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Arkin, Adam

TitleArea Deputy, Faculty
InstitutionLawrence Berkeley National Lab
DepartmentEnviron Genomics & Systems Bio
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/495-2116
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    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 Research 
    Collapse Research Activities and Funding
    Controlled Diversity in Bacterial Stress Response
    NIH/NIGMS R01GM073010Mar 3, 2006 - Aug 31, 2011
    Role: Principal Investigator
    Investigation of Promoter Sequence-Function Relationships in a Model Retrovirus
    NIH/NIGMS R01GM073058Oct 1, 2004 - Mar 31, 2015
    Role: Co-Principal Investigator
    BIOCOMPLEXITY:ANALYSIS, DESIGN, EVOLUTION-COMPLEX GENES
    NIH/NIGMS R01GM063525Jun 2, 2001 - Dec 31, 2004
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    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.
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    1. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin A, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature. 2018 May; 557(7706):503-509. PMID: 29769716.
      View in: PubMed
    2. Paradis CJ, Dixon ER, Lui LM, Arkin A, Parker JC, Istok JD, Perfect E, McKay LD, Hazen TC. Improved Method for Estimating Reaction Rates During Push-Pull Tests. Ground Water. 2018 Apr 15. PMID: 29656383.
      View in: PubMed
    3. Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin A, Elias DA. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. PLoS One. 2018; 13(3):e0194663. PMID: 29558522.
      View in: PubMed
    4. Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin A, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. Elife. 2018 Mar 09; 7. PMID: 29521624.
      View in: PubMed
    5. He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin A, Zhou J. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. MBio. 2018 Feb 20; 9(1). PMID: 29463661.
      View in: PubMed
    6. Liu H, Price MN, Waters RJ, Ray J, Carlson HK, Lamson JS, Chakraborty R, Arkin A, Deutschbauer AM. Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria. mSystems. 2018 Jan-Feb; 3(1). PMID: 29359196.
      View in: PubMed
    7. Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin A. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PLoS Genet. 2018 01; 14(1):e1007147. PMID: 29324779.
      View in: PubMed
    8. Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin A, Zhou J. Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. MBio. 2017 Nov 14; 8(6). PMID: 29138306.
      View in: PubMed
    9. Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin A, Skerker JM, Gladden JM. Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnol Biofuels. 2017; 10:241. PMID: 29075325.
      View in: PubMed
    10. De León KB, Zane GM, Trotter VV, Krantz GP, Arkin A, Butland GP, Walian PJ, Fields MW, Wall JD. Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. MBio. 2017 Oct 17; 8(5). PMID: 29042504.
      View in: PubMed
    11. Rand JM, Pisithkul T, Clark RL, Thiede JM, Mehrer CR, Agnew DE, Campbell CE, Markley AL, Price MN, Ray J, Wetmore KM, Suh Y, Arkin A, Deutschbauer AM, Amador-Noguez D, Pfleger BF. A metabolic pathway for catabolizing levulinic acid in bacteria. Nat Microbiol. 2017 Dec; 2(12):1624-1634. PMID: 28947739.
      View in: PubMed
    12. Price MN, Arkin A. PaperBLAST: Text Mining Papers for Information about Homologs. mSystems. 2017 Jul-Aug; 2(4). PMID: 28845458.
      View in: PubMed
    13. Thorgersen MP, Lancaster WA, Ge X, Zane GM, Wetmore KM, Vaccaro BJ, Poole FL, Younkin AD, Deutschbauer AM, Arkin A, Wall JD, Adams MWW. Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions. Front Microbiol. 2017; 8:1529. PMID: 28848534.
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    14. 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
    15. 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
    16. Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin A. Programming mRNA decay to modulate synthetic circuit resource allocation. Nat Commun. 2017 Apr 26; 8:15128. PMID: 28443619.
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    17. Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin A, Keasling JD, Martín HG. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC Bioinformatics. 2017 Apr 18; 18(1):219. PMID: 28420344.
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    18. Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin A, Keasling JD, Martín HG. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC Bioinformatics. 2017 Apr 05; 18(1):205. PMID: 28381205.
      View in: PubMed
    19. 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 Apr 04; 51(7):3609-3620. PMID: 28300407.
      View in: PubMed
    20. Kim SR, Skerker JM, Kong II, 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 03; 40:176-185. PMID: 28216106.
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    21. King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, 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 Mar 07; 51(5):2879-2889. PMID: 28112946.
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    22. 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
    23. 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
    24. 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 sp. Strain UFO1 Binds Uranium. Appl Environ Microbiol. 2017 Feb 15; 83(4). PMID: 27913415.
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    25. Menezes AA, Vilardi RF, Arkin A, Cohen MJ. Targeted clinical control of trauma patient coagulation through a thrombin dynamics model. Sci Transl Med. 2017 01 04; 9(371). PMID: 28053156.
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    26. Maurer MJ, Sutardja L, Pinel D, Bauer S, Muehlbauer AL, Ames TD, Skerker JM, Arkin A. Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait. ACS Synth Biol. 2017 03 17; 6(3):566-581. PMID: 27936603.
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    27. 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.
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    28. 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.
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    29. 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.
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    30. 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 10 01; 82(19):6046-56. PMID: 27474723.
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    31. Price MN, Arkin A. A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biol Evol. 2016 07 02; 8(6):1917-28. PMID: 27289091; PMCID: PMC4943197.
    32. 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 08; 353(6295):126-7. PMID: 27256881.
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    33. 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 06 15; 82(12):3631-3639. PMID: 27084006.
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    34. 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.
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    35. 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 08 19; 44(14):7006. PMID: 27131373.
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    36. 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 07 15; 5(7):561-8. PMID: 27072506.
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    37. 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 Apr 05; 7(2):e02234-15. PMID: 27048805; PMCID: PMC4817265.
    38. 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 07 15; 5(7):569-76. PMID: 26885935.
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    39. Price MN, Arkin A. Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes. MBio. 2015 Dec 15; 6(6):e01302-15. PMID: 26670382; PMCID: PMC4701828.
    40. Menezes AA, Montague MG, Cumbers J, Hogan JA, Arkin A. Grand challenges in space synthetic biology. J R Soc Interface. 2015 Dec 06; 12(113):20150803. PMID: 26631337; PMCID: PMC4707852.
    41. 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.
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    42. 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 Nov 05; 3(6). PMID: 26543109; PMCID: PMC4645194.
    43. 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.
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    44. 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.
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    45. 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; PMCID: PMC4628106.
    46. 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 01; 112(48):E6634-43. PMID: 26508635; PMCID: PMC4672817.
    47. 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 03; 49(21):12922-31. PMID: 25835088.
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    48. 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. 2016 01 01; 82(1):51-61. PMID: 26452555.
      View in: PubMed
    49. 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 Sep 24; 3(5). PMID: 26404608; PMCID: PMC4582584.
    50. Martín HG, 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; PMCID: PMC4574858.
    51. 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; 81(15):4976-83. PMID: 25979890; PMCID: PMC4495186.
    52. 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 May 14; 3(3). PMID: 25977418; PMCID: PMC4432324.
    53. 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 May 12; 6(3):e00326-15. PMID: 25968645; PMCID: PMC4436078.
    54. 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 May 12; 6(3):e00306-15. PMID: 25968644; PMCID: PMC4436071.
    55. 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 May 12; 6(3):e00233-15. PMID: 25968643; PMCID: PMC4436054.
    56. 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 May 05; 11(5):806. PMID: 25943345; PMCID: PMC4461400.
    57. 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; PMCID: PMC4524159.
    58. 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; PMCID: PMC4611501 [Available on 11/01/16].
    59. 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 Mar 12; 3(2). PMID: 25767232; PMCID: PMC4357754.
    60. 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.
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    61. 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.
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    62. Menezes AA, Cumbers J, Hogan JA, Arkin A. Towards synthetic biological approaches to resource utilization on space missions. J R Soc Interface. 2015 Jan 06; 12(102):20140715. PMID: 25376875; PMCID: PMC4277073.
    63. 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; PMCID: PMC4438318.
    64. 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; PMCID: PMC4215793.
    65. 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; PMCID: PMC4141834.
    66. 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 Aug 19; 3. PMID: 25139909; PMCID: PMC4161972.
    67. 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; 196(20):3643-55. PMID: 25112473; PMCID: PMC4187699.
    68. Shao W, Price MN, Deutschbauer AM, Romine MF, Arkin A. Conservation of transcription start sites within genes across a bacterial genus. MBio. 2014 Jul 01; 5(4):e01398-14. PMID: 24987095; PMCID: PMC4161247.
    69. 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; PMCID: PMC4215863.
    70. 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; 32(6):524-7. PMID: 24911492; PMCID: PMC4112958.
    71. 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 May 27; 5(3):e01041-14. PMID: 24865553; PMCID: PMC4045070.
    72. 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.
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    73. Qi LS, Arkin A. A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol. 2014 May; 12(5):341-54. PMID: 24736794.
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    74. 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; PMCID: PMC4001038.
    75. 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.
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    76. 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 04; 111(9):E836-45. PMID: 24550501; PMCID: PMC3948316.
    77. Guimaraes JC, Rocha M, Arkin A. Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res. 2014 Apr; 42(8):4791-9. PMID: 24510099; PMCID: PMC4005695.
    78. Guimaraes JC, Rocha M, Arkin A, Cambray G. D-Tailor: automated analysis and design of DNA sequences. Bioinformatics. 2014 04 15; 30(8):1087-1094. PMID: 24398007.
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    79. 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; PMCID: PMC3871698.
    80. Arkin A. A wise consistency: engineering biology for conformity, reliability, predictability. Curr Opin Chem Biol. 2013 Dec; 17(6):893-901. PMID: 24268562.
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    81. 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 Nov 01; 14:745. PMID: 24175918; PMCID: PMC3840689.
    82. 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.
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    83. 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.
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    84. 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; PMCID: PMC3807489.
    85. 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 03; 47(17):9841-9. PMID: 23889170.
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    86. 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; PMCID: PMC3752251.
    87. 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; PMCID: PMC3807478.
    88. 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.
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    89. 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; PMCID: PMC3708878.
    90. 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 Jun 18; 9:674. PMID: 23774757; PMCID: PMC3964314.
    91. 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 Apr 16; 9:660. PMID: 23591776; PMCID: PMC3658271.
    92. 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; PMCID: PMC3749499.
    93. 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 Apr 11; 1(2):e0014413. PMID: 23580709; PMCID: PMC3624683.
    94. 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 Apr 02; 14:213. PMID: 23547897; PMCID: PMC3639892.
    95. 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; PMCID: PMC3643576.
    96. 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.
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    97. 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.
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    98. 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.
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    99. 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; PMCID: PMC3664290.
    100. 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; PMCID: PMC3582614.
    101. 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; PMCID: PMC3764933.
    102. 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; PMCID: PMC3551603.
    103. Wang L, Wang X, Arkin A, Samoilov MS. Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinformatics. 2013 Feb 01; 29(3):338-46. PMID: 23271269; PMCID: PMC3562072.
    104. 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; PMCID: PMC3571329.
    105. 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; PMCID: PMC3531168.
    106. 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.
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    107. 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; PMCID: PMC3536172.
    108. 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; PMCID: PMC3497815.
    109. 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; PMCID: PMC3457247.
    110. 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.
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    111. 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.
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    112. 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; PMCID: PMC3430306.
    113. 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; PMCID: PMC3486112.
    114. 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; PMCID: PMC3475374.
    115. 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; PMCID: PMC3394319.
    116. 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 Jun 13; 11:79. PMID: 22694848; PMCID: PMC3460784.
    117. 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; PMCID: PMC3440575.
    118. 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; PMCID: PMC3408205.
    119. 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; PMCID: PMC3362694.
    120. 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 Apr 16; 13:138. PMID: 22507456; PMCID: PMC3431258.
    121. Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin A. Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol. 2012 Mar 25; 8(5):447-54. PMID: 22446835.
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    122. 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; PMCID: PMC3384300.
    123. 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; PMCID: PMC3302606.
    124. 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 09; 287(11):7945-55. PMID: 22253435; PMCID: PMC3318752.
    125. 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; PMCID: PMC3501275.
    126. 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; PMCID: PMC3273024.
    127. 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; PMCID: PMC3219624.
    128. 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 Oct 12; 12(10):R99. PMID: 21992415; PMCID: PMC3333781.
    129. 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; PMCID: PMC3241671.
    130. 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; PMCID: PMC3236048.
    131. Cambray G, Mutalik VK, Arkin A. Toward rational design of bacterial genomes. Curr Opin Microbiol. 2011 Oct; 14(5):624-30. PMID: 21865081.
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    132. 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; PMCID: PMC3187205.
    133. 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; PMCID: PMC3145043.
    134. 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; PMCID: PMC3125180.
    135. 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.
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    136. 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 Jun 15; 12 Suppl 1:S3. PMID: 21810205; PMCID: PMC3223726.
    137. 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 05; 108(27):11069-74. PMID: 21642536; PMCID: PMC3131376.
    138. 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 05; 108(27):11063-8. PMID: 21642531; PMCID: PMC3131332.
    139. 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; PMCID: PMC3125797.
    140. 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; PMCID: PMC3133309.
    141. 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.
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    142. 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; PMCID: PMC3102349.
    143. Arkin A, Schaffer DV. Network news: innovations in 21st century systems biology. Cell. 2011 Mar 18; 144(6):844-9. PMID: 21414475.
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    144. Huang YW, Arkin A, Chandonia JM. WIST: toolkit for rapid, customized LIMS development. Bioinformatics. 2011 Feb 01; 27(3):437-8. PMID: 21258060; PMCID: PMC3031042.
    145. 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.
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    146. Liu CC, Arkin A. Cell biology. The case for RNA. Science. 2010 Nov 26; 330(6008):1185-6. PMID: 21109657.
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    147. 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 Oct 22; 5(10):e13564. PMID: 21042592; PMCID: PMC2962647.
    148. 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.
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    149. 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; PMCID: PMC3008519.
    150. 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 Sep 30; 6(9). PMID: 20941390; PMCID: PMC2947985.
    151. 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 Aug 12; 6(8). PMID: 20711350; PMCID: PMC2920833.
    152. 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; PMCID: PMC2896116.
    153. 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; PMCID: PMC2919733.
    154. 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.
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    155. 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; PMCID: PMC2876650.
    156. Andrews SS, Addy NJ, Brent R, Arkin A. Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol. 2010 Mar 12; 6(3):e1000705. PMID: 20300644; PMCID: PMC2837389.
    157. Price MN, Dehal PS, Arkin A. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010 Mar 10; 5(3):e9490. PMID: 20224823.
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    158. 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 Jan 20; 4(1):1. PMID: 20205762; PMCID: PMC2822740.
    159. 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; PMCID: PMC2832388.
    160. Skerker JM, Lucks JB, Arkin A. Evolution, ecology and the engineered organism: lessons for synthetic biology. Genome Biol. 2009; 10(11):114. PMID: 19941672; PMCID: PMC3091310.
    161. 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; PMCID: PMC2808868.
    162. 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; PMCID: PMC2808921.
    163. 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.
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    164. 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.
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    165. 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; PMCID: PMC2737945.
    166. 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; PMCID: PMC2672531.
    167. 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; PMCID: PMC2672556.
    168. 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; PMCID: PMC2693737.
    169. 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 Mar 25; 10:131. PMID: 19321007; PMCID: PMC2667191.
    170. 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 Mar 25; 10:130. PMID: 19321002; PMCID: PMC2669097.
    171. 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; PMCID: PMC2685097.
    172. 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 01; 102(4):1161-9. PMID: 19031428.
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    173. 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; PMCID: PMC2607019.
    174. 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.
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    175. Price MN, Dehal PS, Arkin A. FastBLAST: homology relationships for millions of proteins. PLoS One. 2008; 3(10):e3589. PMID: 18974889; PMCID: PMC2571987.
    176. 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.
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    177. 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; PMCID: PMC2612455.
    178. 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 Sep 26; 4(9):e1000185. PMID: 18818727; PMCID: PMC2528964.
    179. 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 Jul 30; 3(7):e2815. PMID: 18665232; PMCID: PMC2481393.
    180. Arkin A. Setting the standard in synthetic biology. Nat Biotechnol. 2008 Jul; 26(7):771-4. PMID: 18612298.
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    181. 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; PMCID: PMC2396705.
    182. 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 Feb 27; 3(2):e1700. PMID: 18324309; PMCID: PMC2264733.
    183. Price MN, Dehal PS, Arkin A. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 2008 Jan 07; 9(1):R4. PMID: 18179685.
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    184. 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; PMCID: PMC2168612.
    185. 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.
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    186. 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; PMCID: PMC1971122.
    187. Osterhout RE, Figueroa IA, Keasling JD, Arkin A. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 2007 Aug 31; 7:82. PMID: 17764558; PMCID: PMC2147009.
    188. Anderson JC, Voigt CA, Arkin A. Environmental signal integration by a modular AND gate. Mol Syst Biol. 2007; 3:133. PMID: 17700541; PMCID: PMC1964800.
    189. 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; PMCID: PMC2042090.
    190. Andrews SS, Arkin A. Systems biology: a switch for sex. Curr Biol. 2007 Jun 05; 17(11):R410-2. PMID: 17550765.
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    191. 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; PMCID: PMC1952033.
    192. 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; PMCID: PMC1959564.
    193. Samoilov MS, Price G, Arkin A. From fluctuations to phenotypes: the physiology of noise. Sci STKE. 2006 Dec 19; 2006(366):re17. PMID: 17179490.
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    194. 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; PMCID: PMC1669780.
    195. 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 03; 2(11):e143. PMID: 17083272; PMCID: PMC1630713.
    196. Samoilov MS, Arkin A. Deviant effects in molecular reaction pathways. Nat Biotechnol. 2006 Oct; 24(10):1235-40. PMID: 17033664.
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    197. Onsum MD, Wong K, Herzmark P, Bourne HR, Arkin A. Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification. Phys Biol. 2006 Sep 25; 3(3):190-9. PMID: 17021383.
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    198. Andrews SS, Arkin A. Simulating cell biology. Curr Biol. 2006 Jul 25; 16(14):R523-7. PMID: 16860723.
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    199. Price MN, Arkin A, Alm EJ. The life-cycle of operons. PLoS Genet. 2006 Jun; 2(6):e96. PMID: 16789824; PMCID: PMC1480536.
    200. 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; PMCID: PMC1489655.
    201. 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; PMCID: PMC1482918.
    202. Feeley R, Frenklach M, Onsum M, Russi T, Arkin A, Packard A. Model discrimination using data collaboration. J Phys Chem A. 2006 Jun 01; 110(21):6803-13. PMID: 16722696.
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    203. Ham TS, Lee SK, Keasling JD, Arkin A. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnol Bioeng. 2006 May 05; 94(1):1-4. PMID: 16534780.
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    204. Deutschbauer AM, Chivian D, Arkin A. Genomics for environmental microbiology. Curr Opin Biotechnol. 2006 Jun; 17(3):229-35. PMID: 16650754.
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    205. Price MN, Alm EJ, Arkin A. The histidine operon is ancient. J Mol Evol. 2006 Jun; 62(6):807-8. PMID: 16612542.
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    206. 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; PMCID: PMC1367224.
    207. Price MN, Arkin A, Alm EJ. OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics. 2006 Jan 13; 7:19. PMID: 16412220; PMCID: PMC1397872.
    208. 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; PMCID: PMC1352239.
    209. Arkin A, Fletcher DA. Fast, cheap and somewhat in control. Genome Biol. 2006; 7(8):114. PMID: 16942631; PMCID: PMC1779602.
    210. 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.
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    211. 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; PMCID: PMC1274295.
    212. 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; PMCID: PMC1189734.
    213. 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 09; 102(32):11151-6. PMID: 16076952; PMCID: PMC1183587.
    214. 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.
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    215. Rao CV, Kirby JR, Arkin A. Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles. Phys Biol. 2005 Jul 14; 2(3):148-58. PMID: 16224120.
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    216. 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; PMCID: PMC1172046.
    217. 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; PMCID: PMC1143696.
    218. 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; PMCID: PMC1142471.
    219. Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin A. A latent variable model for chemogenomic profiling. Bioinformatics. 2005 Aug 01; 21(15):3286-93. PMID: 15919724.
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    220. 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.
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    221. 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; PMCID: PMC1065217.
    222. 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; PMCID: PMC548975.
    223. 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; PMCID: PMC549399.
    224. 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.
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    225. 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; PMCID: PMC524878.
    226. 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; PMCID: PMC545781.
    227. 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.
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    228. Voigt CA, Wolf DM, Arkin A. The Bacillus subtilis sin operon: an evolvable network motif. Genetics. 2005 Mar; 169(3):1187-202. PMID: 15466432; PMCID: PMC1449569.
    229. 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; PMCID: PMC409900.
    230. 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.
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    231. 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; PMCID: PMC340952.
    232. 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; PMCID: PMC321760.
    233. 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; PMCID: PMC224590.
    234. Wolf DM, Arkin A. Motifs, modules and games in bacteria. Curr Opin Microbiol. 2003 Apr; 6(2):125-34. PMID: 12732301.
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    235. Alm E, Arkin A. Biological networks. Curr Opin Struct Biol. 2003 Apr; 13(2):193-202. PMID: 12727512.
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    236. 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.
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    237. Rao CV, Wolf DM, Arkin A. Control, exploitation and tolerance of intracellular noise. Nature. 2002 Nov 14; 420(6912):231-7. PMID: 12432408.
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    238. 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.
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    239. 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; PMCID: PMC122859.
    240. 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.
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    241. 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.
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    242. Arkin A. Synthetic cell biology. Curr Opin Biotechnol. 2001 Dec; 12(6):638-44. PMID: 11849948.
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