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Price, M. N., Dehal, P. S., Arkin, A. P. (2010) "FastTree 2--approximately maximum-likelihood trees for large alignments", PLoS One pg. 9490 Novichkov, P. S., Laikova, O. N., Novichkova, E. S., Gelfand, M. S., Arkin, A. P., Dubchak, I., Rodionov, D. A. (2010) "RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes", Nucleic Acids Res pp. 111-8 He, Z., Zhou, A., Baidoo, E., He, Q., Joachimiak, M. P., Benke, P., Phan, R., Mukhopadhyay, A., Hemme, C. L., Huang, K., Alm, E. J., Fields, M. W., Wall, J., Stahl, D., Hazen, T. C., Keasling, J. D., Arkin, A. P., Zhou, J. (2010) "Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation", Appl Environ Microbiol pp. 1574-86 Dehal, P. S., Joachimiak, M. P., Price, M. N., Bates, J. T., Baumohl, J. K., Chivian, D., Friedland, G. D., Huang, K. H., Keller, K., Novichkov, P. S., Dubchak, I. L., Alm, E. J., Arkin, A. P. (2010) "MicrobesOnline: an integrated portal for comparative and functional genomics", Nucleic Acids Res pp. 396-400 Burnett, J. C., Lim, K. I., Calafi, A., Rossi, J. J., Schaffer, D. V., Arkin, A. P. (2010) "Combinatorial latency reactivation for HIV-1 subtypes and variants", J Virol pp. 5958-74 Andrews, S. S., Addy, N. J., Brent, R., Arkin, A. P. (2010) "Detailed simulations of cell biology with Smoldyn 2.1", PLoS Comput Biol pg. 1000705 Anderson, J. C., Dueber, J. E., Leguia, M., Wu, G. C., Goler, J. A., Arkin, A. P., Keasling, J. D. (2010) "BglBricks: A flexible standard for biological part assembly", J Biol Eng pg. 1 Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., Dehal, P., Jacobsen, J., Yang, Z., Palumbo, A. V., Arkin, A. P., Zhou, J. (2009) "Snapshot of iron response in Shewanella oneidensis by gene network reconstruction", BMC Genomics pg. 131 Walker, C. B., Stolyar, S., Chivian, D., Pinel, N., Gabster, J. A., Dehal, P. S., He, Z., Yang, Z. K., Yen, H. C., Zhou, J., Wall, J. D., Hazen, T. C., Arkin, A. P., Stahl, D. A. (2009) "Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity", Environ Microbiol pp. 2244-52 Tang, Y. J., Martin, H. G., Dehal, P. S., Deutschbauer, A., Llora, X., Meadows, A., Arkin, A., Keasling, J. D. (2009) "Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism", Biotechnol Bioeng pp. 1161-9 Ross, J., Arkin, A. P. (2009) "Complex systems: from chemistry to systems biology", Proc Natl Acad Sci U S A pp. 6433-4 Price, M. N., Dehal, P. S., Arkin, A. P. (2009) "FastTree: computing large minimum evolution trees with profiles instead of a distance matrix", Mol Biol Evol pp. 1641-50 Kazakov, A. E., Rodionov, D. A., Alm, E., Arkin, A. P., Dubchak, I., Gelfand, M. S. (2009) "Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria", J Bacteriol pp. 52-64 Jo, W. J., Kim, J. H., Oh, E., Jaramillo, D., Holman, P., Loguinov, A. V., Arkin, A. P., Nislow, C., Giaever, G., Vulpe, C. D. (2009) "Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae", BMC Genomics pg. 130 Elias, D. A., Mukhopadhyay, A., Joachimiak, M. P., Drury, E. C., Redding, A. M., Yen, H. C., Fields, M. W., Hazen, T. C., Arkin, A. P., Keasling, J. D., Wall, J. D. (2009) "Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation", Nucleic Acids Res pp. 2926-39 Burnett, J. C., Miller-Jensen, K., Shah, P. S., Arkin, A. P., Schaffer, D. V. (2009) "Control of stochastic gene expression by host factors at the HIV promoter", PLoS Pathog pg. 1000260 Bischofs, I. B., Hug, J. A., Liu, A. W., Wolf, D. M., Arkin, A. P. (2009) "Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay", Proc Natl Acad Sci U S A pp. 6459-64 Wolf, D. M., Fontaine-Bodin, L., Bischofs, I., Price, G., Keasling, J., Arkin, A. P. (2008) "Memory in microbes: quantifying history-dependent behavior in a bacterium", PLoS ONE pg. 1700 Singh, A. H., Wolf, D. M., Wang, P., Arkin, A. P. (2008) "Modularity of stress response evolution", Proc Natl Acad Sci U S A pp. 7500-5 Price, M. N., Dehal, P. S., Arkin, A. P. (2008) "FastBLAST: homology relationships for millions of proteins", PLoS ONE pg. 3589 Price, M. N., Dehal, P. S., Arkin, A. P. (2008) "Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli", Genome Biol pg. 4 Lucks, J. B., Qi, L., Whitaker, W. R., Arkin, A. P. (2008) "Toward scalable parts families for predictable design of biological circuits", Curr Opin Microbiol pp. 567-73 Jo, W. J., Loguinov, A., Chang, M., Wintz, H., Nislow, C., Arkin, A. P., Giaever, G., Vulpe, C. D. (2008) "Identification of Genes Involved in the Toxic Response of Saccharomyces cerevisiae against Iron and Copper Overload by Parallel Analysis of Deletion Mutants", Toxicol Sci pp. 140-51 Ham, T. S., Lee, S. K., Keasling, J. D., Arkin, A. P. (2008) "Design and construction of a double inversion recombination switch for heritable sequential genetic memory", PLoS ONE pg. 2815 Flaherty, P., Radhakrishnan, M. L., Dinh, T., Rebres, R. A., Roach, T. I., Jordan, M. I., Arkin, A. P. (2008) "A dual receptor crosstalk model of g-protein-coupled signal transduction", PLoS Comput Biol pg. 1000185