geometry" Biophysical Journal 88: 3205-3211
[PubMed] - Hassan SA, Mehler EL "From Quantum Chemistry and the Classical Theory of Polar Liquids to Continuum Approximations in Molecular Mechanics Calculations" Int. J. Quant. Chem. 102:986-1001 (2005) Full Article
- Unser M, Sorzano CO, Thevenaz P, Jonic S, El-Bez C, De Carlo S, Conway JF, Trus BL
"Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions." J Struct Biol. 149(3):243-55
[PubMed] - Davison AJ, Trus BL, Cheng N, Steven AC, Watson MS, Cunningham C, Le Deuff RM, Renault T
"A novel class of herpesvirus with bivalve hosts." J Gen Virol. 86(1):41-53 [PubMed] - Hassan SA, Gracia L, Vasudevan G, Steinbach PJ "Computer Simulation of Protein-Ligand Interactions: Challenges and Applications." Protein-Ligand Interactions: Methods and Applications Nienhaus, G. Ulrich, editor. Humana Press. pp. 451-492 (2005)
- Boguna, M., Basser, P. J., Pajevic, S., Weiss, G. H."A model for noise effects on fibre tract trajectories in diffusion tensor imaging: theory and simulations", New Journal of Physics, 7, 24, 2005
- Freidlin R.Z., Morris H.D., Horkay F., Pierpaoli C., Toyama R., Dawid I.B. and Basser P.J. "Diffusion Tensor MR Microscopy of Adult Zebrafish." Presentation (2004)
- Assaf, Y., Freidlin, R., Rohde, G., and Basser, P."New Modeling and Experimental Framework to Characterize Hindered and Restricted Water Diffusion in Brain White Matter " Magnetic Resonance in Medicine 52:965-978 (2004)
[Abstract] [PubMed] - Dudko OK, Filippov AE, Klafter J, et al.
"Following single molecules by force spectroscopy" ISRAEL J CHEM 44 (4): 363-372 - Trus BL, Cheng N, Newcomb WW, Homa FL, Brown JC, Steven AC
"Structure and polymorphism of the UL6 portal protein of herpes simplex virus type 1." J Virol. 78(22):12668-71
[PubMed] - Dudko OK, Berezhkovskii AM, and Weiss GH
"Diffusion in the presence of periodically spaced permeable membranes." J Chem Phys 121: 11283-11288
[PubMed] - O'Hanlon TP, Koneru B, Bayat E, Love L, Targoff IN, Malley JD, Malley KG, Miller FW
"Immunogenetic Differences between Women who Develop Myositis with and without Silicone Implants." Arthritis Rheum 50(11):3646-50
[PubMed] - Parisi M, Nuttall R, Edwards P, Minor J, Naiman D, Lu J, Doctolero M, Vainer M, Chan C, Malley J, Eastman S, Oliver B
"A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults." Genome Biol. 5(6):R40
[PubMed] - Dudko O, Weiss GH, Chernomordik V, Gandjbakhche A
"Photon Migration in Turbid media with Anisotropic Optical Properties." Phys Med Biol. 49:3979-3989
[PubMed] - Dagdug L, Berezhkovskii AM, Weiss GH
"The kinetics of ligand equilibration between tubular and vesicular parts of the endosome." Phys Rev E. 69:012902
[PubMed] - Dudko O, Berezhkovskii AM, Weiss GH
"Rate constant for diffusion-influenced ligand binding to receptors of arbitrary shape on a cell surface." J Chem Phys. 121:1562-1565
[PubMed] - Wu S, Baxendale V, Chen Y, Pang AL, Stitely T, Munson PJ, Leung M, Ravindranath N, Dym M, Rennert O, Chan W
"Analysis of Mouse Germ Cell Transcriptome at Different Stages of Spermatogenesis by SAGE: Biological Significance." Genomics 84(6):971-81
[PubMed] - Pawliczak R, Woszczek G, Logun C, Barb J, Suffredini AF, Munson PJ, Danner RL, Shelhamer JH
"The influence of interferon gamma on gene expression in human normal bronchial epithelial cells." Am J Respir Crit Care Med. 2004:A675 - Jison ML, Munson PJ, Barb JJ, Suffredini AF, Talwar S, Logun C, Raghavachari N, Beigel JH, Shelhamer JH, Danner RL, Gladwin MT
"Blood mononuclear cell gene expression profiles characterize the oxidant, hemolytic, and inflammatory stress of sickle cell disease." Blood 104(1):270-80
[PubMed] - Gius D, Cui H, Bradbury M, Cook J, Smart DK, Zhao S, Young L, Brandenburg SA, Hu Y, Bisht KS, Ho aS, Mattson D, Sun L, Munson PJ, Chuang EY, Mitchel JB, Feinberg AP
"Distinct Effects on Gene Expression of Chemical and Genetic Manipulation of the Cancer Epigenome Revealed by a Multimodality Approach." Cancer Cell. 6(4):361-71
[PubMed] - Eisenhofer G, Huynh T, Pacak K, Brouwers FM, Walther M, Linehan WM, Munson PJ, Mannelli M, Goldstein DS, Elkahloun AG
"Distinct gene expression profiles in norepinephrine and epinephrine producing hereditary and sporadic pheochromocytomas: Activation of hypoxia-driven angiogenic pathways in von Hippel-Lindau syndrome." Endocrine-Related Cancer 11(4):897-911
[PubMed] - Boissinot S, Entezam A, Young L, Munson PJ, Furano AV
"The insertional history of an active family of L1 retrotransposons in humans." Genome Res. 14(7):1221-31
[PubMed] - Filizola M, Hassan SA, Artoni A, Coller BS, Weinstein H"Mechanistic Insights from a Refined Three-dimensional Model of Integrin aphaIIb-beta3" J. Biol. Chem. 279:24624 (2004)
[PubMed] - Hassan SA "Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium" J. Phys. Chem. B 108:19501 (2004) Full Article
- Kim SH, McQueen PG, Litchman MK, Shevach EM, Parada LA, Misteli T
"Spatial genome organization during T-cell differentiation" Cytogenetic and Genome Research 105:292-301
[PubMed] - Parada LA, McQueen PG, and Misteli T
"Tissue-specific spatial organization of genomes" Genome Biology vol. 5 [PubMed] - McQueen PG and McKenzie EF
"Age-structured red blood cell susceptibility and the dynamics of malaria infections" Proceedings of the National Academy of Sciences 101: 1961-1966
[PubMed] - Trus BL, Newcomb WW, Cheng N, Brown J, Steven AC
"Structure of the HSV-1 Portal Protein by Electron Microscopy." 13th European Microscopy Congress. 3: 295-296 - Sorzano C, Jonic S, Bez EE, Carlo SD, Thevenaz P, Conway J, Trus BL, Unser M
"Volumetric spectral signal-to-noise ratio." 13th European Microscopy Congress. 1:427-8 - Kuszewski J, Schwieters CD, Garrett DS, Byrd RA, Tjandra N, Clore GM
"Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments." J Am Chem Soc. 126:6258-73
[PubMed] - Iwahara J, Schwieters CD, Clore GM
"Characterization of non-specific protein-DNA interactions by 1H paramagnetic relaxation enhancement." J Am Chem Soc. 2004 Oct 13; 126(40):12800-8
[PubMed] - Iwahara J, Schwieters CD, Clore GM
"Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule." J Am Chem Soc. 126:5879-96 - Hemler P, McCreedy ES, McAuliffe MJ "Performance comparison of a new liver vessel segmentation algorithm." International Symposium on Medical Imaging, SPIE 2004 5370:1785-94
- Clore GM, Schwieters CD
"Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements." Biochemistry 43:10678-91
[PubMed] - Clore GM, Schwieters CD
"How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?" J Am Chem Soc. 126:2923-38
[PubMed] - Martino, R.L.
"The Importance of Multidisciplinary Teams In a Large Biomedical Research Program." Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Piscataway, New Jersey: IEEE Press, pp. 5188-5191, September - Lee YS and Krauss M
"Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase." J. Phys. Chem. B. 108: 4508-4515 - Lee YS and Krauss M
"Dynamics of Proton Transfer in Bacteriorhodopsin." J. Am. Chem. Soc. 126: 2225-2230
[PubMed] - Lee YS, Monica GM and Necker L
"Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans-Cis Isomerization of Geldanamycin." Chemistry and Biology 11: 991-8
[PubMed] - J. Tang, S. Stern-Nezer, P.-C. Liu, L. Matyakhina, M. Riordan, N.L.C. Luban, P.J. Steinbach & S.G. Kaler
"Mutation in the Leucine-rich Repeat C-flanking Region of Platelet Glycoprotein Ib-beta Impairs Assembly of von Willebrand Factor Receptor." Thromb. Haemost. 92: 75-88
[PubMed] - P.J. Steinbach
"Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models." Proteins Struct. Funct. Bioinform. 57: 665-677
[PubMed] - Shaohua A Wang, Yang Fann, Huey Cheung, Frank Pecjak, Barg Upender, Adam Frazin, Raj Lingam, Sarada Chintala, Gladys Wang, Marc Kellogg, Robert L. Martino, and Calvin A. Johnson"Performance of Using Oracle XMLDB in the Evaluation of CDISC ODM for a Clinical Study Informatics System." Proceedings 17th IEEE Symposium on Computer-Based Medical Systems 24-25 June 2004, Bethesda, MD; 594-599 Full Article
- Huey Cheung, Yang Fann, Shaohua A. Wang, Barg Upender, Adam Frazin, Raj Lingam, Sarada Chintala, Frank Pecjak, Gladys Wang, Marc Kellogg, Robert L. Martino, and Calvin Johnson"A Web-Based Protocol Tracking Management System For Clinical Research. " 17th IEEE Symposium on Computer Based Medical Systems 24-25 June 2004, Bethesda, MD; 72-77 Full Article
- Johnson CA, Shanthalaxmi Thada, Yongsheng Zhao, Anthony R. Iano-Fletcher, Jeih San Liow, W. Craig Barker, Robert L. Martino, and Richard E. Carson "Software achitecture of the MOLAR-HRRT reconstruction engine." IEEE Nuclear Science Symposium and Medical Imaging Conference Rome, Italy, 2004
- Barker WC, Liow J-S, Zhao Y, Thada S, Iano-Fletcher A, Lenox M, Michel C, Johnson CA, Carson RE "Randoms estimation for list-mode reconstruction for the ECAT HRRT." IEEE Nuclear Science Symposium and Medical Imaging Conference Rome, Italy, 2004
- Souto-Carneiro MM, Longo NS, Russ DE, Sun HW, Lipsky PE."Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER" Journal of Immunology 2004 Jun 1;172(11):6790-6802.
[PubMed] - Becker, K.G., Barnes, K.C., Bright, T.J. & Wang, S.A.
"The Genetic Association Database" Nature Genetics 36: 431-432 [PubMed] - Dagdug, L. and G. H. Weiss
"Suggested Parameter to Estimate the Region Probed by Photons in Laser-Based." Journal of Modern Optics 51(4): 469-478 - Berezhkovskii AM, Batsilas L, Shvartsman SY
"Ligand Trapping in Epithelial Layers and Cell Cultures." Biophys. Chem. 107(3): 221-7
[PubMed] - Berezhkovskii, A. M. and A. V. Barzykin
"Diffusive Escape and Reentry through a Channel in the Cavity Wall." Chem. Phys. Lett. 383(1-2): 6-10 - Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty, Daniel Russ, Edward Suh
"Gene Clustering Based on Clusterwide Mutual Information." Journal of Computational Biology 11:147-161
[PubMed] - Aletras AH, Freidlin RZ, Navon G, Arai AE
"AIR-SPAMM: alternative inversion recovery spatial modulation of magnetization for myocardial tagging." Journal Magn. Reson. 166(2): 236-45
[PubMed] - T. Brody, et al., "A search for targets of the drosophila neuroblast temporal network," Developmental Biology, vol. 259, p. 93, 2003. [Full Article]
- Parada LA, McQueen P, Munson P, Misteli T
"Cell type specific spatial organization of genomes," Fourth European Cytogenetics Conference published in Annales de Genetique, 46:208 - Grigor'ev IV, Makhnovskii YA, Berezhkovskii AM, Zitserman V
"Kinetics of geminate recombination in a cavity." Russ J Phys Chem. 77:1277-1281 - Grigor'ev IV, Makhnovskii YA, Berezhkovskii AM, Zitserman V
"Kinetics of diffusion-controlled ligand binding to a site hidden in a cavity." Chem Phys Rep. 22:49-54 - Miller M, Jerebko AK, Malley JD, Summers RM
"Comparison of stochastic vs. heuristic feature subset selection methods for improving classification algorithms in computer-aided detection." SPIE Medical Imaging 2003: Physiology and Function from Multidimensional Images 5031:102-110 - Larralde H, Weiss GH
"Expected number of sites visited by N random walks in the presence of an absorbing boundary." J. Phys. A. 36:8367-8372 - Dagdug L, Berezhkovskii AM, Weiss GH
"Smoluchowski-like theory for trapping kinetics in a slab." Physica A. 318:341-346 - Berezhkovskii AM, Hummer G
"Unsolved problems in noise and fluctuations. In Random walk model for single-file transport of water molecules through carbon nanotubes." AIP (New York, NY) 267-272 - Talwar S, Munson PJ, Fiuza C, Barb J, Danner RL, Suffredini A
"Gene expression profiling of lung lavage and peripheral blood cells in humans after local pulmonary endotoxin challenge." Am J Respir Crit Care Med. 167:A428 - Nishizuka S, Chen ST, Gwadry FG, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee JK, Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF 3rd, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN
"Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling." Cancer Res. 63(17):5243-50.
[PubMed] - Daoud SS, Munson PJ, Reinhold W, Young L, Prabhu VV, Yu Q, LaRose J, Kohn KW, Weinstein JN, Pommier Y
"Impact of p53 knockout and topotecan treatment on gene expression profiles in human colon carcinoma cells: a pharmacogenomic study." Cancer Res. 63(11):2782-93
[PubMed] - Pajevic S and Basser PJ "Parametric and non-parametric statistical analysis of DT-MRI data" J Magn Reson 161:1-14
[PubMed] - Basser PJ and Pajevic S
"A Normal Distribution for Tensor-valued Random Variables: Applications to Diffusion Tensor MRI" IEEE Trans Med Imag Vol 22, No 7, 785-794 [PubMed] - Carson RE, Barker WC, Liow J-S, Adler S, Johnson CA
"Design of a motion-compensation OSEM List-mode Algorithm for Resolution-Recovery Reconstruction of the HRRT." Conf. Record of the IEEE Nuclear Science Symposium and Medical Imaging Conference Portland, OR, 2003, M16-6. - Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B
"Paucity of Genes on the Drosophilia X Crhomosome Showing Male-Based Expression." Science 299(5607):697-700
[PubMed] - Nishizuka, S., Charboneau, L., Young, L., Kauor, S., Reinhold, W. C., Waltham, M., Kouros-Mehr, H., Bussey, K. J., Lee, J. K., Espina, V., Munson, P. J.,
"Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays." PNAS 100(24): 14229-14234 - Miller, M. T., Jerebko, A. K., Malley, J. D., Summers, R. M.
"Feature Selection for Computer-Aided Detection using Genetic Algorithms." SPIE 2003, Section on Medical Imaging 2003. - Liotta, L. A., Espina, V., Mehta, A. I., Calvert, V., Rosenblatt, K., Geho, D., Munson, P. J., Young, L., Wulfkuhle, J., Petricoin, E. F.,
"Protein microarrays: Meeting Analytical challenges for clinical applications." Cancer Cell 3: 317-324
[PubMed] - Klein AP, Kovac I, Sorant AJ, Baffoe-Bonnie A, Doan BQ, Ibay G, Lockwood E, Mandal D, Santhosh L, Weissbecker K, Woo J, Zambelli-Weiner A, Zhang J, Naiman DQ, Malley J, Bailey-Wilson JE
"Importance Sampling Method of Correction for Multiple Testing in Affectd Sib-pair Linkage Analysis." BMC Genet. 4 Suppl 1:S73 - Jerebko AK, Summers RM, Malley JD, Franaszek M, Johnson CD
"Computer-assisted detection of colonic polyps with CT colongraphy using neural networks and binary classification trees." Medical Physics 30(1):52-60
[PubMed] - Elvevag B, Kerbs M, Malley JD, Seeley E, Goldberg TE
"Autobiographical memory in schizophrenia: an examination of the distribution of memories." Neuropsychology 17(3):402-9
[PubMed] - Earl, P. L., Wyatt, L. S., Montefiori, D. C., Woodward, R., Markham, P. D., Malley, J. D., Vogel, T. U., Allen, T. M., Watkins, D. I., Miller, N., Moss, B.
"Prime Versus Prime-Boost Vaccinations with a Recombinant Replication-Defective Vaccinia Virus (MVA) Expressing SHIV-89.6 Env-Gag-Pol followed by Soluble Oligometric Env Protein." Virology - Dishon M, Taitelbaum H, Weiss GH
"Effects of the scattering Coefficient on width Estimates in a Two Layer Tissue." Journal of Modern Optics 50:2727-40 - Young, L., P. E. Kovanen, et al.
"Scanning the Human Genome Sequence for Clusters of Expressed Genes." Presented at the TGIR conference in Savannah Georgia in September 2003 - Stojilkovic KS, Berezhkovskii AM, Zitserman VY, Bezrukov SM
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"Diffusion in Potential Field in the Presence of Gaussian Sink. Analytical Solution of the Problem." Russ. J. Electrochemistry 39: 53-60 - Berezhkovskii AM, Pustovoit MA, Bezrukov SM
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"Risk Stratification in Diabetic Patients with a Previous Myocardial Infarction." Journal of Electrtocardiol 36 Suppl:121-5
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"A Collaborative Telemedicine Environment for the Ireland - Northern Ireland - National Cancer Institute International Partnership in Cancer Care" EMBS 2003, Proceedings Presented at the 25th International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2003, Proceedings, Institute of Electrical and Electronics Engineers, Inc., New York, 2003, 1350-1353. - Greene JM, Asaki E, Bian X, Bock C, Castillo S, Chandramouli G, Martell R, Meyer K, Ruppert T, Sundaram S, Tomlin J, Yang L, Powell J.
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- Deirdre A. Joy, Xiaorong Feng, Jianbing Mu, Tetsuya Furuya, Kesinee Chotivanich, Antoniana U. Krettli, May Ho, Alex Wang, Nicholas J. White, Edward Suh, Peter Beerli, Xin-zhuan Su
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"Gene Expression Profiling Identifies Strong Feature Genes that Classify de novo CD5+ and CD5- Diffuse Large B-Cell Lymphoma and Mantle Cell Lymphoma." Cancer Research 63:60-66 - Johnson CA, Cook JA, McGarry DP, Devasahayam N, Mitchell JB, Subramanian S, Krishna M
"Maximim Entropy Reconstruction Methods in Electron Paramagnetic Resonance Imaging." Annals of Operations Research 119 (1-4): 101-118 - Yim PJ, McAuliffe MJ, Nosher JL
"Reduction of Intra-Observer Variability of Tumor-Volume Measurement Using the Fuzzy C-Means Algorithm." Radiological Society of North America - Wood BJ, Yanof JH, McAuliffe MJ, Renisch S, Hvizda JL, Cleary K
"PET-CT Treatment Planning Interface for Robot-Assisted Biopsy and Tumor Ablation." Radiological Society of North America - Wood BJ, Hvizda J, Yanof JH, Renisch S, Bitter I, McAuliffe MJ
"Intra-Procedural Real-Time Registration and Fusion of Ultrasound and CT Image-Guided Percutaneous Liver Procedures." Radiological Society of North America - Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM
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"Risk Stratification Applied to CAST Registry Data: Combining 9 Predictors." Journal of Electrocardiology 35: 117-122
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"Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information." Polymer 43: 441-449 - Hecht D, Jung D, Prabhu VV, Munson PJ, Hoffman MP, Kleinman HK
"Metallothionein Promotes Laminin-1-induced Acinar Differentiation in Vitro and Reduces Tumor Growth in Vivo." Cancer Research 65: 5370-5374
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"Both Protein Activation and Gene Expression Are Involved in Early Vascular Tub Formation in Vitro." Clinical Cancer Research 2002 8: 3019-3026
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"Comparison of vaccine strategies using recombinant env-gag-pol MVA with or without an oligomeric Env protein boost in the SHIV rhesus macaque model." Virology 294(2): 270-281
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"A Theoretical framework for the study of the melting transition of DNA using the stochastic matrix method." Physical Review E. - Dagdug, L., A. M. Berezhkovskii, et al.
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"Detailed description of a two-state non-Markov system." Physica A 303: 1-12 - Berezhkovskii, A. M., M. Pustovoit, et al.
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"Risk Stratification Applied to CAST Registry Data: Extended Criteria for Prophylactic Use of ICDs after Myocardial Infarction." The International Society for Computerized Electrocardiology 27th Annual Conference Doorwerth, The Netherlands - Camarano G, Jones M, Freidlin RZ, Panza JA
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"Telemedicine Systems" Chapter 22 in: Principles and Practice of Clinical Research, John I. Gallin, Editor, Academic Press, San Diego, 2002, 361-385. - Jia L, Young MF, Powell J, Yang L, Ho NC, Hotchkiss R, Robey PG, Francomano CA.
"Gene expression profile of human bone marrow stromal cells: high-throughput expressed sequence tag sequencing analysis" Genomics. 79(1):7-17
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"Initiating oncogenic event determines gene-expression patterns of human breast cancer models" Proc Natl Acad Sci USA 99(10):6967-72 - Edgerton ME, Taylor R, Powell JI, Hunter L, Simon R, Liu ET.
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"The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma" N Engl J Med. 346(25):1937-47
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- Hattery D, Gerdelman K, Hekmat F, Chernomordik V, Smith P, Eidsath A, Pursley R, Atkinson J, Mulshine J, Gandjbakhche A; Diffuse Reflectance Spectroscopy to Quantify Inflammation of the Oral Epithelium In Vivo." Progress in Biomedical Optics and Imaging: Optical Biopsy IV 3(5): 59-70
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"Reaction Mechansim of Chorismate Mutase Studied by the Comibined Potentials of Quantum Mechanics and Molecular Mechanics." J. Phys. Chem. B 106: 12059-12065 - P.J. Steinbach, R. Ionescu, & C.R. Matthews
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"Redesign of a Four-helix Bundle Protein by Phage Display Coupled with Proteolysis and Structural Characterization by NMR and X-ray Crystallography." J. Mol. Biol. 323: 253-62
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"Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides." J. Phys. Chem. B 106: 11628-11640 - Suh EB, Wang A, Cheung H, Martino RL
"A Web-based Medical Image Archive System." Proceedings of the Medical Imaging 2002 San Diego, California, International Society for Optical Engineering, February 23-28 Full Article - Suh EB, Russ DE, Dougherty ER, Kim S, Chen Y, Bittner M, Martino RL
"Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene-Expression." Computational and Statistical Approaches to Genomics Wei Zhang and Ilya Shmulevich (Editors), Kluwer Academic Publishers, Boston - Hunsberger S, Albert PS, Follmann DA, Suh EB"Parametric and Semiparametric Approaches to Testing for Seasonal Trend in Serial Count Data." Biostatistics Oxford University Press, June 2002, vol. 3, no. 2.
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"A Latent Autoregressive Model for Longitudinal Binary Data Subject to Informative Missingness." Biometrics 58: 631-642
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"Can Markov Chain Mimic Biological Regulation." Journal of Biological Systems 10 (4): 431-445 - Suh, E.B., D.E. Russ, E.R. Dougherty, S. Kim, M.L. Bittner, Y. Chen, and R.L. Martino
"Parallel Computation for Coefficients of Determination in the Context of Multivariate Gene-Expression Analysis." International Journal of Computer Research 11(4):419-429 - Trus BL, Yamada K, Subramanian S, Cook J, Devasahayam N, Mitchell J, Krishna M
"Improved Quantitation of the Redox State Using Maximum Entropy Methods in Electron Parametric Resonance Imaging." First SIAM Conference on Imaging Science 2002:28 - Seidel J, Vacquero JJ, Pascua J, Desco M, Johnson CA, Green M
"Features of the NIH ATLAS Small Animal PET Scanner and Its Use with a Coaxial Small Animal Volume CT Scanner." IEEE International Symposium on Biomedical Imaging Washington, DC, 2002:TP-P1.9 - Johnson CA, Seidel J, Vaquero JJ, Pascau J, Desco M, Green MV
"Exact Positioning for OSEM Reconstructions on the ATLAS Depth-of-Interaction Small Animal Scanner." Academy of Molecular Imaging Annual Conference 2002 San Diego, CA - Heymann JB, Trus BL, Cheng N, Newcomb WW, Brown JC, Steven AC
"Dynamic Visualization of HSV Capsid Maturation." ICEM 15:1-6 - Heymann JB, Trus BL, Cheng N, Newcomb WW, Brown JC, Steven AC
"Herpes Simplex Virus Capsid Maturation Visualized by time-Lapsed Cryo-EM." Microsc. Microanal 8 (Suppl 2), 844CD-845CD - Green M, Seidel J, Johnson CA, Vaquero JJ, Pascua J, Desco M
"Towards High Performance Small Animal Positron Emission Tomography." IEEE International Symposium on Biomedical Imaging Washington, DC, 2002 TA-SS-1.3 - Clore GM, Kuszewski J
"Chi(1) rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force." J Am Chem Soc 124:2866-7
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"Theoretical and computational advances in biomolecular NMR spectroscopy." Curr Opin Struct Biol 12:146-53
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"Handedness of the herpes simplex virus capsid and procapsid." J Virol 76:855-9
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"Registration of Time-Series Contrast Enhancement Magnetic Resonance Images for Renography." IEEE Computer-Based Medical Systems (CBMS) pp. 516-520. - Yim PJ, Marcos HB, McAuliffe MJ, McGarry D, Heaton Ian, Choyke PL.
"Registration of Time-Series Contrast Enhancement Magnetic Resonance Images for Renography." IEEE Computer-Based Medical Systems (CBMS) pp. 516-520. July 2001. - Pierpaoli C, Barnett A, Pajevic S, et al.
"Water Diffusion Changes in Wallerian Degeneration and Their Dependence on White Matter Architecture" NeuroImage 13:1174-1185
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"Evaluating UMLS strings for natural language processing" Proc AMIA Symp 2001 448-52
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"An Integrated System for Computer-Aided Diagnosis in CT Colonography: Work-In Progress." Proceedings of the 15th International Congress of Computer Assisted Radiology and Surgery - Summers, R. M., Johnson, C. D., Pusanik, L. M., Malley, J. D., Youssef, A., Reed, J. E.
"Automated Polyp Detection at CTColongraphy: Feasibility Assessment in a Human Population." Radiology 219: 51-59
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"Augmentation in Expression of Activation-Induced Genes Differentiates Memory from Naive CD4+ T Cells and Is a Molecular Mechanism for Enhanced Cellular Response of Memory CD4+ T Cells." The American Association of Immunologists 7335-7344
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"Proteomic profiling of the cancer microenvironment by antibody arrays." Proteomics 1: 1271-1278
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"Computer-Assisted Detection of Colonic Polyps in Noisy CT Colonography Data Sets Using Neural Networks and Binary Classification Trees." IEEE Transactrions on Medical Imaging - Blank, P. S., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"A Kinetic Analysis of Calcium-Triggered Exocytosis." J. Gen. Phys. 118(2):145-56
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"Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data." Genetic Epidemiology 21 Suppl 1:S378-83
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"Statistics of Dwell Time in a Reaction with Randomy Fluctuating Rates." Physica A 296: 75-82 - Shrager, R. I. and R. W. Hendler
"Supporting information for "Theory and procedures for finding a correct kinetic model for the bacteriorphdopsim photocycle." Journal of Physical Chemistry 105: 3319 - Makhnovskii, Y. A. and A. M. Berezhkovskii
"Effect of a group of Traps on Fluctuation Assisted Inhibition of Browian Particle Decay." Chem. Phys. Rep. 19: 853-59 - Hendler, R. W., R. I. Shrager, et al.
"Theory and procedures for finding a correct kinetic model for the bacteriorbadopsim photocycle." Journal of Physical Chemistry B 105: 3319-3328 - Bogu¿a, M., A. M. Berezhkovskii, et al.
"Single-Molecule Fluorescence Spectroscopy: Rate Constants for Slow Conformational Transitions and their Sampling Errors." Journal of Physical Chemistry A 105: 4898-4901 - Berezhkovskii, A. M., Y. A. Makhnovskii, et al.
"Trapping of Brownian particles by random spheres of different radii." Journal of Chemical Physics 115: 5376-80 - Berezhkovskii, A. M., H. Larralde, et al.
"Region visited by a pherical Brownian particle in the presence of an abosrbing boundary." Physical Review E 64: 062104-1 - 062104-3 - Berezhkovskii, A. M., M. Bogu¿a, et al.
"Evaluation of Rate Constants for Conformational Transitions using Single-Molecule Fluroescence Spectroscopy." Chemical Physics Letter 336: 321-324 - Bailey, J. J.
"Utility of current risk stratification tests for predicting major arrhythmic events after myocardial infarction." J. Am. Coll Cardiol 1902-1911
[PubMed] - Bailey, J. J.
"Technical Information Report: TIR 24: Acquisition and use of physiological waveform databases for testing of medical devices." Association for the Advancement of Medical Instrumentation monograph - Bailey, J. J.
"Standard Communications Protocol - Computer Assisted Electrocardiography." AAMI EC71: monograph - Schmidt MA, Freidlin RZ, Ohazama CJ, Jones M, Laurienzo JM, Brenneman CL, Norman JE, von Ramm OT, Panza JA
"Anatomic validation of a novel method for left ventricular volume and mass measurements with use of real-time 3-dimensional echocardiography." Journal of the American Society of Echocardiography. 14:(1)1-10 [PubMed] - Kempner, K.M., Govern, F.S., and Martino, R.L.
"A Unique Network Architecture for Global Medical Consultation." Proceedings of the United States Army Medical Department International Telemedicine Meeting, Paper no.6, 1-10 - Kempner, K.M., Chow, D., Elson, J.E., Govern, F.S., Steele, M.E., and Martino, R.L.
"Development of a High-Performance ISDN-to-ATM Telemedicine Gateway in Support of the NCI All Ireland Cancer Consortium (Abstract)" Technology and Health Care Presented at the 2001 Conference of the European Society for Engineering and Medicine, Belfast, N.I., U.K., Technology and Health Care, 9(1-2): 46-47, 2001 - Jia L, Ho NC, Park SS, Powell J, Francomano CA
"Comprehensive resource: Skeletal gene database" Am J Med Genet. 106(4):275-81
[PubMed] - Altarescu G, Moore D, Pursley R, Campia U, Goldstein S, Panza J, Schiffmann R; Enhanced Endothelium-Dependent Vasodilation in Fabry Disease Stroke 32(7): 1559-62
[Abstract] [PubMed] - Moore D, Pursley R, Altarescu G, Schiffmann R, Dimitriadis E; Real Time Peripheral Arterial Flow and Wall Properties Derived by Pulse Waveform Analysis and B-mode Ultrasound Imaging The 14th IEEE Symposium on Computer-Based Medical Systems (CBMS) 2001 pp. 216-221
[Abstract] - Cornelison R., Kakareka J., Wagner U., Kononen J., Hostetter G., Salem G., Leighton S., Pohida T., and Kallioniemi O.
"Automated Construction of Tissue Microarrays Using a Robotic Arrayer" Association for Molecular Pathology Conference - Suh EB, Dougherty ER, Kim S, Russ DE, Martino RL.
"Parallel Computing Methods for Analyzing Gene Expression Relations." Proceedings of the Biomedical Optics (BiOS 2001), San Jose, California, International Society for Optical Engineering. January 20-26 - McGarry DP, Cook J, Subramanian S, Devasahayam N, Cherukuri MK, Johnson CA.
"Reconstruction of electron paramagnetic resonance images using iterative methods" Proc. SPIE 4322:24-29, Medical Imaging 2001: Image Processing, Milan Sonka; Kenneth M. Hanson; Eds - Agarwala R, Schaffer AA, Tomlin JF.
"Towards a complete North American Anabaptist Genealogy II: analysis of inbreeding." Hum Biol. 73(4): 533-45
[PubMed] - G. Reyes-Cruz, J. Hu, P.K. Goldsmith, P.J. Steinbach, & A.M. Spiegel
"Human Ca Receptor Extracellular Domain: Analysis of Function of Lobe I Loop Deletion Mutants." J. Biol. Chem. 276: 32145-32151
[PubMed] - J. Piatigorsky, B. Norman, L.J. Dishaw, L. Kos, J. Horwitz, P.J. Steinbach & Z. Kozmik
"J3-Crystallin of the Jellyfish Lens: Homology to Saposins." Proc. Natl. Acad. Sci. USA 98: 12362-12367 - S. Ganguly, P. Mummaneni, P.J. Steinbach, D.C. Klein & S.L.Coon
"Characterization of the Saccharomyces cerevisiae Homolog of the Melatonin Rhythm Enzyme Arylalkylamine N-acetyltransferase (AANAT, EC 2.3.1.87)." J. Biol. Chem. 276: 47239-47247
[PubMed] - Bailey, J.J. and M. Hodges
"Ambulatory Electrocardiography: Use in Arrhythmia Risk Assessment."¿ In Risk of Arrhythmia and Sudden Death BMJ Publishing, Ltd: 194-201.
[Abstract] - Suh EB, Diougherty ER, Kim S, Russ DE, Martino RL
"Parallel Computing Methods for Microarray Data Analysis." Proceedings of the Biomedical Optics (BiOS) 2001 San Jose, California, International Society for Optical Engineering, January 20-26 - Johnson CA, McGarry D, Cook JA, Subramanian S, Devasahayam N, Mitchell JM, Krishna MC
"Maximum entropy reconstruction methods in electron paramagnetic resonance imaging." Annals of Operations Research - Trus BL, Heymann JB, Nealon K, Cheng N, Newcomb WW, Brown JC, Kedes DH, Steven AC
"Capsid structure of Kaposi’s sarcoma-associated herpesvirus, a gammaherpesvirus, compared to those of an alphaherpesvirus, herpes simplex virus type 1, and a betaherpesvirus, cytomegalovirus." J Virol 75(6):2879-90 [PubMed] - Trus BL
"Reconstruction of electron paramagnetic resonance images." SPIE International Symposium on Medical Imaging 4322:24-29 - McAuliffe MJ, Lalonde F, McGarry DP, Gandler W, Csaky K, Trus BL
"Medical Image Processing, Analysis & Visualization in Clinical Research." 14th IEEE Symposium on Computer-Based Medical Systems (CBMS 2001) 381-386 - Belnap DM, Cheng N, Majeed S, Tsang SK, Filman DJ, McDermott Jr. BM, Trus BL, Kwong PD, Racaniello VR, Hogle JM, Steven AC
"Poliovirus-Receptor Interaction and Conformational Changes During Cell Entry." XVII Biennail Conf on Phage and Virus Assembly June 30-July 5, 2001, Helsinki, Finland 2001:22 - Pajevic S, Aldroubi A, Basser P
"Continuous Tensor Field Approximation of Diffusion Tensor MRI data. In Visualization and Image Processing of Tensor Fields." Springer-Verlag - Summers, R. M., Pusanik, L. M., Malley, J. D., Reed, J. E., Johnson, C. D.
"Method of Labeling Colonic Polys at CT Colonography using Computer-assisted Detection." Proceedings of the 14th International Congress of Computer Assisted Radiology and Surgery (CARS) - Summers, R. M., Beaulieu, C. F., Pusanik, L. M., Malley, J. D., Jeffrey, R. B., Jr., Glazer, D. I., Napel, S.
"An Automated Polyp Detector for CT Colonography - Feasibility Study." Canadian Mathematical Society Conference Proceedings 216: 284-290
[PubMed] - Smith, T. D., Kuczenski, R., George-Friedman, K., Malley, J. D., Foote, S. L.
"In Vivo Microdialysis Assessment of Extracellular Serotonin and Dopamine Levels in Awake Monekys During Sustained Fluoxetine Administration." Synapse 38: 460-470 - Peng, A., Koffman, B. M., Malley, J. D., Dalakas, M. D.
"Disease progression and functional muscle decline in sporadic inclusion body myositis (s-IBM): observations in 78 patients." Neurology 55: 296-298
[PubMed] - Nees, M., Geoghegan, J. M., Munson, P., Prabhu, V., Liu, Y., Androphy, E., Woodworth, C. D.
"Human papillomavirus type 16 E6 and E7 proteins inhibit differentiation-dependent expression of transforming growth factor-beta2 in cervical keratinocytes." Cancer Res 60: 4289-98
[PubMed] - Laks, M. M., Arzbaecher, R., Geselowitz, D. B., Bailey, J. J., Berson, A. S.
"Revisiting the question: Will relaxing safe current limits for electromedical equipment increase hazards to patients?" Circulation 103: 823-5
[PubMed] - Kim HJ, Tisdale JF, Wu T, Takatoku M, Sellers SE, Zickler P, Metzger ME, Agricola BA, Malley JD, Kato I, Donahue RE, Brown KE, Dunbar CE
"Many multi-potential gene-marked progenitor or stem cell clones contribute to hematopoiesis in non-human primates." Blood 96(1):1-8
[PubMed] - Grove, A.D., Lee, F.C., Prabhu, V.V., Young, B.L., Munson, P.J., Kohn, E.C.
"In Validation and application of nylon cDNA microarrays in the analysis of endothelial cell gene expression during tubulogenesis (abstract)" AACR - Boguna, M., Kullman, L., Bezrukov, S. M., Berezhkovskii, A. M., Weiss, G. H."Rate Constants from Uncorrelated Single-Molecule Data." J. Phys. Chem.B 105: 6246-6250
- Bogachev, L. V., Molchanov, S. A., Makhnovskii, Y. A., Berezhkovskii, A. M.
"Correlation Effects in the Trapping Problem: General Approach and Rigorous Results." Canadian Mathematical Society Conference Proceedings 2000 29: 29-42 - Smith RD, Malley JD, Schechter AN
"Quantitative analysis of globin gene expression in single human erythroleukemic cells." Nucleic Acids Research 28(24): 4998-5004
[PubMed] - Selbie, W. S., J. D. Malley, et al.
"Method for segmenting medical images and detecting surface anomalies in anatomical structures" U.S. Patent Application No. 09/136,136 filed August 18, 1998. Accepted: 2000 - Pajevic, S. and P. J. Basser
"Parametric and Non-Parametric Statistical Approaches in Diffusion Tensor Magnetic Resonance Imaging" Journal of Magnetic Resonance - Makhnovskii, Y. A., A. M. Berezhkovskii, et al.
"Trapping by Clusters of traps." Phys. Rev. E 61: 6302-07
[PubMed] - Bezrukov, S. M., A. M. Berezhkovskii, et al.
"Particle Number Fluctuations in a Membrane Channel." J. Chem. Phys. 113(8206-11) - Basser PJ, Pajevic S
"Statistical artifacts in diffusion tensor MRI (DT-MRI) caused by background noise." Magn. Reson. Med. 44(1): 41-50
[PubMed] - Basser PJ, Pajevic S, Pierpaoli C, Duda J, Aldroubi A
"In vivo fiber tractography using DT-MRI data." Magn. Reson. Med. 44(4): 625-632
[PubMed] - Basser, P. J., S. Pajevic, et al.
"Fiber-Tractography in Human Brain Using Diffusion Tensor MRI (DT-MRI)" International Society for Magnetic Resonance in Medicine Annual Meeting Proceedings 784 - Bailey, J. J.
"Signal averaging electrocardiography." Association for the Advancement of Medical Instrumentation Technical Information Report 23: monograph. - G. Chi-Fishman, B.C. Sonies, C.J. Ohazama, R.Z. Freidlin
"Real-Time Three-Dimensional Ultrasound of Lingual Action During Swallowing." Dysphagia Research Society, 8th Annual Scientific Meeting. 15(2)Abst. p 106 - V. Sachdev, I. Ernst, J.M. Laurienzo, R.Z. Freidlin, L. Wood, J.A. Panza
"Improved Reproducibility of Real-Time 3-Dimensional Compared to Conventional 2-Dimensional Echocardiography for the Assessment of Left Ventricular Volumes and Function in Children." Journal of the American Society of Echocardiography. 13:439 - Camarano G, Jones M, Freidlin RZ, Ernst I, Zetts AD, Panza JA
"Temporal evolution of the contractile state of neighboring myocardium in the early phase of acute myocardial infarction." Journal of the American College of Cardiology. 35:(2) 368A-369A - Chamberlin ME, Ubagai T, Pao VY, Pearlstein RA, and Chou JY
"Structural requirements for catalysis and dimerization of human methionine adenosyltransferase I/III." Arch Biochem Biophys 373 (1): 56-62
[Abstract] [PubMed] - Yao R, Seidel J, Johnson CA, Daube-Witherspoon DE, Green MV, Carson RE
"Performance Characteristics of the 3D OSEM Algorithm in the Reconstruction of Small Animal PET Images." IEEE Transactions on Medical Imaging 19: 798-804
[PubMed] - Johnson CA, Sofer A. "A primal-dual method for large-scale image reconstruction in emission tomography." SIAM Journal on Optimization 11: 691-715
- Johnson CA, Seidel J, and Sofer A.
"Interior-point methodology for 3-D PET reconstruction." IEEE Transactions on Medical Imaging, 19: 271-285
[PubMed] - Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC,Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr,Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC,Weisenburger DD, Armitage JO, Warnke R, Staudt LM, et al.
"Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling." Nature. 403(6769): 503-11 - Sugiyama K, Chen Z, Lee YS and Kador PF
"Isolation of a Non-covalent Aldose Reductase-Nucleotide-Inhibitor Complex." Biochem. Pharmacol. 59: 329-336
[PubMed] - J.J. Balbach, J. Yang, D.P. Weliky, P.J. Steinbach, V. Turganov, J. Anglister & R. Tycko
"Probing Hydrogen Bonds in the Antibody-Bound HIV-1 gp120 V3 Loop by Solid State NMR REDOR Measurements." J. Biomol. NMR 16: 313-327
[PubMed] - J. Piatigorsky, Z. Kozmik, J. Horwitz, L. Ding, E. Carosa, W.G. Robison, Jr., P.J. Steinbach & E.R. Tamm
"Omega-Crystallin of the Scallop Lens: A Dimeric Aldehyde Dehydrogenase Class 1/2 Enzyme-Crystallin." J. Biol. Chem. 275: 41064-41073
[PubMed] - Berezhkovskii, A.M., A. Szabo and G.H. Weiss
"Theory of Fluorescence of Single Molecules Undergoing Multistate Conformational Dyanmics." J. Phys. Chem. B104(16): 3776-80
[Abstract] - Wong, M.-L., M.A. Kling, P.J. Munson, S. Listak, et al.
"Pronounced and Sustained Central Hypernoradrenergic Function in Major Depression with Melancholic features: Relation to Hypercortisolism and Corticotropin-releasing Harmone." PNAS 97(1): 325-330 Full Article - Weiss, G.H., M. Boguna and A.M. Berezhkovskii "Occupancy of a Single Site by Many Random Walkers."ý Physical Review E ý62(3): 3250-3256
[Abstract] [PubMed] - Vieira, N.E., R.E. Goans, G.H. Weiss, J.C. Marini, et al.
"Calcium Kinetics in Children with Osteogenesis Imperfecta Type III and IV: Pre- and Post- Growth Harmone Therapy."
[Abstract] - Hendler, R., R. Shrager and S. Bose
"Results from a Search for the Correct Kinetic Model for the Bacteriorhodospin Photocycle."
[Abstract] - Grouse, L.H., P.J. Munson and P.S. Nelson
"Sequence Database and Microarrays as Tools for Identifying Prostate Cancer Biomarkers."
[Abstract] [PubMed] - Gandjbakhche, A.H. and G. H. Weiss
"A Descriptive Parameter for Photon Trajectories in a Turbid Medium."¿ Physical Review E ¿61(6): 6958-6962 [PubMed] - Emmert-Buck, M.R., R.L. Strausberg, D.B. Krizman, M.F. Bonaldo, ..., P.J. Munson, et al.
"Molecular Profiling of Clinical Tissue Specimens Feasibility and Applications." American Journal of Pathology 156(4): 1109-1115 [PubMed] - Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB
"Development of a Prostate cDNA Microarray and Statistical Gene Expression Analysis Package." Molecular Carcinogenesis 28(1):12-22
[Abstract] [PubMed] - Boguna, M., M. Masoliver and G.H. Weiss"The Asympototic Form of the Probability Density of Sojourn Times in Randomly Changing Multistate Systems."
[Abstract] - Boguna, M., A.M. Berezhkovskii and G.H. Weiss"Residence time densities for non-Markovian systems 1. The two-state system." Physica A 282: 475-485
[Abstract] - Bailey, J.J., A.S. Berson, H. Handelsman
"Metanalysis by ROC: ECG Diagnostic Methods Compared."
[Abstract] - Bailey JJ, Berson AS, Handelsman H
"Dysrhythmia hazard after hospitalization for myocardial infarction: two ECG prognostic methods compared." J Electrocardiol 33:151-4
[Abstract] [PubMed] - Newcomb WW, Trus BL, Cheng N, Steven AC, Sheaffer AK, Tenney DJ, Weller SK, Brown JC
"Isolation of Herpes Simplex Virus Procapsids from Cells Infected with a Protease-Deficient Mutant Virus." Virology 74, No.4: 1663-1673 [PubMed] - Iwasaki K, Trus BL, Wingfield PT, Cheng N, Campusano G, Rao VB, Steven AC
"Molecular Architecture of Bacteriophage T4 Capsid: Vertex Structure and Bimodal Binding of the Stabilizing Accessory Protein, Soc." Virology 321-333 [PubMed] - Belnap DM, McDermott BM, Filman DJ, Cheng N, Trus BL, Zuccola HJ, Racaniello VR, Hogle JM, Steven AC
"Three-dimensional structure of poliovirus receptor bound to poliovirus." Proc Natl Acad Sci U S A 97(1):73-8 [PubMed] - Belnap DM, Filman DJ, Trus BL, Cheng N, Booy FP, Conway JF, Curry S, Hiremath CN, Tsang SK, Steven AC, Hogle JM
"Molecular Tectonic Model of Virus Structural Transitions: the Putative Cell Entry States of Poliovirus." Virology 74, No.3: 1342-1354 [PubMed] - Steven AC, Belnap D, Cheng N, Conway JF, Trus BL
"Viral Metamorphosis: Visualization Capsid Proteins and their Maturation." EUREM 12 Brno, Czech Republic, July 9-14, 2000 1:B339-342 - Iwasaki K, Trus BL, Wingfield PT, Cheng N, Campusano G, Rao V, Steven AC
"Morphogenesis of bacteriophage T4 capsid as studied by cryo-electron microscopy and 3D image reconstruction." EUREM 12 Brno, Czech Republic, July 7-14, 2000 1:B343-344 - Summers, R. M., Pusanik, L. M., Malley, J. D., Hoeg, J. M.
"Fractal analysis of virtual endoscopy reconstructions." Proceedings of SPIE 1999 3660: 258-269. - Ioannidis JP, Goedert JJ, McQueen PG, Enger C, Kaslow RA
"Comparison of Viral Load and HLA Statistical and Neural Network Predictive Models for the Rate of Human Immunodeficiency Virus Disease Progression." Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 20: 129-136
[PubMed] - Hecht, D., Jung, D., Munson, P. J., Prabhu, V. V., Kleinman, H. K.
"In Laminin-1 Dependent Gene Expression During Acinar Differentiation of Human Salivary Gland Cells: Analysis Using cDNA Arrays" Pan-pacific connective tissue societies, 4th symposium Queenstown, New Zealand, November 15-19 - Blank, P. S., Coorssen, J. R., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"Calcium-triggered exocytosis: Unifying biophysical, biochemical, and physiological studies." J. Gen. Physiol. - Shrager, R. I.
"On a three term variant of the Lomb periodogram." Astrophysics and Space Science - Pajevic, S. and P. J. Basser
"Parametric Description of Noise in Diffusion Tensor MRI." 7th ISMRM Proceedings 1787 - Pajevic, S. and P. J. Basser
"Non-parametric Statistical Analysis of Diffusion Tensor MRI Data Using the Bootstrap Method." 7th ISMRM Proceedings 1790 - McQueen, PG
"Monte Carlo Methods in Statistical Physics (book review)" Journal of Statistical Physics 97: 1029-1030 - Makhnovskii, Y. A., A. M. Berezhkovskii, et al.
"Role of Trap Clustering in the Trapping Kinetics." J. Chem. Phys 111: 711-20 - Bicout, D. J., A. M. Berezhkovskii, et al.
"First Passage Times in Phase Space for the Strong Collision Model." Physical Review E 59: 3702-3705 - Berezhkovskii, A. M., A. Szabo, et al.
"Reaction dynamics on a thermally fluctuating potential." J. Chem. Phys 111: 9952-9957 - Berezhkovskii, A. M., S. M. Bezrukov, et al.
"The influence of polymer on the diffusion of a spherical tracer." J. Chem. Phys. 111: 5641-5644 - Basser, P. J., S. Pajevic, et al.
"Quantitative Statistical Tests for Assessing Changes in the Trace of the Diffusion Tensor: Clinical and Biological Implications." 7th ISMRM Proceedings 1789 - Basser, P. J., S. Pajevic, et al.
"Methods to reduce Eigenvalue Sorting Bias in DT-MRI." 7th ISMRM Proceedings 1788 - Bailey, J. J.
"Testing and reporting performance results of cardiac rhythm and ST measurement algorithms." Association for the Advancement of Medical Instrumentation American National Standard 2nd ed(EC57): monograph. - Bailey, J.J.
"Ambulatory electrocardiographs" Association for the Advancement of Medical Instrumentation American National Standard 2nd ed(EC38): monograph - V. Sachdev, K.O. Agyeman, J.M. Laurienzo, R.Z. Freidlin, G. Camarano, A.E. Arai, J.A. Panza
"Aortic Root Volume Measurements in Cardiac Patients Using Real-Time Three-Dimensional Echocardiography: Feasibility and Accuracy Compared With Magnetic Resonance Imaging." Journal of the American Society of Echocardiography. 12:401 - G. Camarano, M. Jones, R.Z. Freidlin, P.M. Magno, C.L. Brenneman, J.M. Laurienzo, V. Sachdev, J.A. Panza
"Real-Time Three-Dimensional Myocardial Contrast Echocardiography for the Quantitative Assessment of Left Ventricular Perfusion Defects." American Society of Echocardiography 10th Annual Scientific Session, Washington, DC - V. Sachdev, K.O. Agyeman, P.M. Magno, J.M. Laurienzo, R.Z. Freidlin, A.E. Arai, J.A. Panza
"Left Ventricular Mass Measurements in Cardiac Patients Using Contrast-Enhanced Real-Time Three-Dimensional Echocardiography." American Heart Association. 72nd Scientific Session - M.A. Schmidt, C.J. Ohazama, K.O. Agyeman, R.Z. Freidlin, M. Jones, J.M. Laurienzo, C.L. Brenneman, A.E. Arai, O.T. von Ramm, J.A. Panza
"Real-Time Three-Dimensional Echocardiography for Measurement of Left Ventricular Volumes." American Journal of Cardiology. 84:(12) 1434-1439 [PubMed] - Suarez-Quian C., Goldstein S., Pohida T., Smith P., Peterson J., Wellner E., Ghany M., and Bonner R.
"Laser Capture Mircrodissection of Single Cells From Complex Tissues" Biotechniques 26: 328-335
[PubMed] - Subramanian S., Murugesan R., Devasahayam N., Cook J., Afeworki M., Pohida T., Tschudin R., Mitchell J., and Krishna M.
"High-Speed Data Acquisition System and Receiver Configurations for Time-Domain Radiofrequency Electron Paramagnetic Resonance Spectroscopy and Imaging" Journal of Magnetic Resonance 137: 379-388
[PubMed] - Goldstein S., Pohida T., Smith P., Peterson J., Wellner E., Malekafzali A., Suarez-Quian C., and Bonner R.
"An Instrument for Performing Laser Capture Microdissection of Single Cells" Review of Scientific Instruments 70: 4377-4385 - Rizzo P, Tinello C, Pearlstein RA, and Taniuchi H
"Antibody immunodiversity: A study on the marked specificity difference between two anti-yeast iso-1 cytochrome c monoclonal antibodies whose epitopes are closely related." J Protein Chem. 18 (5): 523-532
[Abstract] [PubMed] - Menotti-Raymond M, David VA, Lyons LA, Schaffer AA, Tomlin JF, Hutton MK, Brien SJ.
"A genetic linkage map of microsatellites in the domestic cat (Felis catus)." Genomics. 57(1): 9-23
[PubMed] - Johnson CA, Sofer A."A Data-Parallel Algorithm for Tomographic Image Recontruction" Proceedings of the 7th Symposium on the Frontiers of Massively Parallel Computation IEEE Computer Society Press, 126-137 Washington Full Article
- Yao R, Seidel J, Johnson CA, Daube-Witherspoon DE, Green MV, Carson RE
"Factors Affecting the Performance of the 3D OSEM Algorithm in the Reconstruction of Small Animal PET Images." the 45th Annual Meeting of the Society of Nuclear Medicine Los Angeles, June - Swalwell J, Emmert-Buck M, Pfeifer J, Johnson C, Wetzel A, Becich M
"Cancer Genome Anatomy Project: an Integrated Web Site for Molecular Profiling of Cancer" The Fourth Annual Conference on Anatomic Pathology Informatics, Imaging and the Interent - Alizadeh A, Eisen M, Davis RE, Ma C, Sabet H, Tran T, Powell JI, Yang L,Marti GE, Moore DT, Hudson JR, Chan WC, Greiner T, Weisenburger D, Armitage JO, Lossos I, Levy R, Botstein D, Brown PO, Staudt LM.
"The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes." Cold Spring Harb Symp Quant Biol. 64: 71-8
[PubMed] - Agarwala R, Biesecker LG, Tomlin JF, Schaffer AA.
"Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources." Am J Med Genet. 86(2): 156-61
[PubMed] - Lee YS, Sugiyama K and Kador PF
"Rotamers of Tolrestat and Their Binding Mode to Aldose Reductase." Adv. Exp. Med. Biol. 463: 465-472
[PubMed] - D.P. Weliky, A.E. Bennett, A. Zvi, J. Anglister, P.J. Steinbach & R. Tycko
"Solid-State NMR Evidence for an Antibody-Dependent Conformation of the V3 Loop of HIV-1 gp120." Nature Struct. Biol. 6: 141-145
[PubMed] - P. Sharma, P.J. Steinbach, M. Sharma, N.D. Amin, J.J. Barchi, Jr. & H.C. Pant
"Identification of Substrate Binding Site of Cyclin-Dependent Kinase 5." J. Biol. Chem. 274: 9600-9606
[PubMed] - K. Ray, B.C. Hauschild, P.J. Steinbach, P.K. Goldsmith, O. Hauache & A.M. Spiegel
"Identification of the Cysteine Residues in the Amino-Terminal Extracellular Domain of the Human Ca Receptor Critical for Dimerization: Implications for Function of Monomeric Ca Receptor." J. Biol. Chem. 274: 27642-27650
[PubMed] - Whitney LW, Becker KG, Tresser NJ, Caballero-Ramos CI, Munson PJ, et al.
"Analysis of gene expression in multiple sclerosis lesions using cDNA microarrays." Annals of Neurology 46(3): 425
[Abstract] [PubMed] - Taitelbaum, H., Z. Koza, T. Yhanir and G.H. Weiss
"Tiger and Rabbits: a single trap and many walkers." Physica A 266: 280-290
[Abstract] - Pajevic S, Pierpaoli C.
"Color Schemes to Represent the Orientation of Anisotropic Tissues from diffusion Tensor Data: Application to White Matter Fiber Tract Mapping in the Human Brain." Magnetic Resonance in Medicine 42: 526-540 [PubMed] - Holbrook, P.G., V. Geetha, M.A. Beaven and P.J. Munson
"Recognizing the Pleckstrin homology doman fold in mammalian phospholipase D using Markov models." FEBS Letters 448: 269-272
[Abstract] Full Article - Geetha, V., V.D. Francesco, J. Garnier and P.J. Munson
"Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologs." Protein Engineering 12(7): 101-108 [PubMed] - DiFrancesco, V., P.J. Munson and J. Garnier
"Foresst: fold recognition from secondary structure predictions of proteins." Bioinformatics 15(2): 131-140 [PubMed] - Burklow, T.R., J.P. Moak, J.J. Bailey and F.T. Makhlouf
"Neurally Mediated Cardiac Syncope: Autonomic Modulation After Normal Saline Infusion." Journal of the American College of Cardiology 33(7): 2059-2066
[Abstract] [PubMed] - Bogu¿a, M., J. Masoliver and G.H. Weiss
"A discrete formulation of the theory of sojourm times in a two-state system."¿¿
[Abstract] - Berezhkovskii, A. M., D. J. Bicout, G. H. Weiss
"Collision Model for Activated Rate Processes: Turnover Behavior of the Rate Constant." J. Chem. Phys 111: 11050-11059
[Abstract] - Berezhkovskii, A.M., A. Szabo and G.H. Weiss
"Theory of single-molecule flourescence spectroscopy of two-state systems." Chemical Physics 110(18): 9145-9150
[Abstract] - Berezhkovskii, A.M., D.J. Bicout and G.H. Weiss
"Target and Trapping Problems: From the Ballistic to the Diffusive Regime." Chemical Physics 110(2): 1112-1122
[Abstract] - Newcomb WW, Homa FL, Thomsen DR, Trus BL, Cheng N, Steven AC, Booy FP, Brown JC.
"Assembly of the Herpes Simplex Virus Procapsid from Purified Components and Identification of Small Complexes Containing the Major Capsid and Scaffolding Proteins." Virology 73, No.5: 4239-4250 [PubMed] - Martino RL, Johnson CA, Kempner KM, Pohida TJ, Powell JI, Suh EB, Trus BL, Yap TK
"Providing Computational Science and Engineering Expertise for a Large Biomedical Research Program." The First Joint Meeting of the Biomedical Engineering Society and the IEEE Engineering in Medicine and Biology Society Atlanta, Georgia, October 1999 - Caston JR, Belnap DM, Steven AC, Trus BL
"A Strategy for Determining the Orientations of Refractory Particles for Reconstruction from Cryo-Electron Micrographs with Particular Reference to Round, Smooth-Surfaced, Icosahedral Viruses." Structural Biology 125:209-215 [PubMed] - Trus BL, Gibson W, Cheng N, Steven AC
"Capsid Structure of Simian Cytomegalovirus from Cryoelectron Microscopy: Evidence for Tegument Attachment Sites." Virology 73, No.3: 2181-2192 [PubMed] - Summers, R. M., Selbie, W. S., Malley, J. D., et al
"Polypoid lesions of airways: early experience with computer-assisted detection by using virtual bronchoscopy and surface curvature." Radiology 208: 331-337
[PubMed] - Summers, R. M., Brune, A. M., Choyke, P. L., Chow, C. K., Patronas, N. J., Miller, F. W., White, P. H., Malley, J. D., Rider, L. G.
"Juvenile Idiopathic inflammatory mypoathy: exercise-induced changes in muscle at short inversion time inversion-recovery MR imaging." Radiology 191-196
[PubMed] - Summers, R. M., Pusanik, L. M., Malley, J. D.
"Automatic detection of endobronchial lesions with virtual bronchoscopy: comparison of two methods." Medical Imaging, Proceedings of SPIE 1998 3338: 327-335 - Radko, S. P., Chrambach, A., Weiss, G. H.
"The asymmetry of protein peaks in capillary zone electrophoresis. Effect of starting zone length and presence of polymer." J. Chromatography A 817: 253-262
[PubMed] - Hecht, D., Jung, D., Munson, P. J., Prabhu, V. V., Kleinman, H. K.
"In Initial array analysis of gene expression during laminin dependent acinar differentiation of a human submandibular gland cell line (Abstract)" Toward a molecular understanding of craniofacial morphogenesis, NIH, Bethesda, MD, November 22-24 - Geetha, V., Di Francesco, V., Garnier, J., Munson, P. J.
"In Comparison of methods for identification of remote homologs in proteins ( Abstract and Poster)" Intelligent Systems in Molecular Biology 98 Montreal, Canada, June 28-July 02 - Geetha, V., Di Francesco, V., Garnier, J., Munson, P. J.
"In Assessment of methods for fold assignment in proteins (abstract)" The Protein Society San Diego, CA, 1998, 159-T. - Blank, P. S., Cho, M. S., Vogel, S. S., Kaplan, D., Kang, A., Malley, J. D., Zimmerberg, J.
"Submaximal responses in calcium-triggered exocytosis are explained by differences in the calcium sensitivity of individual secretory vesicles." J. Gen. Physiol. 112: 559-567
[PubMed] - Blank, P. S., Vogel, S. S., Cho, M. S., Kaplan, D., Bhuva, D., Malley, J. D., Zimmerberg, J.
"The calcium sensitivity of individual secretory vesicles is invariant with the rate of calcium delivery." J. Gen. Physiol. 112: 569-576
[PubMed] - Weiss, G. H., J. M. Porrâ, et al.
"Statistics of the depth probed by cw measurements of photons in a turbid medium." Physical Review E 58(51): 6431-6439 - Weiss, G. H.
"Statistical properties of the penetration depth of photons into a semi-infinite turbid medium: A random walk analysis." Applied Optics 37: 3558-3563 - Weiss, G. H. and J. E. Kiefer
"A numerical study of the statistics of penetration depth of photons re-emitted from irradiated media." J. Mod. Optics 45: 2315-2325 - Weiss, G. H., J. M. Porrâ, et al.
"The continuous-time random walk description of photon motion in an isotropic medium." Optics Comm. 146: 268-276 - Shrager, R. I., G. H. Weiss, et al.
"Selection of optimal measurements for monoexponential T2 determinations in NMR spectroscopy and imaging experiments." NMR in Biomed. 11: 297-305 - Shrager, R. I., G. H. Weiss, et al.
"Optimal time spacings for T2 measurements: monoexpoenential and biexponential systems." NMR in Biomed. 11: 297-305
[PubMed] - Pajevic, S., R. E. Carson, et al.
"Noise Characteristics of 3-D and 2-D Pet Images." IEEE Trans. Med. Imaging 17(1): 9-23
[PubMed] - Pajevic, S. and C. Pierpaoli
"Improved Representation of the Directional Information Contained in the Diffusion Tensor." 6th ISMRM Proceedings 1233 - Norman, J. E., J. J. Bailey, et al.
"NHLBI workshop on the utilization of ECG databases: Preservation and use of existing ECG databases and development of future resources." J. Electrocardiol 31(2): 83-89
[PubMed] - Ioannidis JPA, McQueen PG, Goedert JJ, Kaslow RA
"Use of Neural Networks to Model Complex Immunogenetic Associations of Disease: Human Leukocyte Antigen Impact on the Progression of Human Immunodeficiency Virus Infections." American Journal of Epidemiology 147: 464-471
[PubMed] - Goldstein SR, McQueen PG, Bonner RF.
"Thermal modeling of Laser Capture Microdissection." Applied Optics 37: 7378-7391
[Abstract] - Bicout, D. J., A. M. Berezhkovskii, et al.
"Where do Brownian particles spend their time?" Physica A 258: 352-364 - Bicout, D. J., A. M. Berezhkovskii, et al.
"Turnover in the mean survival time for a particle moving between two traps." Physica A 256: 342-350 - M.A. Schmidt, K.O. Agyeman, J.M. Laurienzo, C.L. Brenneman, R.Z. Freidlin, C.J. Ohazama, A.E. Arai, J.A. Panza
"Left Ventricular Volume Measurements in Humans Using Real-Time Three-Dimensional Echocardiography: Comparison with MRI." American Heart Association 71st Scientific Session, Dallas, Texas - Schmidt MA, Laurienzo JM, Brenneman CL, Freidlin RZ, Ohazamas CJ, Jones M, Panza JA
"Accuracy of left ventricular mass measurements using real-time three-dimensional echocardiography." CIRCULATION 98 (17): 792 Suppl. S OCT 27 - Khan J., Simon R., Bittner M., Chen Y., Leighton S., Pohida T., Smith P., Jiang Y., Gooden G., Trent J., and Meltzer P.
"Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays" Cancer Research 58: 5009-13
[PubMed] - Yao R, Johnson CA, Bacharach SL, Daube-Witherspoon ME.
"Attenuation Correction and Iterative Reconstruction for PET." The Journal of Nuclear Medicine 39: 179P - Norman R. Watts, Manoj Misra, Paul T. Wingfield, Stephen J. Stahl, Naiqian Cheng, Benes L. Trus, and Alasdair C. Steven
"Three-Dimensional Structure of HIV-1 Rev Protein Filaments" Structural Biology 41-52 [PubMed] - Martino RL, Kempner KM, Johnson CA.
"Information technology applications in biomedical research." Proceedings of the IEEE International Conference on Information Technology Applications in Biomedicine 28-34 - Lee YS, Chen Z and Kador PF
"Molecular Modeling Studies of the Binding Modes of Aldose Reductase Inhibitors at the Active Site of Human Aldose Reductase." Bioorg. Med. Chem. 6: 1811-1820
[PubMed] - Lee YS, Hodoscek M, Brooks B and Kador PF
"Catalytic Mechanism of Aldose Reductase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics." Biophys. Chem. 274: 27642-27650
[PubMed] - E. Leroy, R. Boyer, G. Auburger, B. Leube, G. Ulm, E. Mezey, G. Harta, M.J. Brownstein, S. Jonnalagada, T. Chernova, A. Dehejia, C. Lavedan, T. Gasser, P.J. Steinbach, K.D. Wilkinson & M.H Polymeropoulos
"The Ubiquitin Pathway in Parkinson's Disease." Nature 395: 451-452
[PubMed] - Suh EB, Narahari B, Simha R
"Dynamic Load Balancing Schemes for Computing Accessible Surface Areas of Protein Molecules." Proceedings, International Conference on High Performance Computing (HiPC98) December 17-20, 1998, Chennai (Madras), India. - Lanczycki CJ, Johnson CA, Trus BL, Conway JF, Steven AC, Martino RL
"Parallel computing applications for the structural biology of viruses." IEEE Computational Science and Engineering 5:76-9 - Booy FP, Roden RB, Greenstone HL, Schiller JT, Trus BL
"Two Antibodies that Neutralize Papillomavirus by Different Mechanisms Show Distinct Binding Patterns at 13 A Resolution." Molecular Biology 95-106 [PubMed] - Yarmola, E., Calabrese, P. O., Chrambach, A., Weiss, G. H."Interaction with the matrix: The dominant factor in macromolecular band spreading in gel electrophoresis." J. Phys. Chem. 101: 2381-2387
- Summers, R. M., Selbie, W. S., Malley, J. D., et al
"Computer-Assisted Detection of Endobronchial Lesions Using Virtual Bronchoscopy: Application of Concepts from Different Geometry." International Conference on Mathematical Models in Medical and Health Sciences Nashville, TN May 28-31 - Porr¿, J. M., Masoliver, J., Weiss, G. H.
"When the telegrapher's equation furnishes a better approximation to transport equation than the diffusion approximation." Phys. Rev. E 55: 7771-7774 - Laks, M. M., Arzbaecher, R., Bailey, J. J., Geselowitz, D. B., Berson, A. S.
"Special report: Recommendations for safe current limits for electrocardiographs - Response." Circulation 95(1): 277-278. - Blank, P. S., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"Kinetic models for calcium-triggered exocytosis." J. Gen. Phys. 110(1) - Blank, P. S., Vogel, S. S., Malley, J. D., Zimmerberg, J.
"Heterogeneity in calcium-triggered exocytosis." Mol. Biol. Cell 297a - Weiss, G. H. and J. E. Kiefer
"Some properties of a measure of resolution in gel electrophoresis and CZE." Electrophoresis 18: 2008-2011 - Weiss, G. H. and A. H. Gandjbakhche
"Effects of nonlocalized target shape in the random walk description of transillumination experiments for optical imaging." Phys. Rev. E 55: 3451-3459 - Schubert, S. F., S. Pajevic, et al.
"While Body PET Using Overlapped 3D Acquision and Weighted Image Summation." IEEE 1(97): 1284-1289 - Radko SP, Weiss GH, Chrambach A
"Protein band spreading in CZE: Effects of sample zone length and presence of polymer." J. Chromatog. A 781: 277-286
[PubMed] - Munson, P. J. and R. K. Singh
"Multi-body Interactions within the Graph of Protein Structure" ISMB 5: 198-201
[PubMed] - McQueen, PG
"Physics and Fractal Structures (book review)" Journal of Statistical Physics 86: 1397-1398 - Gitterman, M., R. I. Shrager, et al.
"Stochastic resonance and symmetry breaking in a one-dimensional system." Phys. Rev. E 56: 3713-3716 - Di Francesco V, McQueen PG, Garnier J, Munson PJ
"Incorporating global information into secondary structure prediction with hidden Markov models of protein folds." Proc Int Conf Intell Syst Mol Biol. 5:100-3
[PubMed] - Bailey, J. J. and J. P. Moak
"Simultaneous Heart Rate and Blood Pressure Variability Analysis: Insight into Possible Mechanisms Underlying Vasodepressor Synscope." J. Electrocardiol 30: 54 - Cole J., Hendler R., Smith P., Fredrickson H., Pohida T., and Friauf W.
"A High Speed Optical Multichannel Analyzer" Journal of Biochemical and Biophysical Methods 35(3)
[PubMed] - Bonner R., Emmert-Buck M., Cole K., Pohida T., Chuaqui R., Goldstein S., and Liotta L.
"Laser Capture Microdissection: Molecular Analysis of Tissue" Science 278:1230-1
[PubMed] - Lin ZL, Shenker A, and Pearlstein RA
"A model of the lutropin/choriogonadotropin receptor: Insights into the structural and functional effects of constitutively activating mutations." Protein Eng. 10 (5): 501-510
[Abstract] [PubMed] - Johnson CA, Seidel J, Carson RE, Gandler WR, Sofer A, Green MV, Daube-Witherspoon ME.
"Evaluation of 3D Reconstruction Algorithms for a Small Animal PET Camera" IEEE Transactions on Nuclear Science 44 Full Article - Johnson CA, Sofer A.
"Interior Point Methodology for Large Scale Regularized Maximum Likelihood Reconstruction in Emission Tomography" presentation to the University of Pennsylvania Medical Imaging Group July Full Article - Seidel J, Johnson C, Jagoda E, Sha L, Eckelman WC, Green MV.
"A high resolution scanner for investigating technical requirements and selected biological applications in small animal PET" The Journal of Nuclear Medicine 38: 44P - Seidel J, Johnson C, Jagoda E, Sha L, Eckelman WC, Green MV.
"A High Resolution PET Scanner for Investigating Technical Requirements and Selected Biological Applications of Continuous 3-D Detectors in Small Animal Imaging." Journal of Nuclear Medicine 38: 44P - Martino RL, Yap TK, Suh EB
"Parallel Algorithms in Molecular Biology." Proceedings of the High-Performance Computing and Networking (HPCN) Europe '97 Spring-Verlag, 232-240 - Martino RL.
"Parallel computing in molecular biology and medical imaging." Proceedings of the International Symposium on Parallel Computing in Engineering and Science - Liu J, Nau MM, Zucman-Rossi J, Powell JI, Allegra CJ, Wright JJ.
"Line-1 element insertion at the t(11,22) translocation breakpoint of a desmoplastic small round cell tumor," Genes, Chromosomes and Cancer 18(3):232-9 - Kempner KM, Chow D, Choyke P, Cox Jr JR, Johnson CA, Okunieff P, Ostrow H, Pfeifer JC, Martino RL.
"The development of an ATM-based Radiology Consultation WorkStation for radiotherapy treatment planning" SPIE Medical Imaging 1997 Conference Proceedings 3031: 500-11 - Johnson CA, Sofer A.
"Interior Point Methods for Volume PET Reconstruction." Proceedings of the International Symposium on Mathematical Programming, 19 - Johnson CA, Seidel J, Carson RE, Gandler WR, Sofer A, Green MV, Daube-Witherspoon ME.
"Evaluation of 3D Reconstruction Algorithms for a Small Animal PET Camera" IEEE Transactions on Nuclear Science 44: 1303-8 - Johnson CA, Seidel J, Carson RE, Gandler WR, Sofer A, Green MV, Daube-Witherspoon ME.
"Evaluation of 3D Reconstruction Algorithms for a Small Animal PET Camera." '96 IEEE Nuclear Science Symposium Conference Record Alberto Del Guerra, 1481-1485 - Ghosh S, Karanjawala ZE, Hauser ER, Ally D, Knapp JI, Rayman JB, Musick A,Tannenbaum J, Te C, Shapiro S, Eldridge W, Musick T, Martin C, Smith JR,Carpten JD, Brownstein MJ, Powell JI, Whiten R, Chines P, Nylund SJ,Magnuson VL, Boehnke M, Collins FS.
"Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotidemarkers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group." Genome Res. 7(2): 165-78 - Gitterman M, Weiss GH
"An overall view of stochastic resonance."¿ Chaos & Bifurcation ¿7: 911-916 - Gandjbakhche AH, Bonner RF, Nossal RJ, Weiss GH
"Effects of multiple passage probability on fluorescent signals from biological media."¿ Applied Optics 36: 4613-4619 - Bose S, Hendler RW, Shrager RI, Smith PD
"Multichannel analysis of single turnover kinetics of cytochrome aa3 reduction of O2." Biochemistry 36: 2439-2449
[PubMed] - Pajevic S, Bacharach SL, Carson RE, Weiss GH
"Effects of time delay in cardiac blood flow measurements by bolus H2(15)O." IEEE Trans. on Medical Imaging 16:294-300
[Abstract] [PubMed] - Spencer JV, Trus BL, Booy FP, Steven AC, Newcomb WW, Brown JC
"Structure of the Herpes Simplex Virus Capsid: Peptide A862-H880 of the Major Capsid Protein Is Displayed on the Rim of the Capsomer Protrusions." Virology 229-235 [PubMed] - Caston JR, Trus BL, Booy FP, Wickner RB, Wall JS, Steven AC
"Structure of L-A Virus: A Specialized Compartment for the Transcription and Replication of Double-stranded RNA." Cell Biology 138:975-985 [PubMed] - McAuliffe MJ, Eberly D, Fritsch DS, Chaney EL, and Pizer SM.
"Scale-Space Boundary Evolution Initialized by Cores." Proceedings of the Fourth International Conference on Visualization in Biomedical Computing, Lecture Notes in Comp Sci Vol 1131, KH Hohne and R Kikinis (eds), Springer. pp. 173-182, 1996. - McQueen PG, Jin AJ, Pierpaoli C, Basser PJ,
"A Finite Element Model of Molecular Diffusion in Brain Incorporating in vivo Diffusion Tensor MRI Data" Proceedings of the International Society for Magnetic Resonance in Medicine, Fourth Scientific Meeting and Exhibition. 1:193 - McAuliffe MJ, Eberly D, Fritsch DS, Chaney EL, and Pizer SM.
"Scale-Space Boundary Evolution Initialized by Cores." Proceedings of the Fourth International Conference on Visualization in Biomedical Computing, Lecture Notes in Comp Sci Vol 1131, KH Hohne and R Kikinis (eds), Springer. pp. 173-182. - Rosenstein, D. L., Kalogeras, K. T., Kalafut, M., Malley, J. D., Rubinow, D. R.
"Peripheral measures of arginine vasopressin, artial natriuretic peptide, and adrenocorticotropic hormone in premenstrual syndrome." Psychoneuroendocrinology 21: 347-359 - Nunez, S. B., Blye, R. P., Thomas, P. M., Reel, J. R., Barnes, K. M., Malley, J. D., Cutler, G. B.
"Recovery of reproductive function in rats treated with the aromatase inhibitor fadrozole." Reproductive Toxicology 10(5): 373-377
[PubMed] - Magiakou, M. A., Mastorakos, G., Rabin, D., Margioris, A. N., Dubbert, B., Calogero, A. E., Tsigos, C., Munson, P. J., Chrousos, G. P.
"The Maternal Hypothalamic-Pituitary-Adrenal Axis in Third Trimester Human Pregnancy." Clin. Endocrinol. 44: 419-428
[PubMed] - Laks, M. M., Arzbaecher, R., Bailey, J. J., Geselowitz, D. B., Berson, A. S.
"Recommendations for safe current limits for electrocardiographs." Circulation 93: 837-9, A statement for healthcare professionals from the Committee on Electrocardiography, American Heart Association. - Vasudevan, G. and P. J. Munson
"Simplified Representation of Proteins." J. Biomol. Struct. and Dynamics 13(5): 781-793 - McQueen PG, Jin AJ, Pierpaoli C, and Basser PJ
"Development of a Finite Element Model of Molecular Diffusion in Living Brain from in vivo Magnetic Resonance." IEEE Service Center - Proceedings of the 1996 Fifteenth Southern Biomedical Engineering Conference: 289-292. - Yap TK, Frieder O, Martino RL.
"Parallel computing in biomedicine: Genetic and protein sequence analysis." Parallel and Distributed Computing Handbook E: Zomaya AY. New York, McGraw-Hill, 1071-1096 - Yap TK, Frieder O, Martino RL.
"High performance computational methods for biological sequence analysis." Kluwer Academic Publishers Boston, MA - Sofer A, Johnson CA, and Nash SG.
"Nonlinear optimization of the iterative 3-D reconstruction problem" INFORMS Atlanta Fall 1996 Meeting - Mahaukar AA, Vivino MA, Trus BL, Kuehl EM, Datiles MB, Kaiser-Kupfer MI.
"Constructing retinal fundus photomontages," Invest. Ophthal. and Vis. Sci. 37: 1675-1683
[PubMed] - Johnson CA, Nash SG, Sofer A, Carson RE, Daube-Witherspoon ME.
"Optimization for iterative 3D PET reconstructions." Fifth SIAM Conference on Optimization 70 - Bourg J, Mitchell JB, Mirotznik M, Roth B, Subramanian S, Cherukuri M, Zablocky PG, Pohida TJ, Smith PD, Friauf WS, Tschudin RG.
"Pulsed Low Frequency EPR Spectrometer and Imager" US Patent No. 5,502,386 - P.J. Steinbach
"Two-Dimensional Distributions of Activation Enthalpy and Entropy from Kinetics by the Maximum Entropy Method." Biophys. J. 70: 1521-1528
[PubMed] - P.J. Steinbach & B.R. Brooks
"Hydrated Myoglobin's Anharmonic Fluctuations are Not Primarily Due to Dihedral Transitions." Proc. Natl. Acad. Sci. USA 93: 55-59 - Weiss GH, Calabrese P
"Occupation times of a CTRW on a lattice."¿ Physica A 234: 443-454 - Weiss GH "Onsager′s contribution to reaction-rate theory." Physica A 234: 443-454
- Spouge J, Szabo A, Weiss GH
"Single particle survival in gated trapping." Phys Rev E 54: 2248-2255
[PubMed] - Spouge JL, Shrager RI, Dimitrov DS"HIV-1 infection kinetics in tissue cultures." Mathematical Biosciences 138: 1-22
[PubMed] - Masoliver J, Weiss GH
"Finite-velocity diffusion." Eur J Physics 17: 190-196 - Katki H, Weiss GH, Kiefer JE
"Optimization of magnetization transfer experiments to measure first-order rate constants and spin-lattice relaxation times." NMR in Biomed 9(3):135-9.
[PubMed] - Havlin S, Yen A, Kopelman R, Taitelbaum H, Weiss GH
"Effects of bias on the kinetics of A+B C with initially separated reactants."¿ Phys Rev E 54: 5942-5947¿
[PubMed] - Goans RE, Weiss GH, Vieira NE, Sidbury JB, Abrams SA, Yergey AL
"Calcium kinetics in glycogen storage disease type 1a."¿ Calcified Tissue Intl ¿59: 449-453
[PubMed] - Gandjbakhche, A. H., Chernomordik, V., Bonner, R. F., Nossal, R. J., Weiss, G. H., Hebden, J.
"Optical detection of abnormally absorbing regions in tissue." OSA Trends in Optics and Photonics on Advances in Optical Imaging and Photon Migration , Editors: Alfano, RR, and Fujimoto, JG, (OSA, Washington DC) 2, 183-189 - Bryngelson JD, Weiss GH "Polymers with internal length and displacement constraints: Bounds and exact expressions for free energies." Macromolecules 29: 7995-7999
- Weiss GH, Sokoloff H, Zakharov SF, Chrambach A
"Interpretation of electrophoretic band shapes by a partition chromatographic model." Electrophoresis 17:1325-32 - Rovati GE, Shrager RI, Nicosia S, Munson PJ
"KINFIT II: A nonlinear least squares program for analysis of kinetic binding data." Molecular Pharmacology 50:86-95
[PubMed] - Masoliver J, Weiss GH
"Resolution in time of two electrophoretic peaks." Sep Sci & Tech 31:319-26 - Gandjbakhche AH, Bonner RF, Nossal R, Weiss GH, Hebden J
"Optical detection of abnormally absorbing regions in tissue." Advances in Optical Imaging and Photon Migration 1996, Orlando - Gandjbakhche AH, Bonner RF, Nossal RJ, Weiss GH
"Absorptivity contrast in transillumination imaging of tissue abnormalities." Appl Opt 1996 35:1767-74 - Gandjbakhche AH, Bonner RF, Gannot I, Knutson J, Navai R, Nossal R, Weiss GH
"Fluorescent photon migration for turbid biological media." Proceedings of Advances in Laser and Light Spectroscopy to Diagnose Cancer and Other Diseases III: Optical Biopsy SPIE 1996, 2679:8-15 - Carson RE, Yan Y, Shrager RI
"Absolute cerebral blood flow with [150]-water and PET." Quantification of Brain Function Using PET. Myers, Cunningham, Bailey, and Jones (eds.). Academic Press 1996, 185-90. - Burklow TR, Moak JP, Bailey JJ
"Prevention of vasodepressor syncope following normal saline infusion."¿ PACE ¿19:640 - Boguna M, Porrý J, Masoliver J, Weiss GH"Isotropization time for non-Markovian CTRW?s."Physica A 230:149-55
- Berkolaiko G, Havlin S, Larralde H, Weiss GH
"The expected number of distinct sites visited by N discrete L_vy flights on a one-dimensional lattice."¿Phys Rev E¿53:5774-78 - Berezhkovskii AM, Weiss GH
"Average volume of the domain visited by randomly injected spherical particles in d dimensions."¿Phys Rev E¿54:92-9
[PubMed] - Newcomb WW, Homa FL, Thomsen DR, Booy FP, Trus BL, Steven AC, Spencer JV, Brown JC
"Assembly of the Herpes Simplex Virus Capsid: Characterization of Intermediates Observed During Cell-free Capsid Formation." Molecular Biology 432-446 [PubMed] - Vivino M, Laurienzo J, Curiel R, Panza J
"Impact of gain settings on the relation between concentration of ultrasound scatterers and video intensity: implications for clinical studies using myocardial contrast echocardiography." Presentation at the American College of Cardiology Meeting Orlando, FL, 931-119 - Trus BL, Unser M, Vrhel MJ, Conway JF, Gross M, Threvenaz P, Steven AC
"Resolution assessment of 3D reconstructions by spectral signal-to-noise ratio." EUREM Proc. Dublin, Ireland. - Trus BL, Roden RBS, Greenstone HL, Schiller JT, Booy FP
"3D reconstruction of bovine papillomavirus visualized at 9¿." Conf. on Virus Assembly Saxtons River, VT - Trus BL, Roden RBS, Greenstone HL, Schiller JT, Booy FP
"3D reconstruction of bovine papillomavirus visualized at 9¿." Proc. of XIIth International Biophysics Congress in Progress in Biophysics and Molecular Biology 65(1):28. - Trus BL, Kocsis E, Conway JF, Steven AC
"Digital image processing of electron micrographs: The PIC system III." J. Struct. Biol. 116:61-67
[PubMed] - Trus BL, Booy FP, Newcomb WW, Brown JC, Homa FL, Thomsen DR, Steven AC
"The herpes simplex virus procapsid: structure, conformational changes upon maturation, and roles of the triplex proteins VP19c and VP23 in assembly." J. Mol. Biol 263(3):447-62
[PubMed] - Steven AC, Booy FP, Trus BL, Newcomb WW, Homa FL, Thomsen DR, Brown JC
"Visualization of the conformational changes that accompany maturation of the herpesvirus procapsid." EUREM Proc. August, Dublin, Ireland. - Heck DV, Trus BL, Steven AC
"Three-dimensional structure of bordetella pertussis fimbriae." J. Struc. Biol. 116:264-269
[PubMed] - Datiles M, Mahurkar A, Caruso R, Vivino M, Magno B
"Effect of nuclear cataracts on visual function: cone threshold measurements using computer assisted perimetry." ARVO abstracts No.3483,S759 - Conway JF, Trus BL, Booy FP, Newcomb WW, Brown JC, Steven AC
"Visualization of three-dimensional density maps reconstructed from cryo-electron micrographs of viral capsids." J. Struct. Biol. 116:200-208
[PubMed] - Booy FP, Trus BL, Davison AJ, Steven AC
"The capsid architecture of channel catfish virus, an evolutionarily distant herpesvirus, is argely conserved in the absence of discernible sequence homology with herpes simplex virus." Virology 215:134-141
[PubMed] - Booy FP, Greenstone JL, Roden RS, Schiller JT, Steven AC, Trus BL
"High resolution studies of papillomavirus and herpes simplex virus." EUREM Proc. Dublin, Ireland - Fritsch DS, Chaney EL, Boxwala A, McAuliffe MJ, Raghavan S, Thall A, and Earnhart JD.
"Core-based Registration for Automatic Radiotherapy Treatment Verification." International Journal of Radiation Oncology, Biology, Physics. 33 (5), pp. 1287-1300, December 1995. - Johnson CA, Yan Y, Carson RE, Martino RL, Daube-Witherspoon ME.
"A system for the 3D reconstruction of retracted-septa PET data using the EM algorithm." IEEE Transactions on Nuclear Science 42: 1223-1227 Full Article - Yap TK, Munson PJ, Frieder O, Martino RL.
"Parallel multiple sequence alignment using speculative computation." Proceedings of the International Conference on Parallel Processing E: Gallivan KA, Oconomowoc WS. ERC Press - Yap TK, Frieder O, Martino RL.
"Parallel homologous sequence searching in large databases." Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation E: Saltz J. McLean, Virginia, IEEE Computer Society Press: 231-7 - Martino RL, Suh EB.
"How can massively parallel computers help in the prediction of protein structures?." Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation Los Alamitos, CA. IEEE Computer Society Press, 180-1 - Martino RL.
"Issues concerning how can massively parallel computers help in the prediction of protein structures?" the Fifth Symposium on the Frontiers of Massively Parallel Computation. McLean, Virginia - Martino RL.
"High performance parallel computing in biomedicine." Invited Talk at Sandia National Laboratories Albuquerque, NM - Johnson CA, Yan Y, Carson RE, Martino RL, Daube-Witherspoon ME.
"A system for the 3D reconstruction of retracted-septa PET data using the EM algorithm." Conference Record of the '94 IEEE Nuclear Science Symposium and Medical Imaging Conference Trendler RC, Norfolk, VA, IEEE Press: 1325-9 - Bourg J, Mitchell JB, Mirotznik M, Roth B, Subramanian S, Cherukuri M, Zablocky PG, Pohida TJ, Smith PD, Friauf WS, Tschudin RG.
"Pulsed Low Frequency EPR Spectrometer and Imager" US Patent No. 5,387,867 - Weiss GH, Garner M, Yarmola E, Bocek P, Chrambach A
"A comparison of resolution of DNA fragments between agarose gel and capillary zone electrophoresis in agarose solutions." Electrophoresis 16:1345-53
[PubMed] - Weiss GH, Gandjbakhche AH, Masoliver J
"Isotropization length of random walk models of photon migration in turbid media." J of Mod Optics 42:1567-74 - Porr JM, Weiss GH, Masoliver J"A diffusion model incorporating anisotropic properties." Physica A 218:229-36
- Larralde H, Weiss GH
"Expected number of sites visited by a constrained n-step random walk." Phys Rev E 52:1313-17
[PubMed] - Larralde H, Weiss GH
"A generating function for the second moment of the distinct number of sites visited by an n-step lattice random Walk." J Physics A 28:5217-25 - Goans RE, Weiss GH, Abrams SA, Perez MD, Yergey AL
"Calcium tracer kinetics show decreased irreversible flow to bone in glucocorticoid treated patients." Calcified Tissue Intl 56:533-35
[PubMed] - Gitterman M, Weiss GH
"Coherent stochastic resonance in the presence of a field." Phys Rev E 52:5708-11
[PubMed] - Bansil R, Pajevic S, Konak C
"Dynamic light scattering study of linear polyelectrolyte diffusion in gel." Macromolecules 28:7536 - Bailey JJ, Moak JP
"Heart rate variability in patients with neurally medicated syncope: Table- tilt and pharmacological testing." J Electrocardiology 28:89 - Vivino MA, Mahurkar A, Trus B, Lopez ML, Datiles M
"Quantitative analysis of retroillumination images." Eye 9:77-84
[PubMed] - Vivino M
"NIH image and ocular imaging." Ninth Annual Research Symposium presentation at the American Academy of Optometry (AAO) Annual meeting in New Orleans, LA - Trus BL, Homa FL, Thomsen DR, Newcomb WW, Booy FP, Brown JC, Steven AC
"HSV capsid protein VP26 is absent from pentons: difference mapping between VP26 + and VP26 - capsids assembled in a recombinant baculovirus system." Biophys. J. 68(2):A20. - Trus BL, Greenstone HL, Roden RBS, Schiller JT, Booy FP
"Localization of two neutralizing antibodies on bovine papillomavirus." Proceedings of the XIV International Phage/Virus Assembly Conference Gibson U, Hendrix R, Russel M. Johnstown, PA - Trus BL
"Image processing in electron microscopy: High performance computing applied to biological systems." The Second Workshop on Advanced Computing for Biological Imaging Carragler B, Potter C, Urbana-Champaign, IL - Kocsis E, Cerritelli ME, Trus BL, Cheng N, Steven AC
"Improved methods for determination of rotational symmetries in macromolecules." Ultramicroscopy 60:219-228
[PubMed] - Kessel M, Maurizi MR, Kim B, Trus BL, Kocsis E, Singh SK, Steven AC
"Oligomeric Structure of the Clp-AP Protease from E. coli." Proceedings of the 95th General Meeting of the American Society of Microbiology Washington, D.C. - Kessel M, Maurizi RR, Kim B, Kocsis E, Trus BL, Singh SK, Steven AC
"Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome." J. Mol. Biol. 250(5):587-94
[PubMed] - Kessel M, Kim B, Trus BL, Kocsis E, Singh SK, Maurizi M, Steven AC
"Oligomeric structure of the Clp-AP protease from E. coli." Biophys. J. I 68 (suppl 2):A245. - Caston JR, Trus BL, Booy FP, Dinman JD, Wickner RB, Steven AC
"Structural aspects of the capsid of L-A dsRNA virus of yeast." Proceedings of the XIV International Phage/Virus Assembly Conference Gibson U, Hendrix R, Russel M, Johnstown, PA, 6. - Green, M.V., Seidel, J., Stein, S.D., Tedder, T.E., Kempner, K.M., Kertzman, C., and Zeffiro, T.A.
"Head Movement in Normal Subjects During Simulated PET Brain Imaging With and Without Head Restraint" Journal of Nuclear Medicine 35(9): 1538-1546
[PubMed] - Pohida TJ, Fredrickson HA, Tschudin RG, Fessler JF, Krishna MC, Bourg J, Harrington F, Subramanian S.
"High-speed digitizer/averager data-acquisition system for Fourier transform electron paramagnetic resonance spectroscopy," Review of Scrientific Instruments vol.65, No.8: 2500-2504 - Martino RL, Johnson CA, Suh EB, Trus BL, Yap TK.
"The role of high performance parallel computing in biological research." Proceedings of the 16th Annual Conference of the IEEE Engineering in Medicine and Biology Society Editor: Sheppard NF, Eden M, Kantor G. Baltimore, IEEE Computer Society Press,16: 1386-7 - Martino RL.
"Parallel computing in structural biology and medical imaging." 1994 Colloquium Series the George Washington University, Department of Electrical Engineering and Computer Science, Washington, DC - Martino RL.
"Making high performance parallel computing part of the biomedical research process." the 1994 Intel Supercomputer Users Group Conference San Diego, CA - Martino RL
"High performance parallel computing in a biomedical research environment." the ARPA High Performance Computing and Communications Symposium Alexandria, VA - Martino RL.
"High performance computing in biomedical research." the FGIPC Eigth Annual High Performance Computing and Communications Conference Research Triangle Park, NC - Martino RL.
"The high performance computing and communication program: technologies for the national information infrastructure." Panel discussion at the Supercomputing '94 Conference Washington, DC - Martino RL.
"High performance computing and communication and biomedicine at the National Institutes of Health." RCI, Ltd. North American Annual Member Executive Conference. Herndon, VA - Martino RL.
"Applying parallel computing methods to biomedical research problems." Proceedings of the eighth annual Idaho National Engineering Laboratory Computing Symposium National Engineering Laboratory, U.S. Department of Energy; 13..5. 3-13, Idaho Falls, Idaho - Lee YS, Pearlstein R and Kador PF
"Molecular Modeling Studies of Aldose Reductase Inhibitors." J. Med. Chem. 37: 787-792
[PubMed] - P.J. Steinbach & B.R. Brooks
"New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation." J. Comp. Chem. 15: 667-683 - Trus BL, Homa FL, Thomsen DR, Newcomb WW, Booy FP, Brown JC, Steven AC
"Visualization of herpesvirus capsids assembled in a recombinant baculovirus system by cryo-electron microscopy." Proceedings of the 13th International Congress on Electron Microscopy - Trus BL, Davison AJ, Booy FP, Steven AC
"Capsid structure of channel catfish virus, and evolutionarily distant herpesvirus, by cryo-electron microscopy." Proceedings of the 52th Microscopy Society of America Bailey, G.W. - Martino RL, Johnson CA, Suh EB, Trus BL, Yap TK
"Parallel computing in biomedical research." Science 265:902-8
[PubMed] - Johnson CA, Weisenfeld NI, Trus BL, Conway JF, Martino RL, Steven AC
"Orientation determination in the 3-D reconstruction of icosahedral viruses using a parallel computer." Proceedings of Supercomputing 1994 902-8 - Adam, D.R., Kempner, K.M., Vivino, M.A., Tucker, E.E., and Jones, M.
"Correction of Arterial Flow Velocity Doppler Color Mapping in Transverse Cross-Sectional Imaging" Computers in Cardiology 1993 Institute of Electrical and Electronics Engineers, Inc., New York, 1993, 281-284. - Adam, D.R., Kempner, K.M., Vivino, M.A., Tucker, E.E., and Jones, M.
"Measurement of Flow Velocity in a Phantom by Corrected Doppler Color Mapping Technique, Using Transverse Cross-Sectional Imaging" Computers in Cardiology 1993 Institute of Electrical and Electronics Engineers, Inc., New York, 1993, 277-280. - Green, M.V., Seidel, J., Stein, S., Kertzman, C., Zeffiro, T., and Kempner, K.M.
"A Correction Strategy for Head Movement During Brain Imaging (Abstract)" Journal of Nuclear Medicine 34(5):70 - Seidel, J., Gandler, W., Green, M., and Kempner, K.
"An All-Digital Single, Phototube, Small Animal Scintillation Camera (Abstract)" Medical Physics 20(3):910 - Bourg J., Krishna M., Mitchell J., Tschudin R., Pohida T., Friauf W., Smith P., Metcalfe J., Harrington F., and Subramanian S.
"Radiofreqency FT-EPR Spectroscopy and Imaging" Journal of Magnetic Resonance B102 - Y. Osawa, J.F. Darbyshire, P.J. Steinbach, & B.R. Brooks
"Metabolism-Based Transformation of Myoglobin to an Oxidase by BrCCl and Molecular Modeling of the Oxidase Form." J. Biol. Chem. 268: 2953-2959 - P.J. Steinbach & B.R. Brooks
"Protein Hydration Elucidated by Molecular Dynamics Simulation." Proc. Natl. Acad. Sci. USA 90: 9135-9139
[PubMed] - Suh EB, Lee BK, Narahari B, Choudhary A, Martino RL"Parallel computation of solvent accessible surface area of protein molecules." Proceedings of the Seventh International Parallel Processing Symposium IEEE Computer Society, Washington, DC; 1993; 685-689
- Adam, D.R., Kempner, K.M., Vivino, M.A., Tucker, E.E., and Jones, M.
"Cardiovascular Flow Velocity Measurements by 2D Doppler Imaging for Assessment of Vascular Function" Presented at the 8th Henry Goldberg Workshop, December 6-10, 1992, Chapter 38,Interactive Phenomena in the Cardiac System, edited by S. Sideman and R. Beyar, published in the Advances in Experimental Medicine and Biology Series, Vol. 346, Plenum Press, New York, 1993, 393-399.
[PubMed] - Kempner, K.M., Ostrow, H.G., Fessler, J.F., Tucker, E.E.
"Prototype System for Timely Image Distribution in Support of a Cardiology Outpatient Clinic" Computers in Cardiology 1991 Institute of Electrical and Electronics Engineers, Inc., New York, 1992, 85-88. - Hong SY, Kertesz M, Lee YS and Kim OK
"Geometrical and Electronic Structures of Benzimidazobenzophenanthroline-Type Ladder Polymer (BBL)." Macromolecules 25: 5424-5429 - Berger, M.P. and Munson, P.J. "A novel randomized iterative strategy for aligning multiple protein sequences" CABIOS Vol. 7 no. 4 478-484 (1991)
[Abstract] [Full Article] - Palmeri, S.T., Kempner, K.M., Power, J.A., Bacharach, S.L., Choi, B.W., Rosing,D.R., and Bonow, R.O.
"Effects of Percutaneous Transluminal Coronary Angioplasty on Exercise-Induced Changes in R-Wave Amplitude." American Journal of Cardiology 68(1):114-116
[PubMed] - Green, M.V., Stein, S., Yan, Y., Kertzman, C., Zeffiro, T.A., and Kempner, K.M.
"Patterns of Head Movement in Normal Subjects during Simulated Brain Imaging (Abstract)" Journal of Nuclear Medicine 32(5):1064 - Rosenthal J., Jordon M., Ashe F., Conte R., Ibarra J., Jensen W., Kauffman J., Karabelnikoff M., and Pohida T.
"Transformer Failure and Common Mode Loss of Instrument Power at Nine Mile Point Unit 2 on August 13, 1991" Nuclear Regulation Guide 1445 - Martino RL, Johnson CA, Trus BL, Yap TK, Suh EB, Pfeifer JC, Brooks RB
"Highly Parallel Computing at the National Institutes of Health." Proceedings of Supercomputing USA/Pacific 91 - Green, M., Dextras, R., Grady, C., and Kempner, K.
"Correction for Head Motion during Brain Imaging using Simultaneous and Independent Measurements of Head Position: A Feasibility Study (Abstract), European Journal of Nuclear Medicine Supplement." Abstracts of the 5th World Congress of Nuclear Medicine and Biology. 16:S199 - Daube-Witherspoon, M.E., Yan, Y.C., Green, M.V., Carson, R.E., Kempner, K.M., and Herscovitch, P.
"Correction for Motion Distortion in PET by Dynamic Monitoring of Patient Position (Abstract)" Journal of Nuclear Medicine. 31(5):816 - Green, M., Stein, S., Kempner, K., Fessler, J., and Tedder
"The Accuracy of Head Repositioning using a Laser Alignment System:Implications in High-Resolution PET Brain Imaging (Abstract)" Journal of Nuclear Medicine 18(2):137 - Kindle JR, Bartoli FJ, Hoffman CA, Kim OK, Lee YS, Shirk JS and Kafafi ZH
"Nonlinear Optical Properties of Heteroaromatic Ladder Polymers, BBL and BBB at 1.064 um." Appl. Phys. Lett. 56: 712-717 - Lee YS, Kertesz M and Elsenbaumer RL
"The Importance of Energetics in the Design and Synthesis of Small Band Gap Conducting Polymer." Chem. Mater. 2: 526-530