Department of Bioinformatics and Computational Biology  George Mason University

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Publications in 2007


Note: Faculty authors are listed in bold font. Student authors are listed in italics.
For previous year's publications, click here.

Bura, E., D.K. Klimov, and V. Barsegov, Analyzing forced unfolding of protein tandems by ordered variates: 1. Independent unfolding times. Biophysical Journal, 2007. 93: p. 1100-1115.

Choi I. Y., D. L. Hyten, L. K. Matukumalli, Q. Song, J. M. Chaky, C. V. Quigley, K. Chase, K. G. Lark, R. S. Reiter, M. S. Yoon, E, Y. Hwang, S. I. Yi, N. D. Young, R. C. Shoemaker, C. P. van Tassell, J. E. Specht, and P. B. Cregan. "A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis." Genetics 176 (2007): 685-96

Coutinho. L. L., L. K. Matukumalli, . T. S. Sonstegard, C. P. Van Tassell, L. C. Gasbarre, A. V. Capuco. and T. P. Smith. "Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues." Physiol Genomics. 29 (2007): 35-43.

Dong, X., Klimov, D.K., & Blaisten-Barojas, E. 2007. Protein folding with the Adaptive Tempering Monte Carlo method. Mol. Simul., 2007. 33: p. 577-582.

Jafri, M.S., The globalization of biotechnology. Global Studies Review, 2007. 3(3): p. 4-5.

Kostoff, R.N., J.A. Block, 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.

Kostoff, R.N., J.A. Block, Solka, J.L., Briggs, M.B., Rushenberg, R., 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.

Kostoff, R.N., J.L. Solka, Rushenberg, R.L., Wyatt, J.R., Literature-Related Discovery (LRD): Water Purification. Technological Forecasting and Social Change, 2007.

Mahadevan, P. and D. Seto, Comparative genomics using CoreGenes to analyze small bacterial genomes, with an application for the annotation of hypothetical proteins, in International Conference on Bioinformatics and Computational Biology. 2007, CSREA Press.

Masso, M.and I. I. Vaisman. "Accurate prediction of enzyme mutant activity based on a multibody statistical potential". Bioinformatics, 23 (2007): 3155-3161. - Listed by "Faculty of 1000 Biology"

Masso, M.and I. I Vaisman. "A Novel Sequence-Structure Approach for Accurate Prediction of Resistance to HIV-1 Protease Inhibitors." Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007, 952-958.

McKay S. D., R. D. Schnabel, B. M. Murdoch, J. Aerts, C. A. Gill, C. Gao, C. Li, L. K. Matukumalli, P. Stothard, Z. Wang, C. P. Van Tassell, J. L. Williams, J. F. Taylor, and S. S. Moore. "Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping." Anim Genet. 38 (2007):120-5.

McKay S. D., R. D. Schnabel, B. M. Murdoch, L. K. Matukumalli, J. Aerts, W. Coppieters, D. Crews, E. Dias Neto, C. A. Gill, C. Gao, H. Mannen, P. Stothard, Z. Wang, C. P. Van Tassell, J. L. Williams, J. F. Taylor, and S. S. Moore. "Whole genome linkage disequilibrium maps in cattle. " BMC Genet. 8 (2007): 74.

Nguyen, M.T., S.J. Dudycha, and M.S. Jafri, The effects of Ca2+ on cardiac mitochondrial energy production is modulated by Na+ and H+ dynamcis. Am J Physiol Cell Physiol, 2007. 292(6): p. C2004-2020.

Raman, E.P., V. Barsegov, and D.K. Klimov, Folding of tandem-linked domains. Proteins: Struct. Funct. Bioinform., 2007. 67: p. 795-810.

Raman, E.P., T. Takeda, V. Barsegov, and D.K. Klimov, Mechanical unbinding of Abeta peptides from amyloid fibrils. J. Mol. Biol., 2007. 373: p. 785-800

Reck G. and I. I. Vaisman. "Decoy Discrimination Using Contact Potentials Based on Delaunay Tessellation of Hydrated Proteins." Proceedings IEEE-ISVD, 2007, 159-167.

Snelling W. M., R. Chiu, J. E. Schein, M. Hobbs, C. A. Abbey, D. L. Adelson, J. Aerts, G. L. Bennett, I. E. Bosdet, M. Boussaha, R. Brauning, A. R. Caetano, M. M. Costa, A. M. Crawford, B. P. Dalrymple, A. Eggen, A, Everts-van der Wind, S. Floriot, M. Gautier, C. A. Gill, R. D. Green, R. Holt, O. Jann, S. J. Jones, S. M. Kappes, J. W. Keele, P. J. de Jong, D. M. Larkin, H. A. Lewin, J. C. McEwan, S. McKay, M. A. Marra, C. A. Mathewson, L. K. Matukumalli, S. S. Moore, B. Murdoch, F. W. Nicholas, K. Osoegawa, A. Roy, H. Salih, L. Schibler, R. D. Schnabel, L. Silveri, L. C. Skow, T. P. Smith, T. S. Sonstegard, J. F. Taylor, R. Tellam, C. P. Van Tassell, J. L. Williams, J. E. Womack, N. H. Wye, G. Yang, and S. Zhao. International Bovine BAC Mapping Consortium. "A physical map of the bovine genome." Genome Biol. 8 (2007): R165.

Taylor T. and I. I. Vaisman. "Discrimination and Classification of Thermophilic and Mesophilic Proteins.". Proceedings IEEE-ISVD, 2007, 212-221

Takeda, T. and D.K. Klimov, Dissociation of Abeta 16-22 amyloid fibrils probed by molecular dynamics. J. Mol. Biol., 2007. 368: p. 1202-1213.

Wang, G. and J. Kinser. Nonlinear Dimensionality Reduction on 3-D Protein Image Analysis. in ASIMOLAR. 2007.

Wang, P. and D.K. Klimov, Lattice simulations of cotranslational folding of single domain proteins. Proteins: Struct. Funct. Bioinform., 2007.

Williams, G.S., M.A. Huertes, 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, 2007. 92: p. 2311-2328.



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