George Mason University : Bioinformatics and Computational Biology : Pubs

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Publications in 2008

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

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. 94(4):in press

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