| 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 JR; 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] |
| Goldstein B, Coombs D, Faeder JR & Hlavacek W. S. (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). |
Other Years
‣ 2021 Publications
‣ 2020 Publications
‣ 2019 Publications
‣ 2018 Publications
‣ 2017 Publications
‣ 2016 Publications
‣ 2015 Publications
‣ 2014 Publications
‣ 2013 Publications
‣ 2012 Publications
‣ 2011 Publications
‣ 2010 Publications
‣ 2009 Publications
‣ 2008 Publications
‣ 2007 Publications
‣ 2006 Publications
‣ 2005 Publications