Department of Bioinformatics and Computational Biology  George Mason University

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Publications in 2008

Note: Faculty authors are listed in bold font. Student authors are listed in italics.
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Barenboim M., Masso M., Vaisman I.I., and Jamison D.C. Statistical Geometry Based Prediction of Non-Synonymous SNP Functional Effects Using Random Forest and Neuro-Fuzzy Classifiers, Proteins 71 (2008) 1930-1939.

Bura, E., Klimov, D.K., & Barsegov, V. (2008) Analyzing Forced Unfolding of Protein Tandems by Ordered Variates: 2. Dependent Unfolding times. Biophys. J. 94, 2516-2528.

Connor,E.E., Matukumalli,L.K., Chockalingam,A., Bannerman,D.D., Sonstegard,T.S., Thomas,E.D., & Van Tassell,C.P. Association analysis of bovine bactericidal/permeability-increasing protein gene polymorphisms with somatic cell score in Holstein cattle. Anim Genet. (2008).

Hyten,D.L., Song,Q., Choi,I.Y., Yoon,M.S., Specht,J.E., Matukumalli,L.K. , Nelson,R.L., Shoemaker,R.C., Young,N.D., & Cregan,P.B. High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor. Appl. Genet. 116, 945-952 (2008).

J. Kinser, "Python for Bioinformatics", Jones & Bartlett, 2008.

Lavigne, R., Seto, D., Madhadevan, P., Ackermann, H.W. and A.M. Kropinski. (2008). Unifying classical and molecular taxonomy-based classification: A rational classification system for the Podoviridae using BLASTP-based tools. Research in Microbiology 159: 406-414. [Epub 4/18/08].

Mahadevan, P. and Seto, D. (2008). Data mining pathogen genomes using GeneOrder and CoreGenes: gene order, synteny, and proteomes. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology. CSREA Press. H. R. Arabnia and H. Valafar, eds. (Las Vegas, NV. July 14-17, 2008).

Masso M., Mathe E., Hijazi K., Parvez N., and Vaisman I.I. Structure Based Functional Analysis of Bacteriophage f1 Gene V Protein, Proc. IEEE BIBM (2008) 402-406.

Masso M., Hijazi K., Parvez N., and Vaisman I.I. Computational Mutagenesis of Lac Repressor: Insight Into Structure-Function Relationships and Accurate Prediction of Mutant Activity, Proc. ISBRA 2008, Lecture Notes in Bioinformatics 4983 (2008) 390-401.

Masso M. and Vaisman I.I. Accurate Prediction of Stability Changes in Protein Mutants by Combining Machine Learning with Structure Based Computational Mutagenesis, Bioinformatics 24 (2008) 2002-2009.

McKay,S.D., Schnabel,R.D., Murdoch,B.M., Matukumalli,L.K. , Aerts,J., Coppieters,W., Crews,D., Dias,N.E., Gill,C.A., Gao,C., Mannen,H., Wang,Z., Van Tassell,C.P., Williams,J.L., Taylor,J.F., & Moore,S.S. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC. Genet. 9, 37 (2008).

Takeda, T. & Klimov, D. K. (2008) Temperature induced dissociation of Abeta monomers from amyloid fibril. Biophys. J. (published ahead of print on May 23, 2008 as doi:10.1529/biophysj.108.131698).

Van Tassell,C.P., Smith,T.P., Matukumalli,L.K., Taylor,J.F., Schnabel,R.D., Lawley,C.T., Haudenschild,C.D., Moore,S.S., Warren,W.C., & Sonstegard,T.S. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5, 247-252 (2008).

Williams, G. S., M. A. Huertas, E. A. Sobie, M. S. Jafri, and G. D. Smith. 2008. Moment closure for local control models of calcium-induced calcium release in cardiac myocytes. Biophys. J. 95(4):1689-1703

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