2007 Publications

Bahar, I., Chennubhotla, C. and Tobi, D. (2007) Intrinsic Enzyme Motions in the Unbound State and Relation to Allosteric Regulation, Current Opinion Structural Biology, 17 (in press). [JIF: 11.215]

Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. (2007) “Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions” Structure. 15, 741-9. [JIF: 5.738]

Eyal, E., Chennubhotla, C., Yang, L. W., and Bahar, I. (2007) “Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models” Bioinformatics 22, 2619-27. [JIF: 4.894]

Eyal E, Pietrokovski S, Bahar I. (2007) “Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices” Bioinformatics 23, 1837-9. [JIF: 4.894]

Bahar, I., Chennubhotla, C., and Erman, B. (2007) “Reply to comment on elastic network models and proteins” Physical Biology 4, 64-65. [Journal Impact Factor, JIF: 2.773]

Chennubhotla, C. and Bahar, I (2007) “Signal Propagation in Proteins and Relation to Equilibrium Fluctuations” PLoS Computational Biology, accepted. [JIF: 4.914]

Chennubhotla C, Bahar I. (2007) “Markov methods for hierarchical coarse-graining of large protein dynamics” J Comput Biol.14, 765-76. [JIF: 2.000]

Iyer AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. (2007) “Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity” J Cell Physiol. 211, 748-58. [JIF: 3.638]

Lazo, J.S., Skoko, J.J., Werner, S., Mitasev, B., Bakan, A., Koizumi, F, Yellow-Duke, A., Bahar, I, Brummond, K.M. (2007) “Structurally unique inhibitors of human mitogen-activated protein kinase phosphatase-1 identified in a pyrrole carboxamide library” J Pharmacol Exp Ther. 322 940-7. [JIF: 3.956]

Tobi D, Bahar I. (2007) “Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?” BMC Bioinformatics 8, 226. [JIF: 3.617]

Vries, J. K., Liu, X., and Bahar, I. (2007) “Relationship between n-gram patterns and secondary structure” Proteins-Structure Function and Bioinformatics 68, 830-838. [JIF: 3.730]

Benos, P. V., Corcoran, D. L., and Feingold, E. (2007). “Footer: Web-Based Identification of Evolutionary Conserved DNA cis-regulatory Elements” Methods in Molecular Biology/Comparative Genomics, edited by N. Bergman, Totowa, New Jersey: Humana Press, Inc.
Feng, H., Taylor, J.L., Benos, P.V., Newton, R., Downing, R., Waddell, K., Chang, Y., Moore, P.S, (2007) “Subtraction of the human transcriptome to search for human tumor viruses” J Virol (in print). [JIF: 5.341]

Lu, Y., Mahony, S., Benos, P.V., Rosenfeld, R., Simon, I., Breeden, L., Bar-Joseph, Z. (2007) “Combined analysis reveals a core set of cycling genes” Genome Biol. 8, R146. [JIF: 7.172]

Mahony, S. and Benos, P. V. (2007) “STAMP; a web tool for exploring DNA-binding motif similarities” Nucleic Acids Research. [JIF: 6.317] Mahony, S., Corcoran, D. L., Feingold, E., and Benos, P. V. (2007) “Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome” Genome Biology. [JIF: 7.172]

Mahony, S., Auron, P. E., and Benos, P. V. (2007) “DNA Familial binding profiles made easy: Comparison of various motif alignment and clustering strategies” PloS Comput Biology 3, e61. [JIF: 4.914]

Mahony, S., Auron, P.E., Benos, P.V. (2007) “Inferring protein-DNA dependencies using motif alignments and mutual information” Bioinformatics 23, i297-i304. [JIF: 4.894]

Mikkelsen, T.S. and et al. [Benos, P.V.] (2007) “Genome of the marsupial Monodelphia domestica reveals innovation in on-coding sequences” Nature 447, 167-177. [JIF: 26.681]

Ringquist, S., Pecoraro, C., Lu, Y., Styche, A., Rudert, W. A., Benos, P. V., and Trucco, M. (2007). “Web-based primer design software for genome scale SNP mapping by pyrosequencing” Humana Press, Inc., Totowa, New Jersey.

Bueno, M and Camacho CJ (2007) “Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI” Proteins, in press. [JIF: 3.730]

Bueno M, Camacho CJ, Sancho J. (2007) “SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles” Proteins 68, 850-62. [JIF: 3.730]

Camacho, CJ et al. (2007) “A Novel Murine Model of the Anti-synthetase Syndrome Induced by Immunization with Histidyl-tRNA Synthetase: Critical Role of Species-specific Epitopes in Self-directed B and T Cell Responses” accepted.
Champ PC, Camacho CJ. (2007) “FastContact: a free energy scoring tool for protein-protein complex structures” Nucleic Acids Res. 35 (Web Server issue), W556-60. Epub 2007 May 30. [JIF: 6.317]

Iyer AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. (2007) “Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity” J Cell Physiol. 211, 748-58. [JIF: 3.638]

Prasad, J. C., Goldstone, J. V., Camacho, C. J., Vajda, S., and Stegeman, J. J. (2007) “Ensemble modeling of substrate binding to cytochromes p450: Analysis of catalytic differences between CYP1A orthologs” Biochemistry 46, 2640-2654. [JIF: 3.633]

Lee, J., Li, Z., Brower-Sinning, R., John, B. (2007) “Regulatory circuit of human microRNA biogenesis” PLoS Comput Biol. [JIF: 4.914]

Arkhipov, S.N. and Maly, I.V. (2007) “A model for the interplay of receptor recycling and receptor-mediated contact in T cells” PLoS ONE, 2, e633.
Grigoriev, I. , Splinter, D., Keijzer, N., Wulf, P.S., Demmers, J., Ohtsuka, T., Modesti, M., Maly, I.V., Grosveld, F., Hoogenraad, C.C., and Akhmanova, A.. (2007) “Rab6 regulates transport and targeting of exocytotic carriers” Dev. Cell, 13, 305–314. [JIF: 13.523]

Meirovitch H. (2007) “Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation” Curr Opin Struct Biol. 17, 181-6. [JIF: 11.215]

Vries, J. K., Liu, X., and Bahar, I. (2007) “Relationship between n-gram patterns and secondary structure” Proteins-Structure Function and Bioinformatics 68, 830-838. [JIF: 3.73]

Lyman, E. and Zuckerman, D.M. (2007) “Annealed importance sampling of peptides” J. Chem. Phys., in press. [JIF: 3.166]

Lyman, E. and Zuckerman, D.M. (2007) “On the convergence of biomolecular simulations: Determining the effective sample size” J. Phys. Chem. B, in press. [JIF: 4.115]

Ytreberg, F.M., Aroutiounian, S.Kh., and Zuckerman, D.M. (2007) “Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model” J. Chem. Theory Comp., in press; Web Release Date: August 25, 2007. [JIF: 3.627]

Zhang, Bin W., Jasnow, David, and Zuckerman, Daniel M. (2007) “Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin,” Proc Natl Acad Sci (USA), in press.