Mukhopadhyay:Publications

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Refereed Publications

  1. Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, 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
  2. Eudes A, George A, Mukerjee P, et al, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loque D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. 2012
  3. Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Mukhopadhyay A,Petzold CJ, Scheller HV, Loque 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
  4. 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 ω-Hydroxy Fatty Acids in Cutin Polyester. Plant Physiol. 2012 open access
  5. Juminaga D, Baidoo EEK, 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 open access
  6. 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 Biology 2011 open access
  7. Peralta-Yahya P, Ouellet M, Chan R, Mukhopadhyay A, Keasling J, Lee TS. Identification and microbial production of a terpene-based advanced biofuel. Nature Communications 2011 (open access)
  8. 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 (Feature Article)
  9. Ouellet M, Dibble D, et al and Holmes BM*, Mukhopadhyay A. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. Green Chemistry 2011 link Top ten!!!
  10. 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 link
  11. 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
  12. 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(Cover)
  13. 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. 2010
  14. A Zhou, Z He, AM Redding-Johanson, A Mukhopadhyay, CL Hemme, MP Joachimiak, F Luo, Y Deng, KS Bender, Q He, JD Keasling, DA Stahl, MW Fields, TC Hazen, AP Arkin, JD Wall, J Zhou. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol. 2010
  15. J. Ito, C. J. Petzold, A. Mukhopadhyay, J. Heazlewood The role of proteomics in the development of cellulosic biofuels. Current Proteomics. 2010
  16. M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay* A Model for Improving Microbial Biofuel Production using a Synthetic Feedback Loop. Systems and Synthetic Biology. 2010 link
  17. Y. Cong, M. Baker, J. Jakana, D. Woolford, E. Miller, S. Reissmann, R. Kumar, A. Redding-Johanson, T. Batth, A. Mukhopadhyay, S. Ludtke, J. Frydman, W. Chiu. 4.0 Å Resolution Cryo-EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement. PNAS. 2010
  18. B. J. Rutherford, R. Dahl, R. Price, H. L. Szmidt, P. I. Benke, A. Mukhopadhyay*, and J. D. Keasling. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. 2010 link
  19. Z. He, A. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, C. L. Hemme, K. Huang, E.J. Alm, M.W. Fields, J. Wall, D. Stahl, T.C Hazen, J.D. Keasling, A. P. Arkin, J. Zhou. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl Environ Microbiol. 2009
  20. M. Ouellet, P. D. Adams, J. D Keasling and A. Mukhopadhyay*. A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology 2009 link
  21. A. Shaikh, Y. J. Tang, A. Mukhopadhyay, H. García Martín, J. Gin, P. I. Benke, J. D. Keasling. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnology Progress 2009
  22. D.E Elias, A. Mukhopadhyay#, M. Joachimiak#, A. M. Redding,H-C. B. Yen, M. W. Fields, T. C. Hazen , A. P. Arkin, J. D Keasling, J. D. Wall. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Research 2009
  23. S. Borglin, D.C. Joyner, J. S. Jacobsen, A. Mukhopadhyay, T.C. Hazen. Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. J Microbiol Methods. 2009
  24. J.L Fortman#, S. Chhabra#, A. Mukhopadhyay#, H. Chou, T.S. Lee, E. Steen, J.D. Keasling. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol. 2008 Cover
  25. A. Mukhopadhyay#, A.M. Redding#, B.J. Rutherford, J.D. Keasling. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. 2008 link
  26. S. P. Gaucher#, A. M. Redding#, A. Mukhopadhyay, J. D. Keasling, A. K. Singh. Post-translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins. Journal of Proteomic Research 2008
  27. A. S. Shaikh#, Y. J. Tang#, A. Mukhopadhyay, J. D. Keasling*. Isotopomer Distributions in Amino Acids from a Highly Expressed Protein as a Proxy for Those from Total Protein. Analytical Chem 2008 link
  28. A. Mukhopadhyay, A. M. Redding#, M. P. Joachimiak#, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, D. C. Joyner, V. J. J. Martin, J. D. Wall, Z-K. Yang, J. Zhou, J. D. Keasling Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 2007 link
  29. Y. Tang#, F. Pingitore#, A. Mukhopadhyay#, R. Phan, T. C. Hazen, J. D. Keasling Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. J. Bacteriol. 2007
  30. A. Mukhopadhyay, Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Q. He, H-Y. Holman, K. Huang, R. Huang, D. C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. Wall, J. Wei, Z. Yang, H-C. Yen, J. Zhou, J. D. Keasling Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach J. Bacteriol. 2006 link
  31. A. M. Redding, A. Mukhopadhyay, D. C. Joyner, T. C. Hazen, J. D. Keasling Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics. Brief Funct Genomic Proteomic 2006
  32. R. Gao, A. Mukhopadhyay, F. Fang, D. G. Lynn Constitutive Activation of Two-Component Response Regulators: Characterization of VirG Activation in Agrobacterium tumefaciens. J Bacteriol 2006,
  33. A. Mukhopadhyay, R. Gao, D. G. Lynn Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem 2004 link
  34. Y. Wang, A. Mukhopadhyay, V. R. Howitz, A. N. Binns, D. G. Lynn Construction of an efficient expression system for Agrobacterium tumefaciens based on the coliphage T5 promoter. Gene 2000 link

Book Chapters, Invited articles and Reports

  1. Mukhopadhyay A Microbial host engineering: beyond the metabolic pathway 2012 Special Issue: New Science of Synthetic and Systems Biology, Science And Culture Journal (Indian Science News Association) ed. Rupak Bhadra.
  2. Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels 2012 Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs. ed. Z. Lewis Liu, Springer Berlin / Heidelberg. 22: 209-238 link
  3. Rutherford, B.J and Mukhopadhyay, A. 2012 Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In: Arora, R. (ed) Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK.
  4. Mukhopadhyay A, Hauser Loren Workflow 4: Signaling, in the DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science. DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop, Feb. 9–10, 2010

Patents

  1. Dunlop, Mary J.; Keasling, Jay D.; Mukhopadhyay, Aindrila Modified Host Cells with Efflux Pumps U.S. Patent Application Ser. No: 13/115,925 25-May-2011. online or Go to Berkeley lab Tech Transfer

Recent invited talks

  1. Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 Plenary session
  2. Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 Link
  3. Mukhopadhyay A. Study of yeast transcription factors as a strategy to discover new parts for cellular and metabolic engineering. Invited Talk, Yeast Synthetic biology Workshop, UC Mission Bay Campus, San Francisco, Oct 16th 2010. video
  4. Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010.
  5. Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Indo-American Frontiers of Engineering Symposium, Jaypee Palace Hotel, Agra, India, March 10-13, 2010 link
  6. Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Special Departmental Seminar, Department of Chemistry, Indian Institute of Technology, Mumbai, India March 8th, 2010.
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