People

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 ONEpg. 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

Chivian, D., Brodie, E. L., Alm, E. J., Culley, D. E., Dehal, P. S., Desantis, T. Z., Gihring, T. M., Lapidus, A., Lin, L. H., Lowry, S. R., Moser, D. P., Richardson, P. M., Southam, G., Wanger, G., Pratt, L. M., Andersen, G. L., Hazen, T. C., Brockman, F. J., Arkin, A. P., Onstott, T. C. (2008) "Environmental genomics reveals a single-species ecosystem deep within Earth", Science pp. 275-8

Arkin, A. (2008) "Setting the standard in synthetic biology", Nat Biotechnol pp. 771-4

Stolyar, S., He, Q., Joachimiak, M. P., He, Z., Yang, Z. K., Borglin, S. E., Joyner, D. C., Huang, K., Alm, E., Hazen, T. C., Zhou, J., Wall, J. D., Arkin, A. P., Stahl, D. A. (2007) "Response of Desulfovibrio vulgaris to alkaline stress", J Bacteriol pp. 8944-52

Price, M. N., Dehal, P. S., Arkin, A. P. (2007) "Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes", PLoS Comput Biol pg. 175

Osterhout, R. E., Figueroa, I. A., Keasling, J. D., Arkin, A. P. (2007) "Global analysis of host response to induction of a latent bacteriophage", BMC Microbiol pg. 82

Mukhopadhyay, A., Redding, A. M., Joachimiak, M. P., Arkin, A. P., Borglin, S. E., Dehal, P. S., Chakraborty, R., Geller, J. T., Hazen, T. C., He, Q., Joyner, D. C., Martin, V. J., Wall, J. D., Yang, Z. K., Zhou, J., Keasling, J. D. (2007) "Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough", J Bacteriol pp. 5996-6010

Kazakov, A. E., Cipriano, M. J., Novichkov, P. S., Minovitsky, S., Vinogradov, D. V., Arkin, A., Mironov, A. A., Gelfand, M. S., Dubchak, I. (2007) "RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes", Nucleic Acids Res pp. 407-12

Bender, K. S., Yen, H. C., Hemme, C. L., Yang, Z., He, Z., He, Q., Zhou, J., Huang, K. H., Alm, E. J., Hazen, T. C., Arkin, A. P., Wall, J. D. (2007) "Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough", Appl Environ Microbiol pp. 5389-400

Andrews, S. S., Arkin, A. P. (2007) "Systems biology: a switch for sex", Curr Biol pp. 410-2

Anderson, J. C., Voigt, C. A., Arkin, A. P. (2007) "Environmental signal integration by a modular AND gate", Mol Syst Biol pg. 133

Samoilov, M. S., Price, G., Arkin, A. P. (2006) "From fluctuations to phenotypes: the physiology of noise", Sci STKE pg. 17

Samoilov, M. S., Arkin, A. P. (2006) "Deviant effects in molecular reaction pathways", Nat Biotechnol pp. 1235-1240

Price, M. N., Arkin, A. P., Alm, E. J. (2006) "The life-cycle of operons", PLoS Genet pg. 96

Price, M. N., Arkin, A. P., Alm, E. J. (2006) "OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments", BMC Bioinformaticspg. 19

Plyasunov, S., Arkin, A.P. (2006) "Efficient stochastic sensitivity analysis of discrete event systems", Journal of Computational Physics pp. 724-738

Plyasunov, S., Arkin, A.P. (2006) "Averaging Methods For Stochastic Dynamics of Complex Reaction Networks: Description of Multi-scale Couplings", Multiscale Modeling and Simulation pp. 497-513

Onsum, M. D., Wong, K., Herzmark, P., Bourne, H. R., Arkin, A. P. (2006) "Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification", Phys Biolpp. 190-9

Mukhopadhyay, A., He, Z., Alm, E. J., Arkin, A. P., Baidoo, E. E., Borglin, S. C., Chen, W., Hazen, T. C., He, Q., Holman, H. Y., Huang, K., Huang, R., Joyner, D. C., Katz, N., Keller, M., Oeller, P., Redding, A., Sun, J., Wall, J., Wei, J., Yang, Z., Yen, H. C., Zhou, J., Keasling, J. D. (2006) "Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach", J Bacteriol pp. 4068-78

Leaphart, A. B., Thompson, D. K., Huang, K., Alm, E., Wan, X. F., Arkin, A., Brown, S. D., Wu, L., Yan, T., Liu, X., Wickham, G. S., Zhou, J. (2006) "Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH", J Bacteriol pp. 1633-42

He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. (2006) "Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis", Appl Environ Microbiol pp. 4370-81

Ham, T. S., Lee, S. K., Keasling, J. D., Arkin, A. P. (2006) "A tightly regulated inducible expression system utilizing the fim inversion recombination switch", Biotechnol Bioeng pp. 1-4

Feeley, R., Frenklach, M., Onsum, M., Russi, T., Arkin, A., Packard, A. (2006) "Model discrimination using data collaboration", J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory pp. 6803-13

Clark, M. E., He, Q., He, Z., Huang, K. H., Alm, E. J., Wan, X. F., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. Z., Fields, M. W. (2006) "Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion", Appl Environ Microbiol pp. 5578-88

Chhabra, S. R., He, Q., Huang, K. H., Gaucher, S. P., Alm, E. J., He, Z., Hadi, M. Z., Hazen, T. C., Wall, J. D., Zhou, J., Arkin, A. P., Singh, A. K. (2006) "Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough", J Bacteriol pp. 1817-28

Brown, S. D., Martin, M., Deshpande, S., Seal, S., Huang, K., Alm, E., Yang, Y., Wu, L., Yan, T., Liu, X., Arkin, A., Chourey, K., Zhou, J., Thompson, D. K. (2006) "Cellular response of Shewanella oneidensis to strontium stress", Appl Environ Microbiol pp. 890-900

Arkin, A. P., Fletcher, D. A. (2006) "Fast, cheap and somewhat in control", Genome Biol pg. 114

Andrews, S. S., Arkin, A. P. (2006) "Simulating cell biology", Curr Biol pp. 523-7

Anderson, J. C., Clarke, E. J., Arkin, A. P., Voigt, C. A. (2006) "Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria", J Mol Biol pp. 619-627

Wolf, D. M., Vazirani, V. V., Arkin, A. P. (2005) "Diversity in times of adversity: probabilistic strategies in microbial survival games", J Theor Biol pp. 227-53

Wolf, D. M., Vazirani, V. V., Arkin, A. P. (2005) "A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation", J Theor Biol pp. 255-62

Weinberger, L. S., Burnett, J. C., Toettcher, J. E., Arkin, A. P., Schaffer, D. V. (2005) "Stochastic Gene Expression in a Lentiviral Positive-Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity", Cell pp. 169-82

Voigt, C. A., Wolf, D. M., Arkin, A. P. (2005) "The Bacillus subtilis sin Operon: An Evolvable Network Motif", Genetics pp. 1187-202

Samoilov, M., Plyasunov, S., Arkin, A. P. (2005) "Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations", Proc Natl Acad Sci U S A pp. 2310-5

Rodionov, D. A., Dubchak, I. L., Arkin, A. P., Alm, E. J., Gelfand, M. S. (2005) "Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks", PLoS Comput Biol pg. 55

Rao, C. V., Kirby, J. R., Arkin, A. P. (2005) "Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles", Phys Biol pp. 148-58

Price, M. N., Huang, K. H., Arkin, A. P., Alm, E. J. (2005) "Operon formation is driven by co-regulation and not by horizontal gene transfer", Genome Res pp. 809-19

Price, M. N., Huang, K. H., Alm, E. J., Arkin, A. P. (2005) "A novel method for accurate operon predictions in all sequenced prokaryotes", Nucleic Acids Res pp. 880-92

Price, M. N., Alm, E. J., Arkin, A. P. (2005) "Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication", Nucleic Acids Res pp. 3224-34

Liu, Y., Gao, W., Wang, Y., Wu, L., Liu, X., Yan, T., Alm, E., Arkin, A., Thompson, D. K., Fields, M. W., Zhou, J. (2005) "Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions", J Bacteriol pp. 2501-7

Lee, W., St Onge, R. P., Proctor, M., Flaherty, P., Jordan, M. I., Arkin, A. P., Davis, R. W., Nislow, C., Giaever, G. (2005) "Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents", PLoS Genet pg. 24

Flaherty, P., Giaever, G., Kumm, J., Jordan, M. I., Arkin, A. P. (2005) "A latent variable model for chemogenomic profiling", Bioinformatics pp. 3286-93

Alm, E. J., Huang, K. H., Price, M. N., Koche, R. P., Keller, K., Dubchak, I. L., Arkin, A. P. (2005) "The MicrobesOnline Web site for comparative genomics", Genome Res pp. 1015-22

Vlad, M. O., Arkin, A., Ross, J. (2004) "Response experiments for nonlinear systems with application to reaction kinetics and genetics", Proc Natl Acad Sci U S A pp. 7223-8

Rodionov, D. A., Dubchak, I., Arkin, A., Alm, E., Gelfand, M. S. (2004) "Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria", Genome Biolpg. 90

Rao, C. V., Kirby, J. R., Arkin, A. P. (2004) "Design and Diversity in Bacterial Chemotaxis: A Comparative Study in Escherichia coli and Bacillus subtilis", PLoS Biol pg. 49

Rao, C. V., Frenklach, M., Arkin, A. P. (2004) "An allosteric model for transmembrane signaling in bacterial chemotaxis", J Mol Biol pp. 291-303

McAdams, H. H., Srinivasan, B., Arkin, A. P. (2004) "The evolution of genetic regulatory systems in bacteria", Nat Rev Genet pp. 169-78

Giaever, G., Flaherty, P., Kumm, J., Proctor, M., Nislow, C., Jaramillo, D. F., Chu, A. M., Jordan, M. I., Arkin, A. P., Davis, R. W. (2004) "Chemogenomic profiling: identifying the functional interactions of small molecules in yeast", Proc Natl Acad Sci U S A pp. 793-8

Gao, H., Wang, Y., Liu, X., Yan, T., Wu, L., Alm, E., Arkin, A., Thompson, D. K., Zhou, J. (2004) "Global transcriptome analysis of the heat shock response of Shewanella oneidensis", J Bacteriol pp. 7796-803

Arkin, A.P., Doyle, J. (2004) "The old switcheroo: new tricks revealed in ‘Phage Lambda Revisited’", Current Biology pg. 543

Wolf, D. M., Arkin, A. P. (2003) "Motifs, modules and games in bacteria", Curr Opin Microbiol pp. 125-34

Weinberger, L. S., Schaffer, D. V., Arkin, A. P. (2003) "Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection", J Virol pp. 10028-36

Rao, C. V., Arkin, A. P. (2003) "Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm", Journal of Chemical Physics pp. 4999-5010

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., Cuellar, A. A., Dronov, S., Gilles, E. D., Ginkel, M., Gor, V., Goryanin, II, Hedley, W. J., Hodgman, T. C., Hofmeyr, J. H., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., Le Novere, N., Loew, L. M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E. D., Nakayama, Y., Nelson, M. R., Nielsen, P. F., Sakurada, T., Schaff, J. C., Shapiro, B. E., Shimizu, T. S., Spence, H. D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J. (2003) "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models", Bioinformatics pp. 524-31

Alm, E., Arkin, A. P. (2003) "Biological networks", Curr Opin Struct Biol pp. 193-202

Wolf, D. M., Arkin, A. P. (2002) "Fifteen minutes of fim: control of type 1 pili expression in E. coli", Omics pp. 91-114

Vance, W., Arkin, A., Ross, J. (2002) "Determination of causal connectivities of species in reaction networks", Proc Natl Acad Sci U S A pp. 5816-21

Rao, C. V., Wolf, D. M., Arkin, A. P. (2002) "Control, exploitation and tolerance of intracellular noise", Nature pp. 231-7

Gilman, A. G., Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. D., Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., Brown, H. A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., Harden, T. K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., Sambrano, G. R. (2002) "Overview of the Alliance for Cellular Signaling", Nature pp. 703-6

Gilman, A., Arkin, A. P. (2002) "GENETIC "CODE": Representations and Dynamical Models of Genetic Components and Networks", Annu Rev Genomics Hum Genet pp. 341-69

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K. D., Flaherty, P., Foury, F., Garfinkel, D. J., Gerstein, M., Gotte, D., Guldener, U., Hegemann, J. H., Hempel, S., Herman, Z., Jaramillo, D. F., Kelly, D. E., Kelly, S. L., Kotter, P., LaBonte, D., Lamb, D. C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi, S. L., Revuelta, J. L., Roberts, C. J., Rose, M., Ross-Macdonald, P., Scherens, B., Schimmack, G., Shafer, B., Shoemaker, D. D., Sookhai-Mahadeo, S., Storms, R. K., Strathern, J. N., Valle, G., Voet, M., Volckaert, G., Wang, C. Y., Ward, T. R., Wilhelmy, J., Winzeler, E. A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J. D., Snyder, M., Philippsen, P., Davis, R. W., Johnston, M. (2002) "Functional profiling of the Saccharomyces cerevisiae genome", Nature pp. 387-91

Arkin, A. H., Hazer, B. (2002) "Chemical modification of chlorinated microbial polyesters",Biomacromolecules pp. 1327-35

Samoilov, M., Arkin, A., Ross, J. (2001) "On the deduction of chemical reaction pathways from measurements of time series of concentrations", Chaos pp. 108-114

Rao, C. V., Arkin, A. P. (2001) "Control motifs for intracellular regulatory networks", Annu Rev Biomed Eng pp. 391-419

Arkin, A. P. (2001) "Synthetic cell biology", Curr Opin Biotechnol pp. 638-44

McAdams, H. H., Arkin, A. (2000) "Towards a circuit engineering discipline", Curr Biol pp. 318-20

Saito, T. R., Moritani, N., Hashimoto, H., Arkin, A., Takahashi, K. W. (1999) "Simultaneous observation of ingestive and copulatory behavior of the male rat", Exp Anim pp. 285-8

McAdams, H. H., Arkin, A. (1999) "It's a noisy business! Genetic regulation at the nanomolar scale", Trends Genet pp. 65-9

McAdams, H. H., Arkin, A. (1998) "Simulation of prokaryotic genetic circuits", Annu Rev Biophys Biomol Struct pp. 199-224

Arkin, A., Ross, J., McAdams, H. H. (1998) "Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells", Genetics pp. 1633-48

Swanson, C. A., Arkin, A. P., Ross, J. (1997) "An endogenous calcium oscillator may control early embryonic division", Proc Natl Acad Sci U S A pp. 1194-9

McAdams, H. H., Arkin, A. (1997) "Stochastic mechanisms in gene expression", Proc Natl Acad Sci U S A pp. 814-9

Arkin, A.P , .Shen, P.-D., Ross, J. (1997) "A Test Case of Correlation Metric Construction of a Reaction Pathways from Measurements.", Science pg. 1275

Arkin, A. P. , Ross, J. (1994) "Computational functions in biochemical reaction networks",Biophys. J. pp. 560-578

Arkin, A., Ross, J. (1994) "Computational functions in biochemical reaction networks",Biophys J pp. 560-78

Arkin, A.P., Youvan, D.C., Deisenhofer, J., Norris, J.R. (1993) "Digital Imaging Spectroscopy", The Photosynthetic Reaction Center pp. 133-156

Arkin, A. P., Youvan, D. C. (1992) "Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis", Biotechnology (N Y) pp. 297-300

Arkin, A. P., Youvan, D. C. (1992) "An algorithm for protein engineering: simulations of recursive ensemble mutagenesis", Proc Natl Acad Sci U S A pp. 7811-5

Arkin, A. P., Goldman, E. R., Robles, S. J., Goddard, C. A., Coleman, W. J., Yang, M. M., Youvan, D. C. (1990) "Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra", Biotechnology (N Y) pp. 746-9

Zhou, Jizhong; He, Qiang; Hemme, Christopher L.; Mukhopadhyay, Aindrila; Hillesland, Kristina; Zhou, Aifen; He, Zhili; Van Nostrand, Joy D.; Hazen, Terry C.; Stahl, David A.; Wall, Judy D.; Arkin, Adam P. (2011) "How sulphate-reducing microorganisms cope with stress: lessons from systems biology", Nat Rev Micro pg. 452-466

Liu, C. C. Qi, L. Yanofsky, C. Arkin, A. P. (2011) "Regulation of transcription by unnatural amino acids", Nat Biotechnol pg. 164-8

Huang, Y. W. Arkin, A. P. Chandonia, J. M. (2011) "WIST: toolkit for rapid, customized LIMS development", Bioinformatics pg. 437-8

Skupsky, R. Burnett, J. C. Foley, J. E. Schaffer, D. V. Arkin, A. P. (2010) "HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency",PLoS Comput Biol pg. e1000952

Oh, Julia Fung, Eula Price, Morgan N. Dehal, Paramvir S. Davis, Ronald W. Giaever, Guri Nislow, Corey Arkin, Adam P. Deutschbauer, Adam (2010) "A universal TagModule collection for parallel genetic analysis of microorganisms", Nucl. Acids Res. pg. e146-

Novichkov, Pavel S. Rodionov, Dmitry A. Stavrovskaya, Elena D. Novichkova, Elena S. Kazakov, Alexey E. Gelfand, Mikhail S. Arkin, Adam P. Mironov, Andrey A. Dubchak, Inna (2010) "RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach", Nucleic Acids Research pg. W299-W307

Liu, C. C. Arkin, A. P. (2010) "Cell biology. The case for RNA", Science pg. 1185-6

He, Qiang He, Zhili Joyner, Dominique C. Joachimiak, Marcin Price, Morgan N. Yang, Zamin K. Yen, Huei-Che Bill Hemme, Christopher L. Chen, Wenqiong Fields, Matthew M. Stahl, David A. Keasling, Jay D. Keller, Martin Arkin, Adam P. Hazen, Terry C. Wall, Judy D. Zhou, Jizhong (2010) "Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris", International Society for Microbial Ecology pg. 1386–1397

Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, Fields MW. (2012) "Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State.", BMC Genomics pg. in press