2008 Publications

Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. (2008) “Computational insights on the competing effects of nitric oxide in regulating apoptosis.” PLoS ONE, 3, e2249.

Chennubhotla C, Yang Z, Bahar I (2008) “Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL” Molecular Biosystems 4, 287-292. [JIF: 4.121] Eyal, E; Bahar, I, (2008) “Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models” Biophysical Journal 94, 3424-3435. [JIF: 4.627]

Isin, B; Schulten, K; Tajkhorshid, E; Bahar, I, (2008) “Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes” Biophysical Journal 95, 789-803. [JIF: 4.627]

Liu, Y; Eyal, E; Bahar, I, (2008) “Analysis of correlated mutations in HIV-1 protease using spectral clustering” Bioinformatics 24, 1243- 1250. [JIF: 5.039]

Engen JR, Wales TE, Hochrein JM, Meyn MA 3rd, Ozkan, SB, Bahar I, Smithgall TE. (2008) “Structure and dynamic regulation of Src-family kinases.” Cell Mol Life Sci. 65, 3058-3073. [JIF: 5.239]

Shrivastava IH, Jiang J, Amara SG, Bahar I. (2008) “Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter.” J Biol Chem. 283, 28680-90. [JIF: 5.520]

Brower-Sinning R, Carter DM, Crevar CJ, Ghedin E, Ross TM, Benos PV (2009) “The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.” Genome Biol 10 R18. [JIF = 6.153]

Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV (2009) “Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.” PLoS One 4 e5279.

Kadri S, Hinman V, Benos PV. (2009) “HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models.” BMC Bioinformatics. 10 Suppl 1:S35. [JIF = 3.781]

Tchagang AB, Bui KV, McGinnis T, Benos PV. (2009) “Extracting biologically significant patterns from short time series gene expression data.” BMC Bioinformatics 10, 255. [JIF = 3.781]

Bueno M, Camacho CJ, Randhawa PS. (2008) “A molecular modeling approach to develop compounds with anti-BK virus activity” American Journal of Transplantation, 8, Suppl. 2, 284-285. [JIF: 6.423]

Camacho CJ. (2008) “Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation.” PLoS ONE 3, e3342.

Camacho CJ, Katsumata Y, Ascherman DP. (2008) “Structural and thermodynamic approach to peptide immunogenicity.” PLoS Comput Biol. 4, e1000231. [JIF = 5.895]

Chennubhotla C, Yang Z, Bahar I. (2008) “Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL” Molecular Biosystems, 4, 287-292. [JIF: 4.121]

Chennubhotla C, Yang Z, Bahar I. (2008) “PHYS 134-Intrinsic dynamics of proteins and regulation of allosteric communication” Abstracts of Papers of the American Chemical Society 235:134.

An, G; Faeder, J; Vodovotz, Y, (2008) “Translational systems biology: Introduction of an engineering approach to the pathophysiology of the burn patient” Journal of Burn Care & Research 29, 277-285. [JIF: 1.089]

Barua, D; Faeder, JR; Haugh, JM, (2008) “Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase” Journal of Biological Chemistry 283, 7338-7345. [JIF: 5.581]

B. Goldstein, D. Coombs, J. R. Faeder & W. S. Hlavacek. (2008) “Kinetic Proofreading Model.” In Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease, Ed. A. B. Sigalov. Landes Bioscience, Austin, TX.

Scott, A.L., Ghedin, E. (2008). The genome of Brugia malayi – All worms are not created equal. Parasitol Int. [Epub ahead of print] PMC2668601

Alekseev, K.P., Vlasova, A.N., Jung, K., Hasoksuz, M., Zhang, X., Halpin, R., Wang, S., Ghedin, E., Spiro, D., Saif, L.J. (2008) Bovine-like coronaviruses isolated from four species of captive wild ruminants are homologous to bovine coronaviruses based on complete genomic sequences. J. Virol. Oct 8. [Epub ahead of print] PMC2593316

Nelson, M.I., Edelman, L., Spiro, D.J., Boyne, A.R., Bera, J., Halpin, R., Ghedin, E., Miller, M.A., Simonsen, L., Viboud, C., Holmes, E.C. (2008) Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States. PLoS Pathog. 4(8):e1000133. PMC2495036

Dugan, V.G., Chen, R., Spiro, D.J., Sengamalay, N., Zaborsky, J., Ghedin, E., Nolting, J., Swayne, D.E., Runstadler, J.A., Happ, G.M., Senne, D.A., Wang, R., Slemons, R.D., Holmes, E.C., Taubenberger, J.K. (2008) The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. May 30;4(5):e1000076. PMC2387073

Nelson, M.I., Viboud, C., Simonsen, L., Bennett, R.T., Griesemer, S.B., St. George, K., Taylor, J., Spiro, D.J., Sengamalay, N.A., Ghedin, E., Taubenberger, J.K., Holmes, E.C. (2008) Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918. PLoS Pathogens Feb 29;4(2):e1000012. PMC2262849

Ghedin, E., Daehnel. K., Foster, J., Slatko, B. and Lustigman, S. (2008). The symbiotic relationship between filarial parasitic nematodes and their Wolbachia endosymbionts – a resource for a new generation of control measures. Symbiosis. 46: 77-85.

Bringaud, F., Ghedin, E., El-Sayed, N.M., Papadopoulou B. (2008). Role of transposable elements in trypanosomatids. Microbes Infect. 2008 Feb 21. [Epub ahead of print]

Djikeng, A., Halpin, R.A., Kuzmickas, R., Depasse, J., Feldblyum, J., Sengamalay, N., Afonso, C.L., Zhang, X., Anderson, N.G., Ghedin, E, Spiro, D.J. (2008) Viral genome sequencing by random priming methods. BMC Genomics 9:5. PMC2254600

Arkhipov SN, Maly IV. (2008) “Retractile processes in T lymphocyte orientation on a stimulatory substrate: morphology and dynamics” Physical Biology 5, 016006. [JIF: 3.108]

Cheluvaraja, S; Meirovitch, H, (2008) “Stability of the free and bound microstates of a mobile loop of alpha-amylase obtained from the absolute entropy and free energy” Journal of Chemical Theory and Computation, 4, 192-208. [JIF: 4.308]

Cheluvaraja, S; Mihailescu, M; Meirovitch, H (2008) “Entropy and free energy of a mobile protein loop in explicit water” Journal of Physical Chemistry B , 112, 9512-9522. [JIF: 4.086]

White, RP; Meirovitch, H, (2008) “Minimalist explicit solvation models for surface loops in proteins” Journal of Chemical Theory and Computation 4, 216. [JIF: 4.308]

Vries JK, Liu X. (2008) “Subfamily specific conservation profiles for proteins based on n-gram patterns” BMC Bioinformatics 9, 72. [JIF: 3.493]

Ytreberg, FM; Zuckerman, DM (2008) “A black-box re-weighting analysis can correct flawed simulation data” Proceedings of the National Academy of Sciences, USA 105, 7982-7987. [JIF: 9.598]

DM Zuckerman, “Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules,” to appear in Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by GA Voth (Taylor and Francis).