Department of Bioinformatics and Computational Biology  George Mason University

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Publications in 2006

Note: Faculty authors are listed in bold font. Student authors are listed in italics.
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Agan BK, Hanson EH, Kruzelock RP, Lin B, Rowley RK, Seto D, Stenger DA, Thornton J, Tibbetts CJ, Thach D and others; 2006. Re-sequencing pathogen microarray. United States.

Barsegov, V., Klimov, D.K., & Thirumalai, D. 2006. Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: Theory and applications. Biophys. J. 90: 3827-3941.

Chikando A, and Kinser JM. 2006. Adaptation of Fast Marching Methods to Subcellular Imaging. Image Processing: Algorithm and Systems, Neural Networks, and Machine Learning. Proceedings of SPIE6065: 225-233.

Fisher WG, Yang PC, Medikonduri RK, Jafri MS. 2006. NFAT and NFkappaB activation in T lymphocytes: a model of differential activation of gene expression. Ann Biomed Eng. 34(11): 1712-28.

Goswami S.C., Yoon J.H., Abramczyk B.M., Pfeifer G.P. and Postel E.H. 2006. J. Biol. Chem. 281: 32131-32139.

Grefenstette J, Kim S, and Kauffman S. 2006. An analysis of the class of gene regulatory functions implied by a biochemical model. Biosystems 84: 81-90.

Jafri MS, Kotulska M. 2006. Modeling the Mechanism of Metabolic Oscillations in Ischemic Cardiac Myocytes. J. Theor. Biol. 242(4): 801-817.

Kinser JM. 2006. Geodesically Reduced Image Primitive Space. IASTED Proc. on Signal and Image Processing.

Kropinski AM, Borodovsky M, Carver TJ, Cerdeno-Tarraga AM, Darling A, Lomsadze A, Mahadevan P , Stothard P, Seto D , van Domselaar G and others. 2006. In silico Identification of Genes in Bacteriophage DNA. In: Clokie M, Kropinski AM, editors. Bacteriophages: Methods and Protocols: Humana Press.

Leung E, and Bushel PR. 2006. PAGE: phase-shifted analysis of gene expression. Bioinformatics 22: 367-368.

Li MS, Hu CK, Klimov DK, and Thirumalai D. 2006. Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc Natl Acad Sci U S A 103: 93-98.

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., Tibbetts, C. and Stenger, D.A. 2006. Broad spectrum respiratory tract pathogen identification using re-sequencing DNA microarrays. Genome Res. 16: 527-55.

Mahadevan, P. and Seto, D. 2006. Comparative genomics using web-based GeneOrder to determine synteny and to function as an annotation tool. Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology. CSREA Press. H. R. Arabnia and H. Valafar, editors; 566-570. Presented at BioComp06: The 2006 International Conference on Bioinformatics and Computational Biology (Las Vegas, NV. June 26-29, 2006).

Masso M, Lu Z, and Vaisman II. 2006. Computational mutagenesis studies of protein structure-function correlations. Proteins Volume 64(1): 234-245.

Mathe E, Olivier M, Kato S, Ishioka C, Vaisman II, and Hainaut P. 2006. Predicting the transactivation activity of p53 missense mutants using a four-body potential score derived from Delaunay tessellations. Hum Mutat 27: 163-172.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, and Van Tassell CP. 2006a. Application of machine learning in SNP discovery. BMC Bioinformatics 7: 4.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP. 2006b. SNP-PHAGE--High throughput SNP discovery pipeline. BMC Bioinformatics 7: 468.

Packer BR, Yeager M, Burdett L, Welch R, Beerman M, Qi L, Sicotte H, Staats B, Acharya M, Crenshaw A, Eckert A, Puri V, Gerhard DS, and Chanock SJ. 2006. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res 34: D617-621.

Sobie EA, Guatimosim S, Gomez-Viquez L, Song L-S, Hartmann H, Jafri MS, Lederer WJ. 2006. The Ca2+ leak paradox and "rogue ryanodine receptors": SR Ca2+ efflux theory and practice. Prog. Biophys. Mol. Biol. 90: 172-185.

Taylor T., and Vaisman II. 2006. Graph theoretic properties of networks formed by the Delaunay tessellation of protein structures. Physical Review E 73: 041925.

Thirumalai D, Klimov DK. 2006. Intermediates and Transition States in Protein Folding. Methods Mol. Biol. 350: 277-304.

Vora, G.J., Lin, B., Gratwick, K., Meador, C., Hansen, C., Tibbetts, C., Stenger, D.A., Irvine, M., Seto, D., Purkayastha, A., Freed, N., Gibson, M.L., Russell K.L. and Metzgar, D. 2006. Coinfections of multiple adenoviral species in previously vaccinated patients. Emerging Infectious Diseases 12: 921-930.

Wang G, Kinser JM. 2006. Towards Content Based Object Recognition with Image Primitives. Proceedings of the SPIE 6064: 1H-1 - 1H-8.

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