Department of Bioinformatics and Computational Biology  George Mason University

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Publications in 2005


Note: Faculty authors are listed in bold font. Student authors are listed in italics.
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Alkharouf NW, Jamison DC, and Matthews BF. 2005. Online Analytical Processing (OLAP): A Fast and Effective Data Mining Tool for Gene Expression Databases. J Biomed Biotechnol 2005(2):181-188.

Baranova A, Collantes R, Gowder SJ, Elariny H, Schlauch K, Younoszai A, King S, Randhawa M, Pusulury S, Alsheddi T, Ong JP, Martin LM, Chandhoke V, and Younossi ZM. 2005. Obesity-related differential gene expression in the visceral adipose tissue. Obes Surg 15(6):758-765.

Barenboim M, Jamison DC, and Vaisman II. 2005. Statistical geometry approach to the study of functional effects of human nonsynonymous SNPs. Hum Mutat 26(5):471-476.

Baumann RG, Baldwin RL, Van Tassell CPt, Sonstegard TS, and Matukumalli LK. 2005. Characterization of a normalized cDNA library from bovine intestinal muscle and epithelial tissues. Anim Biotechnol 16(1):17-29.

Cheung MS, Klimov D, and Thirumalai D. 2005. Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci U S A 102(13):4753-4758.

Chikando A, and Kinser J. 2005. Optimizing Image Segmentation Using Color Model Mixtures. 34th Applied Imagery and Pattern Recognition Workshop (AIPR 05). p 230-235.

Copley SD, Smith E, and Morowitz HJ. 2005. A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc Natl Acad Sci U S A 102(12): 4442-4447.

Doung D, and Grefenstette J. 2005. SISTER: a Symbolic Interactionist Simulation of Trade and Emergent Roles. Journal of Artificial Societies and Social Simulation 8(1).

Dunlavy DM, O'Leary D P, Klimov D, and Thirumalai D. 2005. HOPE: A Homotopy Optimization Method for Protein Structure Prediction. J Comput Biol 12(10): 1275-1288.

Fryxell KJ, and Moon WJ. 2005. CpG mutation rates in the human genome are highly dependent on local GC content. Mol Biol Evol 22(3): 650-658.

Grefenstette J, Thompson K, Shannon W, and Steinmeyer B. 2005. Genetic algorithms for feature selection using Mantel correlation scoring. Interface 2005: Classification and Clustering 37th Symposium on the Interface. St. Louis, MO.

Guo Y, and Jamison DC. 2005. The distribution of SNPs in human gene regulatory regions. BMC Genomics 6: 140.

Higgs B, Solka JL, and Weller J. 2005a. Deriving meaningful biological structure from spectral embedding and clustering. Computing Science and Statistics: 37.

Higgs B, Weller J, and Solka JL. 2005b. Deriving Meaningful Structure from Spectral Embeddings and Clusterings. Interface 2005: Classification and Clustering 37th Symposium on the Interface. St. Louis, MO.

Higgs B, Weller J, and Solka JL. 2005c. On spectral embedding for extraction of structure in biological data. Joint Statistical Meeting 2005: Using Our Discipline to Enhance Human Welfare. Minneapolis, MN.

Jagota A, and Masso M. 2005. Computational Methods in Phylogenetic Analysis. Bioinformatics by the Bay Press.

Kinser J, and Wang G. 2005. Content Based Object Retrieval with Image Primitive Database. 34th Applied Imagery and Pattern Recognition Workshop (AIPR 05). p 179-183

Kinser JM. 2005. Image Primitives for Content Based Image Retrieval. SWSEAS Transactions on Signal Processing 3(1): 377-384.

Klimov DK, and Thirumalai D. 2005. Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J Mol Biol 353(5): 1171-1186.

Li MS, Klimov DK, and Thirumalai D. 2005. Finite size effects on calorimetric cooperativity of two-state proteins. Physica A: Statistical and Theoretical Physics 350: 38-44.

Lindblad T, and Kinser J. 2005. Image Processing using Pulsed Coupled Neural Networks. Springer-Verlag.

Min W, Lillehoj HS, Ashwell CM, van Tassell CP, Dalloul RA, Matukumalli LK, Han JY, and Lillehoj EP. 2005. Expressed sequence tag analysis of Eimeria-stimulated intestinal intraepithelial lymphocytes in chickens. Mol Biotechnol 30(2): 143-150.

Nguyen M-H, and Jafri MS. 2005a. Cardiac Ventricular Myocyte Mitochndrial Calcium Signaling and Energy Metabolism. Biophys. J.(88): 91a.

Nguyen M-H, and Jafri MS. 2005b. The impact of mitochondrial Ca2+ handling on energy metabolism. Proceedings of the 2005 Conference on Computational and Mathematical Methods on Science and Engineering. p. 608-619.

Nguyen M-H, Ramay HR, Dudycha SJ, and Jafri MS. 2005. Modeling the cellular basis of cardiac excitation-contraction coupling and energy metabolism. Recent Research Developments in Biophysics 3 (Pt 1): 125-145.

Nguyen MH, and Jafri MS. 2005c. Mitochondrial calcium signaling and energy metabolism. Ann N Y Acad Sci 1047: 127-137.

Purkayastha A, Ditty SE, Su J, McGraw J, Hadfield TL, Tibbetts C, and Seto D. 2005a. Genomic and bioinformatics analysis of HAdV-4, a human adenovirus causing acute respiratory disease: implications for gene therapy and vaccine vector development. J Virol 79(4): 2559-2572.

Purkayastha A, Su J, Carlisle S, Tibbetts C, and Seto D. 2005b. Genomic and bioinformatics analysis of HAdV-7, a human adenovirus of species B1 that causes acute respiratory disease: implications for vector development in human gene therapy. Virology 332(1): 114-129.

Purkayastha A, Su J, McGraw J, Ditty SE, Hadfield TL, Seto J, Russell KL, Tibbetts C, and Seto D. 2005c. Genomic and bioinformatics analyses of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease. J Clin Microbiol 43(7): 3083-3094.

Pushkarsky T, Yurchenko V, Vanpouille C, Brichacek B, Vaisman II, Hatakeyama S, Nakayama KI, Sherry B, and Bukrinsky MI. 2005. Cell surface expression of CD147/EMMPRIN is regulated by cyclophilin 60. J Biol Chem 280(30): 27866-27871.

Ramay HR, and Jafri MS. 2005. A Computational Study of the Spread of Calcium Sparks in the Cardiac Myocytes. Biophys. J.,(88): 91a.

Rao CR, Wegman EJ, and Solka JL. 2005. Handbook of Statistics 24: On Data Mining and Visualization: Handbook of Statistics, Elsevier, North Holland.

Ratushna VG, Weller JW, and Gibas CJ. 2005. Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics 6(1): 31.

Skinner J, Zitzewitz Jv, Marquez-Cedillo L, Filichkin T, Szzcs P, Amundsen K, Stockinger E, Thomashow M, Chen T, and Hayes P. 2005. Barley Contains a Large CBF Gene Family Associated with Quantitative Cold Tolerance Traits. In Chen T, Uemura M, Fujikawa S, editors. Cold Hardiness in Plants: Molecular Genetics, Cell Biology and Physiology. Oxon, UK: CAB International. p 30-52.

Skinner JS, von Zitzewitz J, Szucs P, Marquez-Cedillo L, Filichkin T, Amundsen K, Stockinger EJ, Thomashow MF, Chen TH, and Hayes PM. 2005. Structural, functional, and phylogenetic characterization of a large CBF gene family in barley. Plant Mol Biol 59(4): 533-551.

Solka JL, Bryant AC, and Wegman EJ. 2005. Text Data Mining With Minimal Spanning Trees. In EJW C. R. Rao, and J. L. Solka (Ed.): Handbook of Statistics 24 on Data Mining and Visualization, Elsevier, North Holland.

Taylor T, Rivera M, Wilson G, and Vaisman II. 2005. New method for protein secondary structure assignment based on a simple topological descriptor. Proteins 60(3): 513-524.

Thach DC, Agan BK, Olsen C, Diao J, Lin B, Gomez J, Jesse M, Jenkins M, Rowley R, Hanson E, Tibbetts C, Stenger DA, Walter E, and EOS*. 2005. Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes. Genes Immun 6(7): 588-595 (*Seto, D).

Wegman EJ, and Solka JL. 2005a. Statistical Data Mining. In: EJW C. R. Rao, and J. L. Solka, editor. Handbook of Statistics 24 on Data Mining and Visualization, Elsevier, North Holland.

Wegman EJ, and Solka JL. 2005b. Statistical Software for Today and Tomorrow: Encyclopedia of Statistical Sciences, John Wiley.



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