Loading...
Sign in to edit your profile (add interests, overview, photo, etc.)

    Arkin, Adam

    TitleArea Deputy, Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/495-2116
    vCardDownload vCard

      Collapse Biography 
      Collapse Awards and Honors
      2007American Academy of Microbiology Fellow
      University of California Santa Barbara2007Mohammed Dahleh Award

      Collapse Overview 
      Collapse Overview
      The Arkin Lab works on detailed modeling of genetic and biochemical networks with emphasis on developmental systems. The laboratory creates custom genetic circuitry in Saccaromyces cerivisiae and multichannel, protein and small molecule biosensors. The Arkin Lab is interested in the detailed physical analysis of the network of biochemical and genetic reactions that govern cellular development. The goal is to divine the engineering principles of the control systems that determine cell behavior and differentiation in response to internal and external signals. Because of their simplicity (relative to eukaryotic cells), and because many bacterial genome sequencing projects have recently completed, we study mostly bacterial and viral circuitry. Particular biological systems currently under study in my lab include, l-phage/Escherichia coli interactions, the role of stochastic phase-variation of type-1 pili in uropathic E. coli virulence, and analysis of the sporulation initiation and germination pathways in Bacillus subtilis. As the basis for such analyses we examine the detailed mechanisms of the underlying chemical reactions. For example, a rigorous physical analysis of the mechanisms of prokaryotic gene expression revealed that the temporal pattern of protein production from a single gene is an erratic and bursty stochastic process. Analysis of networks of such genes responsible for developmental switches demonstrated that while some architectures generate deterministic outcomes despite this noise, others exploit the noise to produce population diversity to, for example, evade attack by the immune system. In addition to theoretical analyses, the laboratory has started experimental measurements on such systems and has begun design and implementation (in yeast and E. coli) of our own custom genetic circuitry. Thus, the laboratory applies theoretical and computational analyses from dynamical systems, stochastic processes, chemical kinetics and statistical mechanics and methods from molecular biology to determine the principles of cellular signal processing and to aid in design of custom cellular circuitry that may, for example, act as sensitive biosensors.


      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin A, Chakraborty R. Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announc. 2017 Jun 29; 5(26). PMID: 28663297.
        View in: PubMed
      2. Sagawa S, Price MN, Deutschbauer AM, Arkin A. Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS One. 2017; 12(5):e0178258. PMID: 28542589.
        View in: PubMed
      3. Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin A, Stahl DA, Zhou J. Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer. Environ Sci Technol. 2017 Mar 16. PMID: 28300407.
        View in: PubMed
      4. Rin Kim S, Skerker JM, Iok Kong I, Kim H, Maurer MJ, Zhang GC, Peng D, Wei N, Arkin A, Jin YS. Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol. Metab Eng. 2017 Feb 16. PMID: 28216106.
        View in: PubMed
      5. Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin A, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci. 2017; 12:23. PMID: 28194258.
        View in: PubMed
      6. Haliburton JR, Shao W, Deutschbauer A, Arkin A, Abate AR. Genetic interaction mapping with microfluidic-based single cell sequencing. PLoS One. 2017; 12(2):e0171302. PMID: 28170417.
        View in: PubMed
      7. King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn TL, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole FL, Watson DB, W Fields MW, Chandonia JM, Alm EJ, Zhou J, Adams MW, Hazen TC, Arkin A, Elias DA. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environ Sci Technol. 2017 Jan 23. PMID: 28112946.
        View in: PubMed
      8. Menezes AA, Vilardi RF, Arkin A, Cohen MJ. Targeted clinical control of trauma patient coagulation through a thrombin dynamics model. Sci Transl Med. 2017 Jan 04; 9(371). PMID: 28053156.
        View in: PubMed
      9. Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin A, Deutschbauer AM. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PLoS One. 2016; 11(12):e0168719. PMID: 28030630.
        View in: PubMed
      10. Maurer MJ, Sutardja L, Pinel D, Bauer S, Muehlbauer AL, Ames TD, Skerker JM, Arkin A. QTL-guided metabolic engineering of a complex trait. ACS Synth Biol. 2016 Dec 12. PMID: 27936603.
        View in: PubMed
      11. Thorgersen MP, Lancaster WA, Rajeev L, Ge X, Vaccaro BJ, Poole FL, Arkin A, Mukhopadhyay A, Adams MW. A Highly Expressed High Molecular Weight S-Layer Complex of Pelosinus Strain UFO1 Binds Uranium. Appl Environ Microbiol. 2016 Dec 02. PMID: 27913415.
        View in: PubMed
      12. Price MN, Wetmore KM, Deutschbauer AM, Arkin A. A Comparison of the Costs and Benefits of Bacterial Gene Expression. PLoS One. 2016; 11(10):e0164314. PMID: 27711251.
        View in: PubMed
      13. Zhang S, Ito M, Skerker JM, Arkin A, Rao CV. Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation. Appl Microbiol Biotechnol. 2016 Nov; 100(21):9393-9405. PMID: 27678117.
        View in: PubMed
      14. Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin A, Novichkov PS, Wall JD, Adams MW. Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. Appl Environ Microbiol. 2016 Oct 1; 82(19):6046-56. PMID: 27474723.
        View in: PubMed
      15. Price MN, Arkin A. A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biol Evol. 2016; 8(6):1917-28. PMID: 27289091.
        View in: PubMed
      16. Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. GENOME ENGINEERING. The Genome Project-Write. Science. 2016 Jul 8; 353(6295):126-7. PMID: 27256881.
        View in: PubMed
      17. Oh EJ, Skerker JM, Kim SR, Wei N, Turner TL, Maurer MJ, Arkin A, Jin YS. Gene Amplification on Demand Accelerates Cellobiose Utilization in Engineered Saccharomyces cerevisiae. Appl Environ Microbiol. 2016 Jun 15; 82(12):3631-9. PMID: 27084006.
        View in: PubMed
      18. Quarterman J, Skerker JM, Feng X, Liu IY, Zhao H, Arkin A, Jin YS. Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae. J Biotechnol. 2016 Jul 10; 229:13-21. PMID: 27140870.
        View in: PubMed
      19. Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin A, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res. 2016 Aug 19; 44(14):7006. PMID: 27131373.
        View in: PubMed
      20. Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik VK, Arkin A, Gill RT. Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli. ACS Synth Biol. 2016 Jul 15; 5(7):561-8. PMID: 27072506.
        View in: PubMed
      21. Hemme CL, Green SJ, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutschbauer AM, Van Nostrand JD, Wu L, He Z, Jordan IK, Hazen TC, Arkin A, Kostka JE, Zhou J. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. MBio. 2016; 7(2). PMID: 27048805.
        View in: PubMed
      22. Kosina SM, Danielewicz MA, Mohammed M, Ray J, Suh Y, Yilmaz S, Singh AK, Arkin A, Deutschbauer AM, Northen TR. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. ACS Synth Biol. 2016 Jul 15; 5(7):569-76. PMID: 26885935.
        View in: PubMed
      23. Price MN, Arkin A. Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes. MBio. 2015; 6(6). PMID: 26670382.
        View in: PubMed
      24. Menezes AA, Montague MG, Cumbers J, Hogan JA, Arkin A. Grand challenges in space synthetic biology. J R Soc Interface. 2015 Dec 6; 12(113). PMID: 26631337.
        View in: PubMed
      25. Zhang S, Skerker JM, Rutter CD, Maurer MJ, Arkin A, Rao CV. Engineering Rhodosporidium toruloides for increased lipid production. Biotechnol Bioeng. 2016 May; 113(5):1056-66. PMID: 26479039.
        View in: PubMed
      26. Stephens CM, Skerker JM, Sekhon MS, Arkin A, Riley LW. Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections. Genome Announc. 2015; 3(6). PMID: 26543109.
        View in: PubMed
      27. Freed EF, Winkler JD, Weiss SJ, Garst AD, Mutalik VK, Arkin A, Knight R, Gill RT. Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits. ACS Synth Biol. 2015 Nov 20; 4(11):1244-53. PMID: 26478262.
        View in: PubMed
      28. Venturelli OS, Egbert RG, Arkin A. Towards Engineering Biological Systems in a Broader Context. J Mol Biol. 2016 Feb 27; 428(5 Pt B):928-44. PMID: 26546279.
        View in: PubMed
      29. Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin A, Zhou J. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol. 2015; 6:1205. PMID: 26583008.
        View in: PubMed
      30. Rubin BE, Wetmore KM, Price MN, Diamond S, Shultzaberger RK, Lowe LC, Curtin G, Arkin A, Deutschbauer A, Golden SS. The essential gene set of a photosynthetic organism. Proc Natl Acad Sci U S A. 2015 Dec 1; 112(48):E6634-43. PMID: 26508635.
        View in: PubMed
      31. Zhang P, Van Nostrand JD, He Z, Chakraborty R, Deng Y, Curtis D, Fields MW, Hazen TC, Arkin A, Zhou J. A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction. Environ Sci Technol. 2015 Nov 3; 49(21):12922-31. PMID: 25835088.
        View in: PubMed
      32. Vaccaro BJ, Thorgersen MP, Lancaster WA, Price MN, Wetmore KM, Poole FL, Deutschbauer A, Arkin A, Adams MW. Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Appl Environ Microbiol. 2015; 82(1):51-61. PMID: 26452555.
        View in: PubMed
      33. De León KB, Utturkar SM, Camilleri LB, Elias DA, Arkin A, Fields MW, Brown SD, Wall JD. Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum. Genome Announc. 2015; 3(5). PMID: 26404608.
        View in: PubMed
      34. García Martín H, Kumar VS, Weaver D, Ghosh A, Chubukov V, Mukhopadhyay A, Arkin A, Keasling JD. A Method to Constrain Genome-Scale Models with 13C Labeling Data. PLoS Comput Biol. 2015 Sep; 11(9):e1004363. PMID: 26379153.
        View in: PubMed
      35. Thorgersen MP, Lancaster WA, Vaccaro BJ, Poole FL, Rocha AM, Mehlhorn T, Pettenato A, Ray J, Waters RJ, Melnyk RA, Chakraborty R, Hazen TC, Deutschbauer AM, Arkin A, Adams MW. Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments. Appl Environ Microbiol. 2015 Aug 1; 81(15):4976-83. PMID: 25979890.
        View in: PubMed
      36. Ray J, Waters RJ, Skerker JM, Kuehl JV, Price MN, Huang J, Chakraborty R, Arkin A, Deutschbauer A. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announc. 2015; 3(3). PMID: 25977418.
        View in: PubMed
      37. Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin A, Fields MW, Zhou J, Alm EJ, Hazen TC. Natural bacterial communities serve as quantitative geochemical biosensors. MBio. 2015; 6(3). PMID: 25968645.
        View in: PubMed
      38. Wetmore KM, Price MN, Waters RJ, Lamson JS, He J, Hoover CA, Blow MJ, Bristow J, Butland G, Arkin A, Deutschbauer A. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio. 2015; 6(3). PMID: 25968644.
        View in: PubMed
      39. Melnyk RA, Youngblut MD, Clark IC, Carlson HK, Wetmore KM, Price MN, Iavarone AT, Deutschbauer AM, Arkin A, Coates JD. Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase. MBio. 2015; 6(3). PMID: 25968643.
        View in: PubMed
      40. Dey SS, Foley JE, Limsirichai P, Schaffer DV, Arkin A. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci. Mol Syst Biol. 2015; 11(5):806. PMID: 25943345.
        View in: PubMed
      41. Zhang P, Wu WM, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt CW, Watson D, Jardine P, Criddle CS, Brooks S, Marsh TL, Tiedje JM, Arkin A, Zhou J. Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Appl Environ Microbiol. 2015 Jun 15; 81(12):4164-72. PMID: 25862231.
        View in: PubMed
      42. Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin A, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J. 2015 Nov; 9(11):2360-72. PMID: 25848870.
        View in: PubMed
      43. Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin A, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, Fields MW. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announc. 2015; 3(2). PMID: 25767232.
        View in: PubMed
      44. Carlson HK, Stoeva MK, Justice NB, Sczesnak A, Mullan MR, Mosqueda LA, Kuehl JV, Deutschbauer AM, Arkin A, Coates JD. Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms. Environ Sci Technol. 2015 Mar 17; 49(6):3727-36. PMID: 25698072.
        View in: PubMed
      45. Korte HL, Saini A, Trotter VV, Butland GP, Arkin A, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Environ Sci Technol. 2015 Jan 20; 49(2):924-31. PMID: 25534748.
        View in: PubMed
      46. Menezes AA, Cumbers J, Hogan JA, Arkin A. Towards synthetic biological approaches to resource utilization on space missions. J R Soc Interface. 2015 Jan 6; 12(102):20140715. PMID: 25376875.
        View in: PubMed
      47. Carlson HK, Kuehl JV, Hazra AB, Justice NB, Stoeva MK, Sczesnak A, Mullan MR, Iavarone AT, Engelbrektson A, Price MN, Deutschbauer AM, Arkin A, Coates JD. Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. ISME J. 2015 Jun; 9(6):1295-305. PMID: 25405978.
        View in: PubMed
      48. Price MN, Ray J, Wetmore KM, Kuehl JV, Bauer S, Deutschbauer AM, Arkin A. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Front Microbiol. 2014; 5:577. PMID: 25400629.
        View in: PubMed
      49. Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin A, Wall JD. Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH. J Bacteriol. 2015 Jan 1; 197(1):29-39. PMID: 25313388.
        View in: PubMed
      50. Lee S, Geller JT, Torok T, Wu CH, Singer M, Reid FC, Tarjan DR, Hazen TC, Arkin A, Hillson NJ. Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models. PLoS One. 2014; 9(8):e105689. PMID: 25148472.
        View in: PubMed
      51. Ryan OW, Skerker JM, Maurer MJ, Li X, Tsai JC, Poddar S, Lee ME, DeLoache W, Dueber JE, Arkin A, Cate JH. Selection of chromosomal DNA libraries using a multiplex CRISPR system. Elife. 2014; 3. PMID: 25139909.
        View in: PubMed
      52. Deutschbauer A, Price MN, Wetmore KM, Tarjan DR, Xu Z, Shao W, Leon D, Arkin A, Skerker JM. Towards an informative mutant phenotype for every bacterial gene. J Bacteriol. 2014 Oct 15; 196(20):3643-55. PMID: 25112473.
        View in: PubMed
      53. Shao W, Price MN, Deutschbauer AM, Romine MF, Arkin A. Conservation of Transcription Start Sites within Genes across a Bacterial Genus. MBio. 2014; 5(4). PMID: 24987095.
        View in: PubMed
      54. Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin A, Deutschbauer AM, Patti GJ, Siuzdak G. Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses. Anal Chem. 2014 Jul 15; 86(14):6931-9. PMID: 24934772.
        View in: PubMed
      55. Rinehart D, Johnson CH, Nguyen T, Ivanisevic J, Benton HP, Lloyd J, Arkin A, Deutschbauer AM, Patti GJ, Siuzdak G. Metabolomic data streaming for biology-dependent data acquisition. Nat Biotechnol. 2014 Jun 9; 32(6):524-7. PMID: 24911492.
        View in: PubMed
      56. Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin A, Deutschbauer A. Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20. MBio. 2014; 5(3). PMID: 24865553.
        View in: PubMed
      57. Whitaker WR, Lee H, Arkin A, Dueber JE. Avoidance of Truncated Proteins from Unintended Ribosome Binding Sites within Heterologous Protein Coding Sequences. ACS Synth Biol. 2015 Mar 20; 4(3):249-57. PMID: 24931615.
        View in: PubMed
      58. Korte HL, Fels SR, Christensen GA, Price MN, Kuehl JV, Zane GM, Deutschbauer AM, Arkin A, Wall JD. Genetic basis for nitrate resistance in Desulfovibrio strains. Front Microbiol. 2014; 5:153. PMID: 24795702.
        View in: PubMed
      59. Qi LS, Arkin A. A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol. 2014 Apr 16; 12(5):341-54. PMID: 24736794.
        View in: PubMed
      60. Meyer B, Kuehl JV, Price MN, Ray J, Deutschbauer AM, Arkin A, Stahl DA. The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environ Microbiol. 2014 Nov; 16(11):3463-86. PMID: 24447568.
        View in: PubMed
      61. Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, Arkin A. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci U S A. 2014 Mar 4; 111(9):E836-45. PMID: 24550501.
        View in: PubMed
      62. Guimaraes JC, Rocha M, Arkin A. Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res. 2014 Apr 1; 42(8):4791-9. PMID: 24510099.
        View in: PubMed
      63. Guimaraes JC, Rocha M, Arkin A, Cambray G. D-Tailor: automated analysis and design of DNA sequences. Bioinformatics. 2014 Apr 15; 30(8):1087-1094. PMID: 24398007.
        View in: PubMed
      64. Somenahally AC, Mosher JJ, Yuan T, Podar M, Phelps TJ, Brown SD, Yang ZK, Hazen TC, Arkin A, Palumbo AV, Van Nostrand JD, Zhou J, Elias DA. Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities. PLoS One. 2013; 8(12):e83909. PMID: 24376771.
        View in: PubMed
      65. Arkin A. A wise consistency: engineering biology for conformity, reliability, predictability. Curr Opin Chem Biol. 2013 Dec; 17(6):893-901. PMID: 24268562.
        View in: PubMed
      66. Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin A, Dubchak I, Rodionov DA. RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013; 14:745. PMID: 24175918.
        View in: PubMed
      67. Louie KB, Bowen BP, Cheng X, Berleman JE, Chakraborty R, Deutschbauer A, Arkin A, Northen TR. "Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Anal Chem. 2013 Nov 19; 85(22):10856-62. PMID: 24111681.
        View in: PubMed
      68. Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin A, Price MN, Rodionov DA. Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environ Microbiol. 2014 Jan; 16(1):1-8. PMID: 24118949.
        View in: PubMed
      69. Meyer B, Kuehl JV, Deutschbauer AM, Arkin A, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. J Bacteriol. 2013 Nov; 195(21):4900-14. PMID: 23974031.
        View in: PubMed
      70. Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin A, Zhou J. StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Environ Sci Technol. 2013 Sep 3; 47(17):9841-9. PMID: 23889170.
        View in: PubMed
      71. Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin A, Endy D, Church GM. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A. 2013 Aug 20; 110(34):14024-9. PMID: 23924614.
        View in: PubMed
      72. Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin A, Wall JD, Mukhopadhyay A, Novichkov PS. New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol. 2013 Oct; 195(19):4466-75. PMID: 23913324.
        View in: PubMed
      73. Cardinale S, Joachimiak MP, Arkin A. Effects of genetic variation on the E. coli host-circuit interface. Cell Rep. 2013 Jul 25; 4(2):231-7. PMID: 23871664.
        View in: PubMed
      74. Miller-Jensen K, Skupsky R, Shah PS, Arkin A, Schaffer DV. Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression. PLoS Comput Biol. 2013; 9(7):e1003135. PMID: 23874178.
        View in: PubMed
      75. Skerker JM, Leon D, Price MN, Mar JS, Tarjan DR, Wetmore KM, Deutschbauer AM, Baumohl JK, Bauer S, Ibáñez AB, Mitchell VD, Wu CH, Hu P, Hazen T, Arkin A. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates. Mol Syst Biol. 2013; 9:674. PMID: 23774757.
        View in: PubMed
      76. Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, Kuehl JV, Shao W, Arkin A. Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol. 2013; 9:660. PMID: 23591776.
        View in: PubMed
      77. Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin A, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J. 2013 Sep; 7(9):1790-802. PMID: 23575373.
        View in: PubMed
      78. Brown SD, Utturkar SM, Arkin A, Deutschbauer AM, Elias DA, Hazen TC, Chakraborty R. Draft Genome Sequence for Desulfovibrio africanus Strain PCS. Genome Announc. 2013 Mar-Apr; 1(2):e0014413. PMID: 23580709.
        View in: PubMed
      79. Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin A, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics. 2013; 14:213. PMID: 23547897.
        View in: PubMed
      80. Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin A, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res. 2013 May; 41(9):5139-48. PMID: 23511967.
        View in: PubMed
      81. Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai QA, Tran AB, Paull M, Keasling JD, Arkin A, Endy D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods. 2013 Apr; 10(4):354-60. PMID: 23474465.
        View in: PubMed
      82. Mutalik VK, Guimaraes JC, Cambray G, Mai QA, Christoffersen MJ, Martin L, Yu A, Lam C, Rodriguez C, Bennett G, Keasling JD, Endy D, Arkin A. Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods. 2013 Apr; 10(4):347-53. PMID: 23474467.
        View in: PubMed
      83. Huh JH, Kittleson JT, Arkin A, Anderson JC. Modular design of a synthetic payload delivery device. ACS Synth Biol. 2013 Aug 16; 2(8):418-24. PMID: 23654275.
        View in: PubMed
      84. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin A, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28; 152(5):1173-83. PMID: 23452860.
        View in: PubMed
      85. Kim SR, Skerker JM, Kang W, Lesmana A, Wei N, Arkin A, Jin YS. Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. PLoS One. 2013; 8(2):e57048. PMID: 23468911.
        View in: PubMed
      86. Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin A, Mavromatis K, Malfatti S, Tringe S, Hazen TC. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Stand Genomic Sci. 2013; 7(3):382-98. PMID: 24019987.
        View in: PubMed
      87. Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin A, Aitchison JD, Adams MW, Baliga NS. Metallochaperones regulate intracellular copper levels. PLoS Comput Biol. 2013; 9(1):e1002880. PMID: 23349626.
        View in: PubMed
      88. Wang L, Wang X, Arkin A, Samoilov MS. Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinformatics. 2013 Feb 1; 29(3):338-46. PMID: 23271269.
        View in: PubMed
      89. Meyer B, Kuehl J, Deutschbauer AM, Price MN, Arkin A, Stahl DA. Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J Bacteriol. 2013 Mar; 195(5):990-1004. PMID: 23264581.
        View in: PubMed
      90. Chivian D, Dehal PS, Keller K, Arkin A. MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res. 2013 Jan; 41(Database issue):D648-54. PMID: 23203984.
        View in: PubMed
      91. Baran R, Bowen BP, Price MN, Arkin A, Deutschbauer AM, Northen TR. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chem Biol. 2013 Jan 18; 8(1):189-99. PMID: 23082955.
        View in: PubMed
      92. Kazakov AE, Rodionov DA, Price MN, Arkin A, Dubchak I, Novichkov PS. Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol. 2013 Jan; 195(1):29-38. PMID: 23086211.
        View in: PubMed
      93. Whitaker WR, Davis SA, Arkin A, Dueber JE. Engineering robust control of two-component system phosphotransfer using modular scaffolds. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):18090-5. PMID: 23071327.
        View in: PubMed
      94. Bowen De León K, Young ML, Camilleri LB, Brown SD, Skerker JM, Deutschbauer AM, Arkin A, Fields MW. Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction. J Bacteriol. 2012 Oct; 194(19):5456-7. PMID: 22965085.
        View in: PubMed
      95. Liu CC, Qi L, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VK, Arkin A. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nat Methods. 2012 Nov; 9(11):1088-94. PMID: 23023598.
        View in: PubMed
      96. Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin A. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012 Oct; 30(10):1002-6. PMID: 22983090.
        View in: PubMed
      97. Brown SD, Podar M, Klingeman DM, Johnson CM, Yang ZK, Utturkar SM, Land ML, Mosher JJ, Hurt RA, Phelps TJ, Palumbo AV, Arkin A, Hazen TC, Elias DA. Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. J Bacteriol. 2012 Sep; 194(18):5147-8. PMID: 22933770.
        View in: PubMed
      98. Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak MP, He Z, Zhou J, Arkin A, Wall JD, Stahl DA. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J Bacteriol. 2012 Nov; 194(21):5783-93. PMID: 22904289.
        View in: PubMed
      99. Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin A, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA. Functional responses of methanogenic archaea to syntrophic growth. ISME J. 2012 Nov; 6(11):2045-55. PMID: 22739494.
        View in: PubMed
      100. Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin A, Dubchak I, Rodionov DA. RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W604-8. PMID: 22700702.
        View in: PubMed
      101. McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin A, Petzold CJ, Adams PD, Keasling JD, Chhabra SR. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microb Cell Fact. 2012; 11:79. PMID: 22694848.
        View in: PubMed
      102. Cardinale S, Arkin A. Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems. Biotechnol J. 2012 Jul; 7(7):856-66. PMID: 22649052.
        View in: PubMed
      103. Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin A, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem. 2012 Jul 20; 287(30):25335-43. PMID: 22645145.
        View in: PubMed
      104. Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin A, Schaffer DV. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-?B mediated viral gene expression. Integr Biol (Camb). 2012 Jun; 4(6):661-71. PMID: 22555315.
        View in: PubMed
      105. Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin A, Mukhopadhyay A, Fields MW. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics. 2012; 13:138. PMID: 22507456.
        View in: PubMed
      106. Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin A. Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol. 2012 May; 8(5):447-54. PMID: 22446835.
        View in: PubMed
      107. Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin A. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012 Jul; 40(12):5775-86. PMID: 22383579.
        View in: PubMed
      108. Mosher JJ, Phelps TJ, Podar M, Hurt RA, Campbell JH, Drake MM, Moberly JG, Schadt CW, Brown SD, Hazen TC, Arkin A, Palumbo AV, Faybishenko BA, Elias DA. Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Appl Environ Microbiol. 2012 Apr; 78(7):2082-91. PMID: 22267668.
        View in: PubMed
      109. Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin A, Schaffer DV. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. J Biol Chem. 2012 Mar 9; 287(11):7945-55. PMID: 22253435.
        View in: PubMed
      110. Chen D, Arkin A. Sequestration-based bistability enables tuning of the switching boundaries and design of a latch. Mol Syst Biol. 2012; 8:620. PMID: 23089683.
        View in: PubMed
      111. Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumohl JK, He Q, Fields MW, Arkin A, Wall JD, Hazen TC, Zhou J. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 2012 Feb; 78(4):1168-77. PMID: 22156435.
        View in: PubMed
      112. Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin A. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet. 2011 Nov; 7(11):e1002385. PMID: 22125499.
        View in: PubMed
      113. Rajeev L, Luning EG, Dehal PS, Price MN, Arkin A, Mukhopadhyay A. Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biol. 2011; 12(10):R99. PMID: 21992415.
        View in: PubMed
      114. Jajamovich GH, Wang X, Arkin A, Samoilov MS. Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites. Nucleic Acids Res. 2011 Nov; 39(21):e146. PMID: 21948794.
        View in: PubMed
      115. Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin A, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Hazen TC. Complete genome sequence of "Enterobacter lignolyticus" SCF1. Stand Genomic Sci. 2011 Oct 15; 5(1):69-85. PMID: 22180812.
        View in: PubMed
      116. Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, Singer M, Ouellet M, Szakal ED, Jorgens D, Price MN, Witkowska HE, Beller HR, Arkin A, Hazen TC, Biggin MD, Auer M, Wall JD, Keasling JD. Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Appl Environ Microbiol. 2011 Nov; 77(21):7595-604. PMID: 21908633.
        View in: PubMed
      117. Cambray G, Mutalik VK, Arkin A. Toward rational design of bacterial genomes. Curr Opin Microbiol. 2011 Oct; 14(5):624-30. PMID: 21865081.
        View in: PubMed
      118. Price MN, Deutschbauer AM, Kuehl JV, Liu H, Witkowska HE, Arkin A. Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol. 2011 Oct; 193(20):5716-27. PMID: 21840973.
        View in: PubMed
      119. Liu P, Meagher RJ, Light YK, Yilmaz S, Chakraborty R, Arkin A, Hazen TC, Singh AK. Microfluidic fluorescence in situ hybridization and flow cytometry (µFlowFISH). Lab Chip. 2011 Aug 21; 11(16):2673-9. PMID: 21755095.
        View in: PubMed
      120. Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin A, Wall JD, Singh AK, Keasling JD. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PLoS One. 2011; 6(6):e21470. PMID: 21738675.
        View in: PubMed
      121. Miller-Jensen K, Dey SS, Schaffer DV, Arkin A. Varying virulence: epigenetic control of expression noise and disease processes. Trends Biotechnol. 2011 Oct; 29(10):517-25. PMID: 21700350.
        View in: PubMed
      122. Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin A, Dubchak I, Osterman AL, Gelfand MS. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011; 12 Suppl 1:S3. PMID: 21810205.
        View in: PubMed
      123. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin A. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A. 2011 Jul 5; 108(27):11063-8. PMID: 21642531.
        View in: PubMed
      124. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin A, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011 Jul 5; 108(27):11069-74. PMID: 21642536.
        View in: PubMed
      125. Bates JT, Chivian D, Arkin A. GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W400-5. PMID: 21624891.
        View in: PubMed
      126. Gerasimova A, Kazakov AE, Arkin A, Dubchak I, Gelfand MS. Comparative genomics of the dormancy regulons in mycobacteria. J Bacteriol. 2011 Jul; 193(14):3446-52. PMID: 21602344.
        View in: PubMed
      127. Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin A. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol. 2011 Jun; 9(6):452-66. PMID: 21572460.
        View in: PubMed
      128. Lucks JB, Qi L, Mutalik VK, Wang D, Arkin A. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A. 2011 May 24; 108(21):8617-22. PMID: 21555549.
        View in: PubMed
      129. Arkin A, Schaffer DV. Network news: innovations in 21st century systems biology. Cell. 2011 Mar 18; 144(6):844-9. PMID: 21414475.
        View in: PubMed
      130. Huang YW, Arkin A, Chandonia JM. WIST: toolkit for rapid, customized LIMS development. Bioinformatics. 2011 Feb 1; 27(3):437-8. PMID: 21258060.
        View in: PubMed
      131. Liu CC, Qi L, Yanofsky C, Arkin A. Regulation of transcription by unnatural amino acids. Nat Biotechnol. 2011 Feb; 29(2):164-8. PMID: 21240267.
        View in: PubMed
      132. Liu CC, Arkin A. Cell biology. The case for RNA. Science. 2010 Nov 26; 330(6008):1185-6. PMID: 21109657.
        View in: PubMed
      133. Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin A, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One. 2010; 5(10):e13564. PMID: 21042592.
        View in: PubMed
      134. Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin A, Wall JD, Zhou J. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol. 2010 Oct; 12(10):2645-57. PMID: 20482586.
        View in: PubMed
      135. Hemme CL, Mouttaki H, Lee YJ, Zhang G, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Kyrpides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin A, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Xing D, Ren N, Wang A, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, Zhou J. Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol. 2010 Dec; 192(24):6494-6. PMID: 20889752.
        View in: PubMed
      136. Skupsky R, Burnett JC, Foley JE, Schaffer DV, Arkin A. HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput Biol. 2010; 6(9). PMID: 20941390.
        View in: PubMed
      137. Aviran S, Shah PS, Schaffer DV, Arkin A. Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Comput Biol. 2010; 6(8). PMID: 20711350.
        View in: PubMed
      138. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin A, Mironov AA, Dubchak I. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W299-307. PMID: 20542910.
        View in: PubMed
      139. Oh J, Fung E, Price MN, Dehal PS, Davis RW, Giaever G, Nislow C, Arkin A, Deutschbauer A. A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res. 2010 Aug; 38(14):e146. PMID: 20494978.
        View in: PubMed
      140. He Q, He Z, Joyner DC, Joachimiak M, Price MN, Yang ZK, Yen HC, Hemme CL, Chen W, Fields MM, Stahl DA, Keasling JD, Keller M, Arkin A, Hazen TC, Wall JD, Zhou J. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. ISME J. 2010 Nov; 4(11):1386-97. PMID: 20445634.
        View in: PubMed
      141. Burnett JC, Lim KI, Calafi A, Rossi JJ, Schaffer DV, Arkin A. Combinatorial latency reactivation for HIV-1 subtypes and variants. J Virol. 2010 Jun; 84(12):5958-74. PMID: 20357084.
        View in: PubMed
      142. Andrews SS, Addy NJ, Brent R, Arkin A. Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol. 2010 Mar; 6(3):e1000705. PMID: 20300644.
        View in: PubMed
      143. Price MN, Dehal PS, Arkin A. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMID: 20224823.
        View in: PubMed
      144. Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin A, Keasling JD. BglBricks: A flexible standard for biological part assembly. J Biol Eng. 2010; 4(1):1. PMID: 20205762.
        View in: PubMed
      145. He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, Keasling JD, Arkin A, Zhou J. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Appl Environ Microbiol. 2010 Mar; 76(5):1574-86. PMID: 20038696.
        View in: PubMed
      146. Skerker JM, Lucks JB, Arkin A. Evolution, ecology and the engineered organism: lessons for synthetic biology. Genome Biol. 2009; 10(11):114. PMID: 19941672.
        View in: PubMed
      147. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin A. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010 Jan; 38(Database issue):D396-400. PMID: 19906701.
        View in: PubMed
      148. Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin A, Dubchak I, Rodionov DA. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010 Jan; 38(Database issue):D111-8. PMID: 19884135.
        View in: PubMed
      149. Tang YJ, Martin HG, Deutschbauer A, Feng X, Huang R, Llora X, Arkin A, Keasling JD. Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations. Biotechnol Prog. 2009 Sep-Oct; 25(5):1254-9. PMID: 19610125.
        View in: PubMed
      150. Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HC, Zhou J, Wall JD, Hazen TC, Arkin A, Stahl DA. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environ Microbiol. 2009 Sep; 11(9):2244-52. PMID: 19737303.
        View in: PubMed
      151. Walker CB, He Z, Yang ZK, Ringbauer JA, He Q, Zhou J, Voordouw G, Wall JD, Arkin A, Hazen TC, Stolyar S, Stahl DA. The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol. 2009 Sep; 191(18):5793-801. PMID: 19581361.
        View in: PubMed
      152. Ross J, Arkin A. Complex systems: from chemistry to systems biology. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6433-4. PMID: 19380716.
        View in: PubMed
      153. Bischofs IB, Hug JA, Liu AW, Wolf DM, Arkin A. Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6459-64. PMID: 19380751.
        View in: PubMed
      154. Price MN, Dehal PS, Arkin A. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009 Jul; 26(7):1641-50. PMID: 19377059.
        View in: PubMed
      155. Jo WJ, Kim JH, Oh E, Jaramillo D, Holman P, Loguinov AV, Arkin A, Nislow C, Giaever G, Vulpe CD. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics. 2009; 10:130. PMID: 19321002.
        View in: PubMed
      156. Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin A, Zhou J. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics. 2009; 10:131. PMID: 19321007.
        View in: PubMed
      157. Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin A, Keasling JD, Wall JD. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Res. 2009 May; 37(9):2926-39. PMID: 19293273.
        View in: PubMed
      158. Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A, Arkin A, Keasling JD. Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism. Biotechnol Bioeng. 2009 Mar 1; 102(4):1161-9. PMID: 19031428.
        View in: PubMed
      159. Burnett JC, Miller-Jensen K, Shah PS, Arkin A, Schaffer DV. Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathog. 2009 Jan; 5(1):e1000260. PMID: 19132086.
        View in: PubMed
      160. Lucks JB, Qi L, Whitaker WR, Arkin A. Toward scalable parts families for predictable design of biological circuits. Curr Opin Microbiol. 2008 Dec; 11(6):567-73. PMID: 18983935.
        View in: PubMed
      161. Price MN, Dehal PS, Arkin A. FastBLAST: homology relationships for millions of proteins. PLoS One. 2008; 3(10):e3589. PMID: 18974889.
        View in: PubMed
      162. Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin A, Onstott TC. Environmental genomics reveals a single-species ecosystem deep within Earth. Science. 2008 Oct 10; 322(5899):275-8. PMID: 18845759.
        View in: PubMed
      163. Flaherty P, Radhakrishnan ML, Dinh T, Rebres RA, Roach TI, Jordan MI, Arkin A. A dual receptor crosstalk model of G-protein-coupled signal transduction. PLoS Comput Biol. 2008; 4(9):e1000185. PMID: 18818727.
        View in: PubMed
      164. Kazakov AE, Rodionov DA, Alm E, Arkin A, Dubchak I, Gelfand MS. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol. 2009 Jan; 191(1):52-64. PMID: 18820024.
        View in: PubMed
      165. Ham TS, Lee SK, Keasling JD, Arkin A. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS One. 2008; 3(7):e2815. PMID: 18665232.
        View in: PubMed
      166. Arkin A. Setting the standard in synthetic biology. Nat Biotechnol. 2008 Jul; 26(7):771-4. PMID: 18612298.
        View in: PubMed
      167. Singh AH, Wolf DM, Wang P, Arkin A. Modularity of stress response evolution. Proc Natl Acad Sci U S A. 2008 May 27; 105(21):7500-5. PMID: 18495925.
        View in: PubMed
      168. Wolf DM, Fontaine-Bodin L, Bischofs I, Price G, Keasling J, Arkin A. Memory in microbes: quantifying history-dependent behavior in a bacterium. PLoS One. 2008; 3(2):e1700. PMID: 18324309.
        View in: PubMed
      169. Price MN, Dehal PS, Arkin A. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 2008; 9(1):R4. PMID: 18179685.
        View in: PubMed
      170. Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin A, Stahl DA. Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol. 2007 Dec; 189(24):8944-52. PMID: 17921288.
        View in: PubMed
      171. Jo WJ, Loguinov A, Chang M, Wintz H, Nislow C, Arkin A, Giaever G, Vulpe CD. Identification of genes involved in the toxic response of Saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants. Toxicol Sci. 2008 Jan; 101(1):140-51. PMID: 17785683.
        View in: PubMed
      172. Price MN, Dehal PS, Arkin A. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol. 2007 Sep; 3(9):1739-50. PMID: 17845071.
        View in: PubMed
      173. Osterhout RE, Figueroa IA, Keasling JD, Arkin A. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 2007; 7:82. PMID: 17764558.
        View in: PubMed
      174. Anderson JC, Voigt CA, Arkin A. Environmental signal integration by a modular AND gate. Mol Syst Biol. 2007; 3:133. PMID: 17700541.
        View in: PubMed
      175. Bender KS, Yen HC, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin A, Wall JD. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 2007 Sep; 73(17):5389-400. PMID: 17630305.
        View in: PubMed
      176. Andrews SS, Arkin A. Systems biology: a switch for sex. Curr Biol. 2007 Jun 5; 17(11):R410-2. PMID: 17550765.
        View in: PubMed
      177. Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin A, Borglin SE, Dehal PS, Chakraborty R, Geller JT, Hazen TC, He Q, Joyner DC, Martin VJ, Wall JD, Yang ZK, Zhou J, Keasling JD. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J Bacteriol. 2007 Aug; 189(16):5996-6010. PMID: 17545284.
        View in: PubMed
      178. Andrews SS, Arkin A. A mechanical explanation for cytoskeletal rings and helices in bacteria. Biophys J. 2007 Sep 15; 93(6):1872-84. PMID: 17513368.
        View in: PubMed
      179. Samoilov MS, Price G, Arkin A. From fluctuations to phenotypes: the physiology of noise. Sci STKE. 2006 Dec 19; 2006(366):re17. PMID: 17179490.
        View in: PubMed
      180. Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 2007 Jan; 35(Database issue):D407-12. PMID: 17142223.
        View in: PubMed
      181. Alm E, Huang K, Arkin A. The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLoS Comput Biol. 2006 Nov 3; 2(11):e143. PMID: 17083272.
        View in: PubMed
      182. Samoilov MS, Arkin A. Deviant effects in molecular reaction pathways. Nat Biotechnol. 2006 Oct; 24(10):1235-40. PMID: 17033664.
        View in: PubMed
      183. Onsum MD, Wong K, Herzmark P, Bourne HR, Arkin A. Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification. Phys Biol. 2006 Sep; 3(3):190-9. PMID: 17021383.
        View in: PubMed
      184. Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan XF, Hazen TC, Arkin A, Wall JD, Zhou JZ, Fields MW. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Appl Environ Microbiol. 2006 Aug; 72(8):5578-88. PMID: 16885312.
        View in: PubMed
      185. Andrews SS, Arkin A. Simulating cell biology. Curr Biol. 2006 Jul 25; 16(14):R523-7. PMID: 16860723.
        View in: PubMed
      186. Price MN, Arkin A, Alm EJ. The life-cycle of operons. PLoS Genet. 2006 Jun; 2(6):e96. PMID: 16789824.
        View in: PubMed
      187. Mukhopadhyay A, He Z, Alm EJ, Arkin A, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, Oeller P, Redding A, Sun J, Wall J, Wei J, Yang Z, Yen HC, Zhou J, Keasling JD. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol. 2006 Jun; 188(11):4068-78. PMID: 16707698.
        View in: PubMed
      188. Feeley R, Frenklach M, Onsum M, Russi T, Arkin A, Packard A. Model discrimination using data collaboration. J Phys Chem A. 2006 Jun 1; 110(21):6803-13. PMID: 16722696.
        View in: PubMed
      189. He Q, Huang KH, He Z, Alm EJ, Fields MW, Hazen TC, Arkin A, Wall JD, Zhou J. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl Environ Microbiol. 2006 Jun; 72(6):4370-81. PMID: 16751553.
        View in: PubMed
      190. Ham TS, Lee SK, Keasling JD, Arkin A. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnol Bioeng. 2006 May 5; 94(1):1-4. PMID: 16534780.
        View in: PubMed
      191. Deutschbauer AM, Chivian D, Arkin A. Genomics for environmental microbiology. Curr Opin Biotechnol. 2006 Jun; 17(3):229-35. PMID: 16650754.
        View in: PubMed
      192. Price MN, Alm EJ, Arkin A. The histidine operon is ancient. J Mol Evol. 2006 Jun; 62(6):807-8. PMID: 16612542.
        View in: PubMed
      193. Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou J, Arkin A, Singh AK. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol. 2006 Mar; 188(5):1817-28. PMID: 16484192.
        View in: PubMed
      194. Leaphart AB, Thompson DK, Huang K, Alm E, Wan XF, Arkin A, Brown SD, Wu L, Yan T, Liu X, Wickham GS, Zhou J. Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. J Bacteriol. 2006 Feb; 188(4):1633-42. PMID: 16452448.
        View in: PubMed
      195. Price MN, Arkin A, Alm EJ. OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics. 2006; 7:19. PMID: 16412220.
        View in: PubMed
      196. Brown SD, 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 DK. Cellular response of Shewanella oneidensis to strontium stress. Appl Environ Microbiol. 2006 Jan; 72(1):890-900. PMID: 16391131.
        View in: PubMed
      197. Arkin A, Fletcher DA. Fast, cheap and somewhat in control. Genome Biol. 2006; 7(8):114. PMID: 16942631.
        View in: PubMed
      198. Anderson JC, Clarke EJ, Arkin A, Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol. 2006 Jan 27; 355(4):619-27. PMID: 16330045.
        View in: PubMed
      199. Rodionov DA, Dubchak IL, Arkin A, Alm EJ, Gelfand MS. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol. 2005 Oct; 1(5):e55. PMID: 16261196.
        View in: PubMed
      200. Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin A, Davis RW, Nislow C, Giaever G. Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet. 2005 Aug; 1(2):e24. PMID: 16121259.
        View in: PubMed
      201. Schwartz P, Adalsteinsson D, Colella P, Arkin A, Onsum M. Numerical computation of diffusion on a surface. Proc Natl Acad Sci U S A. 2005 Aug 9; 102(32):11151-6. PMID: 16076952.
        View in: PubMed
      202. Weinberger LS, Burnett JC, Toettcher JE, Arkin A, Schaffer DV. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005 Jul 29; 122(2):169-82. PMID: 16051143.
        View in: PubMed
      203. Rao CV, Kirby JR, Arkin A. Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles. Phys Biol. 2005 Sep; 2(3):148-58. PMID: 16224120.
        View in: PubMed
      204. Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin A. The MicrobesOnline Web site for comparative genomics. Genome Res. 2005 Jul; 15(7):1015-22. PMID: 15998914.
        View in: PubMed
      205. Price MN, Alm EJ, Arkin A. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res. 2005; 33(10):3224-34. PMID: 15942025.
        View in: PubMed
      206. Price MN, Huang KH, Arkin A, Alm EJ. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res. 2005 Jun; 15(6):809-19. PMID: 15930492.
        View in: PubMed
      207. Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin A. A latent variable model for chemogenomic profiling. Bioinformatics. 2005 Aug 1; 21(15):3286-93. PMID: 15919724.
        View in: PubMed
      208. Wolf DM, Vazirani VV, Arkin A. A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation. J Theor Biol. 2005 May 21; 234(2):255-62. PMID: 15757682.
        View in: PubMed
      209. Liu Y, Gao W, Wang Y, Wu L, Liu X, Yan T, Alm E, Arkin A, Thompson DK, Fields MW, Zhou J. Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions. J Bacteriol. 2005 Apr; 187(7):2501-7. PMID: 15774893.
        View in: PubMed
      210. Samoilov M, Plyasunov S, Arkin A. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A. 2005 Feb 15; 102(7):2310-5. PMID: 15701703.
        View in: PubMed
      211. Price MN, Huang KH, Alm EJ, Arkin A. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 2005; 33(3):880-92. PMID: 15701760.
        View in: PubMed
      212. Wolf DM, Vazirani VV, Arkin A. Diversity in times of adversity: probabilistic strategies in microbial survival games. J Theor Biol. 2005 May 21; 234(2):227-53. PMID: 15757681.
        View in: PubMed
      213. Gao H, Wang Y, Liu X, Yan T, Wu L, Alm E, Arkin A, Thompson DK, Zhou J. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol. 2004 Nov; 186(22):7796-803. PMID: 15516594.
        View in: PubMed
      214. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 2004; 5(11):R90. PMID: 15535866.
        View in: PubMed
      215. Rao CV, Frenklach M, Arkin A. An allosteric model for transmembrane signaling in bacterial chemotaxis. J Mol Biol. 2004 Oct 15; 343(2):291-303. PMID: 15451661.
        View in: PubMed
      216. Voigt CA, Wolf DM, Arkin A. The Bacillus subtilis sin operon: an evolvable network motif. Genetics. 2005 Mar; 169(3):1187-202. PMID: 15466432.
        View in: PubMed
      217. Vlad MO, Arkin A, Ross J. Response experiments for nonlinear systems with application to reaction kinetics and genetics. Proc Natl Acad Sci U S A. 2004 May 11; 101(19):7223-8. PMID: 15123834.
        View in: PubMed
      218. McAdams HH, Srinivasan B, Arkin A. The evolution of genetic regulatory systems in bacteria. Nat Rev Genet. 2004 Mar; 5(3):169-78. PMID: 14970819.
        View in: PubMed
      219. Rao CV, Kirby JR, Arkin A. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol. 2004 Feb; 2(2):E49. PMID: 14966542.
        View in: PubMed
      220. Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin A, Davis RW. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A. 2004 Jan 20; 101(3):793-8. PMID: 14718668.
        View in: PubMed
      221. Weinberger LS, Schaffer DV, Arkin A. Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection. J Virol. 2003 Sep; 77(18):10028-36. PMID: 12941913.
        View in: PubMed
      222. Wolf DM, Arkin A. Motifs, modules and games in bacteria. Curr Opin Microbiol. 2003 Apr; 6(2):125-34. PMID: 12732301.
        View in: PubMed
      223. Alm E, Arkin A. Biological networks. Curr Opin Struct Biol. 2003 Apr; 13(2):193-202. PMID: 12727512.
        View in: PubMed
      224. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin A, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003 Mar 1; 19(4):524-31. PMID: 12611808.
        View in: PubMed
      225. Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, Ross EM, Stull JT, Taussig R, Bourne HR, Arkin AP, Cobb MH, Cyster JG, Devreotes PN, Ferrell JE, Fruman D, Gold M, Weiss A, Stull JT, Berridge MJ, Cantley LC, Catterall WA, Coughlin SR, Olson EN, Smith TF, Brugge JS, Botstein D, Dixon JE, Hunter T, Lefkowitz RJ, Pawson AJ, Sternberg PW, Varmus H, Subramaniam S, Sinkovits RS, Li J, Mock D, Ning Y, Saunders B, Sternweis PC, Hilgemann D, Scheuermann RH, DeCamp D, Hsueh R, Lin KM, Ni Y, Seaman WE, Simpson PC, O'Connell TD, Roach T, Simon MI, Choi S, Eversole-Cire P, Fraser I, Mumby MC, Zhao Y, Brekken D, Shu H, Meyer T, Chandy G, Heo WD, Liou J, O'Rourke N, Verghese M, Mumby SM, Han H, Brown HA, Forrester JS, Ivanova P, Milne SB, Casey PJ, Harden TK, Arkin AP, Doyle J, Gray ML, Meyer T, Michnick S, Schmidt MA, Toner M, Tsien RY, Natarajan M, Ranganathan R, Sambrano GR. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12; 420(6916):703-6. PMID: 12478301.
        View in: PubMed
      226. Rao CV, Wolf DM, Arkin A. Control, exploitation and tolerance of intracellular noise. Nature. 2002 Nov 14; 420(6912):231-7. PMID: 12432408.
        View in: PubMed
      227. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin A, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kötter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002 Jul 25; 418(6896):387-91. PMID: 12140549.
        View in: PubMed
      228. Vance W, Arkin A, Ross J. Determination of causal connectivities of species in reaction networks. Proc Natl Acad Sci U S A. 2002 Apr 30; 99(9):5816-21. PMID: 11983885.
        View in: PubMed
      229. Gilman A, Arkin A. Genetic "code": representations and dynamical models of genetic components and networks. Annu Rev Genomics Hum Genet. 2002; 3:341-69. PMID: 12142360.
        View in: PubMed
      230. Wolf DM, Arkin A. Fifteen minutes of fim: control of type 1 pili expression in E. coli. OMICS. 2002; 6(1):91-114. PMID: 11881836.
        View in: PubMed
      231. Arkin A. Synthetic cell biology. Curr Opin Biotechnol. 2001 Dec; 12(6):638-44. PMID: 11849948.
        View in: PubMed
      232. Samoilov M, Arkin A, Ross J. On the deduction of chemical reaction pathways from measurements of time series of concentrations. Chaos. 2001 Mar; 11(1):108-114. PMID: 12779446.
        View in: PubMed
      233. Rao CV, Arkin A. Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng. 2001; 3:391-419. PMID: 11447069.
        View in: PubMed
      234. Arkin A, Saito TR, Takahashi K, Amao H, Takahashi KW. Marking behavior is innate and not learned in the Mongolian gerbil. Exp Anim. 2000 Jul; 49(3):205-9. PMID: 11109543.
        View in: PubMed
      235. McAdams HH, Arkin A. Towards a circuit engineering discipline. Curr Biol. 2000 Apr 20; 10(8):R318-20. PMID: 10801411.
        View in: PubMed
      236. Arkin A, Saito TR, Takahashi K, Sugiyama M, Aokikomori S, Amao H, Takahashi KW. Observation of marking-like behavior, marking behavior, and growth of the scent gland in young Mongolian gerbils (Meriones unguiculatus) of an inbred strain. Exp Anim. 1999 Oct; 48(4):269-76. PMID: 10591007.
        View in: PubMed
      237. McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999 Feb; 15(2):65-9. PMID: 10098409.
        View in: PubMed
      238. Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 1998 Aug; 149(4):1633-48. PMID: 9691025.
        View in: PubMed
      239. McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annu Rev Biophys Biomol Struct. 1998; 27:199-224. PMID: 9646867.
        View in: PubMed
      240. Swanson CA, Arkin A, Ross J. An endogenous calcium oscillator may control early embryonic division. Proc Natl Acad Sci U S A. 1997 Feb 18; 94(4):1194-9. PMID: 9037029.
        View in: PubMed
      241. McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A. 1997 Feb 4; 94(3):814-9. PMID: 9023339.
        View in: PubMed
      242. Arkin A, Ross J. Computational functions in biochemical reaction networks. Biophys J. 1994 Aug; 67(2):560-78. PMID: 7948674.
        View in: PubMed
      243. Arkin A, Youvan DC. An algorithm for protein engineering: simulations of recursive ensemble mutagenesis. Proc Natl Acad Sci U S A. 1992 Aug 15; 89(16):7811-5. PMID: 1502200.
        View in: PubMed
      244. Arkin A, Youvan DC. Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis. Biotechnology (N Y). 1992 Mar; 10(3):297-300. PMID: 1368102.
        View in: PubMed
      245. Arkin A, Goldman ER, Robles SJ, Goddard CA, Coleman WJ, Yang MM, Youvan DC. Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra. Biotechnology (N Y). 1990 Aug; 8(8):746-9. PMID: 1366901.
        View in: PubMed

      Collapse ORNG Applications 
      Collapse Websites

      A U.S. Department of Energy National Laboratory Managed by the University of California

      This site is running Profiles RNS version v2.10.1-414-g6fb82b0a.