2009 Publications

Bakan A, Bahar I. (2009). The intrinsic dynamics of enzymes plays a dominant role in determinint the structural changes induced upon inhibitor binding. Proc Natl Acad Sci USA, 106: 14349-54. [JIF=9.380]

Gu Y, Shrivastava IH, Amara SG, Bahar I (2009). Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Proc Natl Acad Sci U SA, 106: 2589-94. [JIF=9.380]

Lezon TR, Sali A, Bahar I. (2009). Global motions of the nuclear pore complex: insights from elastic network models. PLoS Comput Biol., 9:e1000496 [JIF=5.895]

Liu L, Koharudin LM, Gronenborn AM, Bahar I. (2009). A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations. Proteins, July 6 [Epub ahead of print]. [JIF=3.419]

Molina G, Vogt A, Bakan A, Dai W, de Oliveira PQ, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. (2009) Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages. Nat Chem Biol, 5: 680-7. [JIF=14.612]

Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I. (2009). Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model. J Med Chem, 52: 1247-50. [JIF=4.898]

Yang LW, Eyal E, Bahar I, Kitao A. (2009). Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics, 25: 606-14. [JIF=4.328]

Yang Z, Bahar I, Widom M. (2009). Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity. Biophys J, 96: 4438-48. [JIF=4.683]

Yang Z, Májek P, Bahar I. (2009). Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol, 5: e1000360. [JIF = 5.895]

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.

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]

Hofmann WA, Arduini A, Nicol SM, Camacho CJ, Lessard JL, Fuller-Pace FV, de Lanerolle P. (2009) “SUMOylation of nuclear actin.” J Cell Biol, 186: 193-200. [JIF=9.120]

Temiz NA, Camacho CJ (2009). “Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Res, 37: 4076-88. [JIF=6.878]

Zheng G, Bueno M, Camacho CJ, Ramaswami B, Luo C, Randhawa P. (2009). Validation of BKV large T-antigen ATP-binding site as a target for drug discovery. Antiviral Res., 2: 184-7. [JIF = 3.613]

Barua D, Faeder JR, Haugh JM. (2009). A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLoS Comput Biol., 5: e1000364. [JIF=6.236]

Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG. (2009). Simulation of large-scale rule-based models. Bioinformatics, 25: 910-7. [JIF = 4.328]

Faeder JR, Blinov ML, Hlavacek WS (2009). Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol, 500: 113-67.

Hlavacek WS, Faeder JR. (2009). The complexity of cell signaling and the need for a new mechanics. Sci Signal, 2: pe46.

Hu B, Matthew Fricke G, Faeder JR, Posner RG, Hlavacek WS. (2009). GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics, 25: 1257-60. [JIF = 4.328]

Indest KJ, Buchholz WG, Faeder JR, Setlow P. (2009). Workshop report: modeling the molecular mechanism of bacterial spore germination and elucidating reasons for germination heterogeneity. J Food Sci, 74: R73-8. [JIF = 1.601]

Nag A, Monine MI, Faeder JR, Goldstein B. (2009). Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys J., 96: 2604-23. [JIF = 4.683]

Nelson, M., Spiro, D.J., Wentworth, D., Beck, E., Fan, J., Ghedin, E., Halpin, R., Bera, J., Hine, E., Proudfoot, K., Stockwell, T., Lin, X., Griesemer, S., Kumar, S., Bose, M., Viboud, C., Holmes, E., Henrickson, K. (2009). The early diversification of influenza A/H1N1pdm. PLoS Currents Influenza., 9: RRN1126.

Brindley, P.J., Mitreva, M., Ghedin, E., Lustigman, S. (2009). Helminth genomics: the implications for human health. PLoS Negl. Trop. Dis., 3(10): e538.

Ghedin, E., Hailemariam, T., DePasse, J., Zhang, X., Oksov, Y., Unnasch, T.R., Lustigman, S. (2009). Brugia malayi gene expression in response to the targeting of the Wolbachia endosymbiont by tetracycline treatment. PLoS Negl. Trop. Dis. 3(10): e525.

Liu, C., Oliveira, A., Chauhan, C., Ghedin, E., Unnasch, T.R. (2009). Functional analysis of putative operons in Brugia malayi. Int. J. Parasitol., 40: 63-71.

Berriman, M., Haas, B.J., LoVerde, P.T., Wilson, R.A., Dillon, G.P., Cerqueira, G.C., Mashiyama, S.T., Al-Lazikani, B., Andrade, L.F., Ashton, P.D., Aslett, M.A., Bartholomeu, D.C., Blandin, G., Caffrey, C.R., Coghlan, A., Coulson, R., Day, T.A., Delcher, A., DeMarco, R., Djikeng, A., Eyre, T., Gamble, J.A., Ghedin, E, et al., (2009). The Genome of the blood fluke Schistosoma mansoni. Nature. 460: 352-358.

Ghedin, E., Fitch, A., Boyne, A., Griesemer, S., DePasse, J., Bera, J., Zhang, X., Halpin, R.A., Smit, M., Jennings, L., St George, K., Holmes, E.C., Spiro, D.J. (2009). Mixed Infection and the Genesis of Influenza Virus Diversity. J. Virology, 83: 8832-8841.

Brower-Sinning, R., Carter, D.M., Crevar, C.J., Ghedin, E., Ross, T.M., Benos, P.V. (2009). The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. Genome Biology, 10: R18.

Li Z, Kim SW, Lin Y, Moore PS, Chang Y, John B. (2009). Characterization of viral and human RNAs smaller than canonical MicroRNAs. J Virol, 83: 12751-8. [JIF = 5.150] Kim MJ, Maly IV (2009). Deterministic mechanical model of T-killer cell polarization reproduces the wandering of aim between simultaneously engaged targets. PLoS Comput Biol, 5: e1000260. [JIF = 5.895]

Maly IV (2009). Introduction: a practical guide to the systems approach in biology. Methods Mol Biol, 500: 3-13.

Meirovitch H, Cheluvaraja S, White RP (2009). Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding. Curr Protein Pept Sci, 10: 229-43.

Mihailescu M, Meirovitch H. (2009) Absolute free energy and entropy of a mobile loop of the enzyme acetylcholinesterase. J Phys Chem B, 113: 7950-64. [JIF = 4.189]

Tastan O, Klein-Seetharaman J, Meirovitch H. (2009). The effect of loops on the structural organization of alpha-helical membrane proteins. Biophys J. 96, 2299-312. [JIF = 4.683]

Giuliano, K.A., Premkumar, D., Strock, C., Johnston, P.A., and D. L. Taylor. (2009). Cellular Systems Biology Applied to Cellular Models of Disease. Combinatorial Chemistry and High Throughput Screening, 12: 838-48.

Critchley-Thorne, R. J., Miller, S. M., Taylor, D. L., and W. Lingle. (2009). Applications of Cellular Systems Biology in Breast Cancer Stratification and Diagnostics. Combinatorial Chemistry and High Throughput Screening, 12: 860-869.

Molina, G.#, Vogt, A. #, Bakan, A. #, Dai, W., Queiroz de Olivera, P.E., Znosko, W., Smithgall, T.G., Bahar, I., Lazo, J.S., Day, B.W., and Tsang, M. Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages. Nature Chemical Biology 5, 680-687 (2009) (# equal contribution) PMID: 1957833
Highlighted in Nature “Research Highlights” 460:p308. July 16th, 2009 issue
“Featured article” in UCSD-Nature Signaling Gateway July 31st, 2009 issue
(http://www.signaling-gateway.org/)

*Vogt, A., McPherson, P.A., Shen, X., Balachandran, R., Raccor, B., Tsang, M., Day, B.W., and Nelson, S.G. (2009) High-content analysis of cancer-cell specific apoptosis and inhibition of in vivo angiogenesis by synthetic (–)-pironetin analogs. Chemical Biology and Drug Design 74 (4), 358-368 (2009)PMID: 19691472

Vogt, A., Cholewinski, A., Nelson, S.G., Tsang, M., Lazo, J.S., and Hukriede, N.A. Automated image-based phenotypic analysis in zebrafish embryos. Developmental Dynamics 238 (3), 656-663 (2009) PMID: 19235725
Cited in “Highlights in DD” in Developmental Dynamics July 17th 2009 issue

Albert, B.J., McPherson, P.A., O’Brien, K., Czaicki, N.L., DeStefino, V., Osman, S., Li, M., Day, B.W., Grabowski, P.J., Moore, M., *Vogt, A., and *Koide, K. (2009) Meayamycin Inhibits pre-mRNA Splicing and Exhibits Picomolar Activity Against Multidrug Resistant Cells (Molecular Cancer Therapeutics 8 (8), 2308-2318 (2009) PMID: 19671752

Zou, H., Thomas, S.M., Yan, Z.-W., Grandis, J.R., Vogt. A., and Li, L. Human Rhomboid Family-1 Gene RHBDF1 Participates in GPCR-Mediated Transactivation of EGFR Growth Signals in Head and Neck Squamous Cancer Cells. FASEB J. 23 (2), 425-432 (2009) PMID: 18832597

Bhatt D, Zuckerman DM. (2009). Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method. J Chem Phys, 131: 214110.
Grossfield A, Zuckerman DM. (2009). Quantifying uncertainty and sampling quality in biomolecular simulations. Annual Reports in Computational Chemistry. 5: 23-48.

Lyman E, Zuckerman DM. (2009). Resampling improves the efficiency of a “fast-switch” equilibrium sampling protocol. J Chem Phys., 130: 081102. [JIF = 3.149]

Mamonov AB, Bhatt D, Cashman DJ, Ding Y, Zuckerman DM (2009). General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models. J Phys Chem B, 113: 10891-10904. [JIF = 4.189]

Zhang X, Mamonov AB, Zuckerman DM. (2009). Absolute free energies estimated by combining precalculated molecular fragment libraries. J Comput Chem., 30: 1680-91. [JIF = 3.390]

Lezon TR, Sali A, Bahar I. (2009). Global motions of the nuclear pore complex: insights from elastic network models. PLoS Comput Biol., 9:e1000496 [JIF=5.895]

Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I (2009). Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model. J Med Chem. 52: 1247-50. [JIF = 4.898]

Sharlow ER, Mustata G. (2009). Identification of potent chemotypes targeting Leishmania major using a high-throughput, low-stringency, computationally enhanced, small molecule screen. PLoS Negl Trop Dis, 3: e540.

Gu Y, Shrivastava IH, Amara SG, Bahar I (2009). Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Proc Natl Acad Sci U SA, 106: 2589-94. [JIF=9.380]