Department of Bioinformatics and Computational Biology  George Mason University

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Publications in 2010

Note: Faculty authors are listed in bold font. Student authors are listed in italics.
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Arnold, J., Janoska, M., Kajon, A.E., Metzgar, D., Hudson, N.R., Torres, S., Harrach, B., Seto, D., Chodosh, J. and Jones, M.S. (2010). Genomic characterization of human adenovirus 36, a putative obesity agent. Virus Research 149: 152-161. [Epub 01/28/10].

Brister, J.R., Bao, Y., Kuiken, C., Lefkowitz, E., Le Mercier, P., Leplae, R., Madupu, R., Scheuermann, R., Schobel, S., Seto, D., Shrivastava, S., Sterk, P., Zeng, Q., Klimke W. and T. Tatusova. (2010). Towards viral genome annotation standards, Report from the 2010 NCBI Annotation Workshop. Viruses 2(10): 2258-2268. (Editorial).

Chang, W. E., Takeda, T., Raman, E. P., & Klimov, D.K. (2010) Molecular dynamics simulations of anti-aggregation effect of ibuprofen. Biophys. J. (in press).

Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LC, Smith TP, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW. Analysis of copy number variations among diverse cattle breeds. Genome Res. 2010 Apr 5. [Epub ahead of print]

Mahadevan, P. and Seto, D. (2010). Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. BMC Research Notes 3:41. [Epub 02/23/10]

Mahadevan, P. and D. Seto. (2010). In silico bioinformatic tools for determining core genes from sets of genomes. Drug Development Research 72: 1-6. (Review).

Mahadevan, P. and Seto, D. (2010). "Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes." Adv Exp Med Biol. 680: 379-385. in Advances in Experimental Medicine and Biology. Arabnia, H.R. (Ed.). ISBN 978-1-4419-5912-6. (Book chapter).

Mahadevan, P., Seto, J., Tibbetts, C. and D. Seto. (2010). Natural variants of human adenovirus type 3 provide evidence for relative genome stability across time and geographic space. Virology 397: 113-118. [Epub 11/23/09].

Masso M. Overcoming the Curse of Dimensionality in a Statistical Geometry Based Computational Protein Mutagenesis, Proc. IEEE ICDM BioDM Workshop (2010) 719-725.

Masso M. Improving Prediction Accuracy via Subspace Modeling in a Statistical Geometry Based Computational Protein Mutagenesis, Int J Knowl Disc Bioinformatics 1 (2010) 54-68.

Masso M. and Vaisman I.I. Structure-Based Machine Learning Models for Computational Mutagenesis, in Introduction to Protein Structure Prediction: Methods and Algorithms (eds: H. Rangwala and G. Karypis), Wiley Book Series on Bioinformatics, December 2010. ISBN: 9780470470596 (Textbook)

Masso M. and Vaisman I.I. Accurate and Efficient gp120 V3 Loop Structure Based Models for the Determination of HIV-1 Co-receptor Usage, BMC Bioinformatics 11 (2010) 494.

Masso M. and Vaisman I.I. Knowledge-Based Computational Mutagenesis for Predicting the Disease Potential of Human Non-Synonymous Single Nucleotide Polymorphisms, J Theor Biol 266 (2010) 560-568.

Masso M. and Vaisman I.I. AUTO-MUTE: Web-Based Tools for Predicting Stability Changes in Proteins Due to Single Amino Acid Replacements, Protein Eng Des Sel 23 (2010) 683-687.

Ramay, H. R., M. S. Jafri, W. J. Lederer, and E. A. Sobie. 2010. Predicting local SR Ca2+ dynamics during Ca2+ wave propagation in ventricular myocytes. Biophys. J. 98(11):(in press)

Robinson, C.M., Gurdeep, S., Henquell, C., Walsh, M.P., Peigue-Lafeuille, H., Seto, D., Jones, M.S., Dyer, D.W. and J. Chodosh. (2010). Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. In press, Virol. [Epub 11/05/10].

Seto, D. (2010). Viral genomics and bioinformatics. Viruses 2: 2587-2593. (Editorial).

Seto, J., Walsh, M.P., Mahadevan, P. , Zhang, Q. and D. Seto. (2010). Applying genomic and bionformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery. Viruses 2: 1-26.

Seto, J*., Walsh, M.P*., Metzgar, D. and Seto, D. (2010). Computational analysis of adenovirus serotype 5 (HAdV-C5) from a HAdV coinfection shows genome stability after 45 years of circulation. Virology 404: 180-186. [Epub 06/03/10]. *equal contributions.

Takeda, T., & Klimov, D.K. (2010) Computational backbone mutagenesis of Abeta peptides: Probing the role of backbone hydrogen bonds in aggregation. J. Phys. Chem. B 114, 4755-4762.

Takeda, T. & Klimov, D. K. (2010) Side chain interactions can impede amyloid fibril growth: Replica exchange simulations of Abeta peptide mutant. Biophys. J. 98, 649.

Torres, S., Chodosh, J., Seto, D. and M.S. Jones. (2010). The revolution in viral genomics as exemplified by the bioinformatic analysis of human adenoviruses. Viruses 2(7): 1367-1381. (Review).

Walsh, M.P., Seto, J., Jones, M.S., Chodosh, J., Xu, W.and D. Seto. (2010). Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J Clin Microbiol. 48: 991-993. [Epub 12/30/09]

Walsh, M.P., Seto, J., Tirado, D., Chodosh, J., Seto, D*. and Jones, M.S. (2010). Computational analysis of human adenovirus type 18. Virology 404: 284-292. [Epub 06/07/10]. *corresponding author.

Williams, G. S., G. D. Smith, E. A. Sobie, and M. S. Jafri. 2010. Models of cardiac excitation-contraction coupling in ventricular myocytes. Math. Biosci. 226(1):1-15.

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