Refereed Publications
- 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 (accepted)
- 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)
- 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
- 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
- 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
- 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)
- 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
- 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
- J. Ito, C. J. Petzold, A. Mukhopadhyay, J. Heazlewood The role of proteomics in the development of cellulosic biofuels. Current Proteomics. 2010
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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,
- A. Mukhopadhyay, R. Gao, D. G. Lynn Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem 2004 link
- 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
- Mukhopadhyay A Microbial host engineering: beyond the metabolic pathway 2011 Special Issue: New Science of Synthetic and Systems Biology, Science And Culture Journal (Indian Science News Association) ed. Rupak Bhadra.
- Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels 2011 Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs (Springer series) ed. Z. Lewis Liu
- 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.
- 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
- 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
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