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    Mukhopadhyay, Aindrila

    TitleBiological Engineer Senior Sci
    SchoolLawrence Berkeley National Lab
    DepartmentBiological Systems & Eng
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/495-2628
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      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. Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H. The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization. ACS Synth Biol. 2017 Sep 08. PMID: 28826210.
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      2. Shymansky CM, Wang G, Baidoo EEK, Gin J, Apel AR, Mukhopadhyay A, García Martín H, Keasling JD. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. Front Bioeng Biotechnol. 2017; 5:31. PMID: 28596955.
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      3. Parisutham V, Chandran SP, Mukhopadhyay A, Lee SK, Keasling JD. Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries. Bioresour Technol. 2017 Sep; 239:496-506. PMID: 28535986.
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      4. Liang Y, Richardson S, Yan J, Benites VT, Cheng-Yue C, Tran T, Mortimer J, Mukhopadhyay A, Keasling JD, Scheller HV, Loqué D. Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants. ACS Synth Biol. 2017 May 19; 6(5):806-816. PMID: 28094975.
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      5. Thorgersen MP, Lancaster WA, Rajeev L, Ge X, Vaccaro BJ, Poole FL, Arkin AP, 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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      6. Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EE, Petzold CJ, Keasling JD, Mukhopadhyay A. Engineering glucose metabolism of Escherichia coli under nitrogen starvation. NPJ Syst Biol Appl. 2017; 3:16035. PMID: 28725483.
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      7. Reider Apel A, d'Espaux L, Wehrs M, Sachs D, Li RA, Tong GJ, Garber M, Nnadi O, Zhuang W, Hillson NJ, Keasling JD, Mukhopadhyay A. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae. Nucleic Acids Res. 2017 Jan 09; 45(1):496-508. PMID: 27899650.
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      8. Eudes A, Mouille M, Robinson DS, Benites VT, Wang G, Roux L, Tsai YL, Baidoo EE, Chiu TY, Heazlewood JL, Scheller HV, Mukhopadhyay A, Keasling JD, Deutsch S, Loqué D. Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast. Microb Cell Fact. 2016 Nov 21; 15(1):198. PMID: 27871334.
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      9. Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EE, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ. Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using ?pfk mutants. Biotechnol Biofuels. 2016; 9:212. PMID: 27766116.
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      10. Kothari A, Charrier M, Wu YW, Malfatti S, Zhou CE, Singer SW, Dugan L, Mukhopadhyay A. Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization. FEMS Microbiol Lett. 2016 Oct; 363(20). PMID: 27664055.
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      11. Brown ME, Mukhopadhyay A, Keasling JD. Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol. ACS Synth Biol. 2016 12 16; 5(12):1485-1496. PMID: 27403844.
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      12. Fortman JL, Mukhopadhyay A. The Future of Antibiotics: Emerging Technologies and Stewardship. Trends Microbiol. 2016 Jul; 24(7):515-7. PMID: 27229181.
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      13. Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl. 2016; 2:16009. PMID: 28725470.
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      14. Reider Apel A, Ouellet M, Szmidt-Middleton H, Keasling JD, Mukhopadhyay A. Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae. Sci Rep. 2016 Jan 19; 6:19512. PMID: 26781725; PMCID: PMC4726032.
      15. Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS. s54-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics. 2015 Nov 10; 16:919. PMID: 26555820; PMCID: PMC4641369.
      16. 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.
      17. Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A. Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium. J Bacteriol. 2015 Nov; 197(21):3400-8. PMID: 26283774; PMCID: PMC4621071.
      18. Mukhopadhyay A. Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends Microbiol. 2015 Aug; 23(8):498-508. PMID: 26024777.
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      19. Chubukov V, Mingardon F, Schackwitz W, Baidoo EE, Alonso-Gutierrez J, Hu Q, Lee TS, Keasling JD, Mukhopadhyay A. Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC. Appl Environ Microbiol. 2015 Jul; 81(14):4690-6. PMID: 25934627; PMCID: PMC4551201.
      20. Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Front Microbiol. 2015; 6:277. PMID: 25926821; PMCID: PMC4396413.
      21. Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A. Improving olefin tolerance and production in E. coli using native and evolved AcrB. Biotechnol Bioeng. 2015 May; 112(5):879-88. PMID: 25450012; PMCID: PMC4406151.
      22. Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS, Leong S, Mukhopadhyay A. Improving microbial biogasoline production in Escherichia coli using tolerance engineering. MBio. 2014 Nov 04; 5(6):e01932. PMID: 25370492; PMCID: PMC4222104.
      23. Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. PLoS Comput Biol. 2014 Sep; 10(9):e1003827. PMID: 25188426; PMCID: PMC4154649.
      24. Rajeev L, Luning EG, Altenburg S, Zane GM, Baidoo EE, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. Front Microbiol. 2014; 5:382. PMID: 25120537; PMCID: PMC4114195.
      25. Rajeev L, Luning EG, Mukhopadhyay A. DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. J Vis Exp. 2014 Jul 21; (89). PMID: 25079303; PMCID: PMC4233932.
      26. Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One. 2014; 9(7):e101115. PMID: 24983352; PMCID: PMC4077768.
      27. Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson JJ, Auer M, Wall JD, Mukhopadhyay A. Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. Front Microbiol. 2014; 5:77. PMID: 24639670; PMCID: PMC3944678.
      28. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol. 2013 Nov; 31(11):1039-46. PMID: 24142050.
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      29. Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, 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.
      30. Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J. 2013 Nov; 7(11):2178-91. PMID: 23739051; PMCID: PMC3806265.
      31. Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, 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.
      32. Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling JD. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng. 2012 Nov; 14(6):653-60. PMID: 23026122.
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      33. Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, 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.
      34. Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, Batth T, Benke PI, D'haeseleer P, Sun N, Sale KL, Keasling JD, Lee TS, Petzold CJ, Mukhopadhyay A, Singer SW, Simmons BA, Gladden JM. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One. 2012; 7(5):e37010. PMID: 22649505; PMCID: PMC3359315.
      35. Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, 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.
      36. Eudes A, George A, Mukerjee P, Kim JS, Pollet B, Benke PI, Yang F, Mitra P, Sun L, Cetinkol OP, Chabout S, Mouille G, Soubigou-Taconnat L, Balzergue S, Singh S, Holmes BM, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loqué D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. 2012 Jun; 10(5):609-20. PMID: 22458713.
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      37. Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, Heazlewood JL. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol. 2012 May; 159(1):12-26. PMID: 22430844; PMCID: PMC3375956.
      38. Rautengarten C, Ebert B, Ouellet M, Nafisi M, Baidoo EE, Benke P, Stranne M, Mukhopadhyay A, Keasling JD, Sakuragi Y, Scheller HV. Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of ?-hydroxy fatty acids in cutin polyester. Plant Physiol. 2012 Feb; 158(2):654-65. PMID: 22158675; PMCID: PMC3271757.
      39. Juminaga D, Baidoo EE, Redding-Johanson AM, Batth TS, Burd H, Mukhopadhyay A, Petzold CJ, Keasling JD. Modular engineering of L-tyrosine production in Escherichia coli. Appl Environ Microbiol. 2012 Jan; 78(1):89-98. PMID: 22020510; PMCID: PMC3255607.
      40. Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, 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.
      41. Peralta-Yahya PP, Ouellet M, Chan R, Mukhopadhyay A, Keasling JD, Lee TS. Identification and microbial production of a terpene-based advanced biofuel. Nat Commun. 2011 Sep 27; 2:483. PMID: 21952217; PMCID: PMC3195254.
      42. Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP. 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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      43. Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol. 2011 May 10; 7:487. PMID: 21556065; PMCID: PMC3130554.
      44. Rautengarten C, Ebert B, Herter T, Petzold CJ, Ishii T, Mukhopadhyay A, Usadel B, Scheller HV. The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis. Plant Cell. 2011 Apr; 23(4):1373-90. PMID: 21478444; PMCID: PMC3101560.
      45. Ito J, Batth TS, Petzold CJ, Redding-Johanson AM, Mukhopadhyay A, Verboom R, Meyer EH, Millar AH, Heazlewood JL. Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism. J Proteome Res. 2011 Apr 01; 10(4):1571-82. PMID: 21166475.
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      46. Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ. Targeted proteomics for metabolic pathway optimization: application to terpene production. Metab Eng. 2011 Mar; 13(2):194-203. PMID: 21215324.
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      47. 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 AP, 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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      48. Cong Y, Baker ML, Jakana J, Woolford D, Miller EJ, Reissmann S, Kumar RN, Redding-Johanson AM, Batth TS, Mukhopadhyay A, Ludtke SJ, Frydman J, Chiu W. 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci U S A. 2010 Mar 16; 107(11):4967-72. PMID: 20194787; PMCID: PMC2841888.
      49. Dunlop MJ, Keasling JD, Mukhopadhyay A. A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol. 2010 Jun; 4(2):95-104. PMID: 20805930; PMCID: PMC2923299.
      50. Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD. Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol. 2010 Mar; 76(6):1935-45. PMID: 20118358; PMCID: PMC2838030.
      51. Shaikh AS, Tang YJ, Mukhopadhyay A, Martín HG, Gin J, Benke PI, Keasling JD. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnol Prog. 2010 Jan-Feb; 26(1):52-6. PMID: 19899123.
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      52. 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 AP, 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.
      53. Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A. A rapid and inexpensive labeling method for microarray gene expression analysis. BMC Biotechnol. 2009 Nov 25; 9:97. PMID: 19939278; PMCID: PMC2790446.
      54. Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin AP, 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.
      55. Borglin S, Joyner D, Jacobsen J, Mukhopadhyay A, Hazen TC. Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. J Microbiol Methods. 2009 Feb; 76(2):159-68. PMID: 18996155.
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      56. Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. 2008 Jun; 19(3):228-34. PMID: 18515068.
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      57. Fortman JL, Chhabra S, Mukhopadhyay A, Chou H, Lee TS, Steen E, Keasling JD. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol. 2008 Jul; 26(7):375-81. PMID: 18471913.
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      58. Gaucher SP, Redding AM, Mukhopadhyay A, Keasling JD, Singh AK. Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins. J Proteome Res. 2008 Jun; 7(6):2320-31. PMID: 18416566.
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      59. Shaikh AS, Tang YJ, Mukhopadhyay A, Keasling JD. Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein. Anal Chem. 2008 Feb 01; 80(3):886-90. PMID: 18179240.
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      60. Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin AP, 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.
      61. Tang Y, Pingitore F, Mukhopadhyay A, Phan R, Hazen TC, Keasling JD. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry. J Bacteriol. 2007 Feb; 189(3):940-9. PMID: 17114264; PMCID: PMC1797301.
      62. Gao R, Mukhopadhyay A, Fang F, Lynn DG. Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens. J Bacteriol. 2006 Jul; 188(14):5204-11. PMID: 16816192; PMCID: PMC1539974.
      63. Mukhopadhyay A, He Z, Alm EJ, Arkin AP, 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.
      64. Redding AM, Mukhopadhyay A, Joyner DC, Hazen TC, Keasling JD. Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics. Brief Funct Genomic Proteomic. 2006 Jun; 5(2):133-43. PMID: 16772278.
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