Department of Bioinformatics and Computational Biology  George Mason University

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Publications in 2009


Note: Faculty authors are listed in bold font. Student authors are listed in italics.
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Alexander LJ, Kuehn LA, Smith TP, Matukumalli LK, Mote B, Koltes JE, Reecy J, Geary TW, Rule DC, Macneil MD. A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F2 population. J Anim Sci. 2009 May;87(5):1576-81. Epub 2009 Feb 11. PubMed PMID: 19213716.

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 Jan 10, in press.

Bertram, R. P. Budu-Grajdeanu, and M. S. Jafri. 2009. Using Phase Relations to Identify Potential Mechanisms for Metabolic Oscillations in Isolated รข-Cell Mitochondria. Islets 1(2):87-4

Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guig R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, C mara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Mor DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8. PubMed PMID: 19390049.

Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, Matukumalli LK, McEwan JC, Nazareth LV, Schnabel RD, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JF, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LO, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song XZ, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, Barbosa da Silva M, Lau LP, Liu GE, Lynn DJ, Panzitta F, Dodds KG. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24;324(5926):528-32. PubMed PMID: 19390050; PubMed Central PMCID: PMC2735092.

Lavigne, R., Darius, P., Summer, E.J., Seto, D., Madhadevan, P., Nilsson, A.S., Ackermann, H.W. and A.M. Kropinski. (2009). Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiology 9:224. [Epub 10/26/09]

Mahadevan, P., Seto, J., Tibbetts, C. and D. Seto. (2009). Natural variants of human adenovirus type 3 provide evidence for relative genome stability across time and geographic space. Virology [Epub 11/23/09].

Masso M., Mathe E., Parvez N., Hijazi K., and Vaisman I.I. Modeling the Functional Consequences of Single Residue Replacements in Bacteriophage f1 Gene V Protein, PEDS 22 (2009) 665-671.

Masso M., Alsheddi T., and Vaisman I.I. Accurate Prediction of Stability Changes in Bacteriophage T4 Lysozyme Upon Single Amino Acid Replacements, IEEE Proc. BIBM (2009) 26-30.

Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TP, Sonstegard TS, Van Tassell CP. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One. 2009;4(4):e5350. Epub 2009 Apr 24. PubMed PMID: 19390634; PubMed Central PMCID: PMC2669730.

McDaneld TG, Smith TP, Doumit ME, Miles JR, Coutinho LL, Sonstegard TS, Matukumalli LK, Nonneman DJ, Wiedmann RT. MicroRNA transcriptome profiles during swine skeletal muscle development. BMC Genomics. 2009 Feb 10;10:77. PubMed PMID: 19208255; PubMed Central PMCID: PMC2646747.

Raman, E. P., Takeda, T., & Klimov, D.K. (2009) Molecular dynamics simulations of ibuprofen binding to Abeta peptides. Biophys. J. 97,2070-2079

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.

Takeda, T. & Klimov, D. K. (2009) Replica exchange simulations of the thermodynamics of Abeta fibril growth. Biophysical J. 96, 442-452.

Takeda, T. & Klimov, D.K. (2009) Interpeptide interactions induce helix to strand structural transition in Abeta peptides. Proteins Struct. Funct. (accepted, doi 10.1002/prot.22406).

Takeda, T., & Klimov, D.K. (2009) Probing energetics of Abeta fibril elongation by molecular dynamics simulations. Biophys. J. doi:10.1016/j.bpj.2009.03.015.

Takeda, T., & Klimov, D.K. (2009) Probing the effect of amino-terminal truncation for Abeta1-40 Peptides. J. Phys. Chem. B 113, 6692-6702.

Takeda, T., & Klimov, D.K. (2009) Side chain interactions can impede amyloid fibril growth: Replica exchange simulations of Abeta peptide mutant. J. Phys. Chem. B 113,11848-11857.

Thompson KJ, Deshmukh H, Solka JL, Weller JW. A white-box approach to microarray probe response characterization: the BaFL pipeline. BMC Bioinformatics. 2009 Dec 29;10:449. PubMed PMID: 20040098; PubMed Central PMCID: PMC2804686.

Villa-Angulo R, Matukumalli LK, Gill CA, Choi J, Van Tassell CP, Grefenstette JJ. High-resolution haplotype block structure in the cattle genome. BMC Genet. 2009 Apr 24;10:19. PubMed PMID: 19393054; PubMed Central PMCID: PMC2684545.

Walsh, M.P., Seto, J., Jones, M.S., Chodosh, J., Xu, W.and D. Seto. (2009). Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J Clin Microbiol. [Epub 12/30/09]

Wiggans GR, Sonstegard TS, VanRaden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS, Van Tassell CP. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. J Dairy Sci. 2009 Jul;92(7):3431-6. PubMed PMID: 19528621.



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