Bioinformatics and Computational Biology

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2007

Bura, E., Klimov, D.K., Barsegov, V., "Analyzing forced unfolding of protein tandems by ordered variates: 1. Independent unfolding times", Biophysical Journal, vol. 93, pp. 1100-1115, 2007 [BCB]
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Blair, D., Grefenstette, J., Nash, H., Newfield, D., Lucien, D., Apparatus and method for providing sequence database comparison, , US, June 12, 2007 [BCB]
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Dong, X., Klimov, D.K., Blaisten-Barojas, E., "Protein folding with the Adaptive Tempering Monte Carlo method", Mol. Simul., vol. 33, pp. 577-582, 2007 [BCB]
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Jafri, M.S., "The globalization of biotechnology", Global Studies Review, vol. 3, no. 3, pp. 4-5, 2007 [BCB]
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Kostoff, R.N., Block, J.A., Solka, J.L., Briggs, M.B., Rushenberg, R., Stump, J.A., Dustin, J., Lyons, T., Wyatt, J., "Literature-Related Discovery(LRD): Methodology", Technological Forecasting and Social Change, 2007 [BCB]
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Kostoff, R.N., Block, J.A., Solka, J.L., Briggs, M.B., Rushenberg, R.L., Stump, J.A., Johnson, D., Arndt, C.M., Lyons, T.J., Wyatt, J.R., "Literature-Related Discovery (LRD):Lessons Learned and Future Directions", Technological Forecasting and Social Change, 2007 [BCB]
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Kostoff, R.N., Solka, J.L., Rushenberg, R.L., Wyatt, J.R., "Literature-Related Discovery (LRD): Water Purification", Technological Forecasting and Social Change, 2007 [BCB]
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Mahadevan, P., Seto, D., "Comparative genomics using CoreGenes to analyze small bacterial genomes, with an application for the annotation of hypothetical proteins", International Conference on Bioinformatics and Computational Biology: CSREA Press, 2007 [BCB]
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Nguyen, M. T., Dudycha, S.J., Jafri, M.S., "The effects of Ca2+ on cardiac mitochondrial energy production is modulated by Na+ and H+ dynamcis", Am J Physiol Cell Physiol, vol. 292, no. 6, pp. C2004-2020, 2007 [BCB]
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Raman, E.P., Barsegov, V., Klimov, D.K., "Folding of tandem-linked domains", Proteins: Struct. Funct. Bioinform., vol. 67, pp. 795-810, 2007 [BCB]
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Raman, E.P., Takeda, T., Barsegov, V., Klimov, D.K., "Mechanical unbinding of Abeta peptides from amyloid fibrils", J. Mol. Biol., vol. 373, pp. 785-800, 2007 [BCB]
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Takeda, T., Klimov, D.K., "Dissociation of Abeta 16-22 amyloid fibrils probed by molecular dynamics", J. Mol. Biol., vol. 368, pp. 1202-1213, 2007 [BCB]
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Williams, G.S., Huertas, M.A., Sobie, E.A., Jafri, M.S., Smith, G.D., "A probability density approach to modeling local control of calcium-induced calcium release in cardiac myocytes", Biophys J, vol. 92, pp. 2311-2328, 2007 [BCB]
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Wang, P., Klimov, D.K., "Lattice simulations of cotranslational folding of single domain proteins", Proteins: Struct. Funct. Bioinform., 2007 [BCB]
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Wang, G., Kinser, J., "Nonlinear Dimensionality Reduction on 3-D Protein Image Analysis", ASIMOLAR, 2007 (Invited) [BCB]
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2006

Agan, B.K., Hanson, E.H., Kruzelock, R.P., Lin, B., Rowley, R.K., Seto, D., Stenger, D.A., Thornton, J., Tibbetts, C.J., Thach, D., Vora, G.J., Walter, E.A., Wang, Z., Re-sequencing pathogen microarray, , no. 11/177,64, United States , 2006 [BCB]
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Barsegov, V., Klimov, D.K., Thirumalai, D., "Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: Theory and applications", Biophys. J., vol. 90, pp. 3827-3941., 2006 [BCB]
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Chikando, A., Kinser, J.M., "Adaptation of Fast Marching Methods to Subcellular Modeling", Proceedings of the SPIE, vol. 6065, 2006 [BCB]
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Fisher, W.G., Yang, P.C., Medikonduri, R.K., Jafri, M.S., "NFAT and NFkappaB activation in T lymphocytes: a model of differential activation of gene expression", Ann Biomed Eng., vol. 34, no. 11, pp. 1712-28, 2006 [BCB]
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Grefenstette, J., Kim, S., Kauffman, S., "An analysis of the class of gene regulatory functions implied by a biochemical model", Biosystems, vol. 84, no. 81-90, 2006 [BCB]
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Goswami, S.C., Yoon, J.H., Abramczyk, B.M., Pfeifer, G.P., Postel, E.H., "Molecular and functional interactions between Escherichia coli nucleoside-diphosphate kinase and the uracil-DNA glycosylase Ung", J. Biol. Chem., vol. 281, pp. 32131-32139, 2006 [BCB]
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Jafri, M.S., Kotulska, M., "Modeling the Mechanism of Metabolic Oscillations in Ischemic Cardiac Myocytes", J. Theor. Biol. , vol. 242, no. 4, pp. 801-817, 2006 [BCB]
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Kropinski, A.M., Borodovsky, M., Carver, T.J., Cerdeno-Tarraga, A.M., Darling, A., Lomsadze, A., Mahadevan, P., Stothard, P., Seto, D., van Domselaar, G., Wishart, D.S., "In silico Identification of Genes in Bacteriophage DNA", Bacteriophages: Methods and Protocols: Humana Press, 2006 [BCB]
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Klimov, D.K., "Invited Opening Talk", Workshop on Rigidity, Flexibility and Motion in Biomolecules, Tempe, AZ, 2006 [BCB]
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Lin, B., Wang, Z., Vora, G.J., Thornton, J.A., Schnur, J.M., Thach, D.C., Mueller, K.M., Ligler, A.G., Malanoski, A.P., Santiago, J., Walter, E.A., Agan, B.K., Metzgar, D., Seto, D., Daum, L.T., Kruzelock, R., Rowley, R.K., Hanson, E.H., Ti,, "Broad spectrum respiratory tract pathogen identification using re-sequencing DNA microarrays", Genome Res., vol. 16, pp. 527-555, 2006 [BCB]
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