2006 Publications

Yang, LeeWei, Rader, AJ, Liu, X, Jursa, CJ, Chen, SC, Karimi, HA and Bahar, Ivet. oGNM: Online Computation of Structural Dynamics Using the Gaussian Network Model, Nucleic Acids Res 34, W24-31, 2006. [JIF: 6.317]

Bagci, E. Z., Vodovotz, Y., Billiar,T. R., Ermentrout, G. B. and Bahar, I. Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores. Biophys J 90, 1546-1559, 2006. [JIF: 4.757]

Chennubhotla, C. and Bahar, I. “Markov Propagation of Allosteric Effects in Biomolecular Systems” Molecular Systems Biology, 2, 36, 2006. [JIF: 7.941]

Chennubhotla,, Chakra and Bahar, Ivet. Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB’06, accepted. Lecture Notes in Computer Science 3909, 379-393 2006.

Cui, Q & Bahar, Ivet (Eds). Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 2006.

Eyal, E., Yang, L. W., and Bahar, I. (2006) “Anisotropic network model: systematic evaluation and a new web interface” Bioinformatics 22, 2619-2627. [JIF: 4.894]

Farkas, I. J., Wu, C., Chennubhotla, C., Bahar, I., and Oltvai, Z. N. (2006) “Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae” BMC Bioinformatics 7. Published online 2006 October 28. [JIF: 3.617]

Isin, B., Rader, A. J., Dhiman, H. K., Klein-Seetharaman, J., and Bahar, I. (2006) “Predisposition of the dark state of rhodopsin to functional changes in structure” Proteins-Structure Function and Bioinformatics 65, 970-983. [JIF: 3.73]

Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR, Bahar I. An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnol Prog. 22(1):179-85, 2006. [JIF: 2.102]

Rader, AJ, Chennubhotla, Chakra, Yang, Lee-Wei and Bahar, Ivet. The Gaussian Network Model: Theory and Applications, in Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems, Eds Qiang Cui and I Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006.

Shrivastava, Indira H. and Bahar, Ivet. Common Mechanism of Pore Opening Shared by Five Different Potassium Channels. Biophys J 90, 3929-3940, 2006. [JIF: 4.757]

Tobi, Dror and Bahar, Ivet. Optimal Design of Protein Docking Potentials: Efficiency and Limitations, Proteins: Structure, Function, and Bioinformatics, 62, 970-981, 2006. [JIF: 3.73]

Belov, K., Deakin, J. E., Papenfuss, A. T., Baker, M. L., Melman, S. D., Siddle, H. V., Gouin, N., Goode, D. L., Sargeant, T. J., Robinson, M. D., Wakefield, M. J., Mahony, S., Cross, J. G. R., Benos, P. V., Samollow, P. B., Speed, T. P., Graves, J. A. M., and Miller, R. D. (2006) “Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex” PloS Biology 4, 317-328. [JIF: 14.101]

Mahony, S., Benos, P. V., Smith, T. J., and Golden, A. (2006) “Self-organizing neural networks to support the discovery of DNA-binding motifs” Neural Networks 19, 950-962. [JIF: 2.000]

Camacho, C. J., Ma, H., and Champ, P. C. (2006) “Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions” Proteins-Structure Function and Bioinformatics 63, 868-877. [JIF: 3.73]

John,B., Sander,C., and Marks,D.S. 2006. Prediction of human microRNA targets. Methods in Molecular Biology. 342:101-113.

Arkhipov, S. N. and Maly, I. V. (2006) “Contribution of whole-cell optimization via cell body rolling to polarization of T cells” Physical Biology 3, 209-219. [JIF: 2.773]

Arkhipov, S. N. and Maly, I. V. (2006) “Quantitative analysis of the role of receptor recycling in T cell polarization” Biophysical Journal 91, 4306-4316. [JIF: 4.757]

Cheluvaraja, S. and Meirovitch, H. (2006) “Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method” Journal of Chemical Physics 125 024905. [JIF: 3.166]

Szarecka A, Meirovitch H. Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins. J. Phys. Chem. B. 2006:110, 2869-2880. [JIF: 4.115]

White, R. P. and Meirovitch, H. (2006) “Minimalist explicit solvation models for surface loops in proteins” Journal of Chemical Theory and Computation 2, 1135-1151. [JIF: 3.627]

White, R. P. and Meirovitch, H. (2006) “Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids” Journal of Chemical Physics 124 204108. [JIF: 3.166]

Lyman, E., Ytreberg, F.M. and Zuckerman, D. M., Resolution Exchange Simulation, Phys. Rev. Lett. 96:028105 (2006). [JIF: 7.072]

Lyman, E. and Zuckerman, D. M. (2006) “A second look at canonical sampling of biomolecules using replica exchange simulation” Journal of Chemical Theory and Computation 2, 1200-1202. [JIF: 3.627]

Lyman, E. and Zuckerman, D. M., Resolution exchange simulation with incremental coarsening, J. Chem. Theory Comp. 2:656-666 (2006). [JIF: 3.627]

Lyman, E. and Zuckerman, D. M., Ensemble-based convergence analysis of biomolecular trajectories, Biophysical J., 91:164-172 (2006). [JIF: 4.757]

Ytreberg, F.M., Swendsen, R.H. and Zuckerman, D.M. (2006) “Comparison of free energy methods for molecular systems,” J. Chem. Phys 125, 184114. [JIF:3.166 ]

Ytreberg, F.M. and Zuckerman, D.M. (2006) “BlackBox Reweighting” arXiv:physics/0609194v1 [physics.comp-ph].

Ytreberg, F. M. and Zuckerman, D. M. Simple estimation of absolute free energies for biomolecules, J. Chem. Phys. 124:104015 (2006). [JIF: 3.166]