From OpenWetWare

Jump to: navigation, search

About us            Contact            People            Research            Pubs etc            Internal           


Refereed Publications

n= 62 h-impact 27

M group pubs

  1. Frederix M, Mingardon F, Sun N, Pray T, Singh S, Simmons BA, Keasling JD, Mukhopadhyay A* Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass. Green Chemistry 2016 (in press)
  2. Fortman JL and Mukhopadhyay A*, The Future of Antibiotics: Emerging Technologies and Stewardship, Trends in Microbiology 2016
  3. Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Garcia-Martín HG * Synthetic and systems biology for microbial production of commodity chemicals, Nature Systems Biology and Applications 2016
  4. Reider-Apel, Ouellet M, Szmidt-Middleton H, Keasling JD, Mukhopadhyay A*, Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae Nature. Sci Rep 2016 open access
  5. 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 Bacteriology. 2015 online
  6. Mukhopadhyay A* Tolerance engineering in bacteria for the production of advanced biofuels and chemicals Trends in Microbiology 2015 open access
  7. Chubukov V, Mingardon F, Schackwitz W, Baidoo EEK, Alonso-Gutierrez J, Hu Q, Lee TS, Keasling JD, MukhopadhyayA* Acute limonene toxicity in Escherichia coli is caused by limonene-hydroperoxide and alleviated by a point mutation in alkyl hydroperoxidase (AhpC) AEM 2015 online
  8. 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. Biotechnology and Bioengineering. 2015 online
  9. Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS,Leong SSJ, Mukhopadhyay A*. Improving microbial bio-gasoline production in Escherichia coli using tolerance engineering. mBio 2014 open access
  10. 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. Frontiers in Microbiology 5. 2014 open access
  11. Frederix M, Hutter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch H, 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 online
  12. Rajeev, L.*, Luning, E. G., Mukhopadhyay, A. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems. J. Vis. Exp. 2014
  13. Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson J, Auer M, Wall JD, Mukhopadhyay A* Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility Frontiers in Microbiology 2014open access
  14. Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A*. Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-Butanediol CES 2013 open access
  15. Rajeev L, da Rocha U, Klitgord N, Luning E, Fortney J, Axen S, Shih P, Bouskill N, Bowen B, Kerfeld C, Garcia-Pichel F, Brodie E, Northen T*, Mukhopadhyay A*. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J 2013 open access
  16. 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* and Stahl DA. Functional Responses of Methanogenic Archaea to Syntrophic Growth. ISME J 2012 open access
  17. 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
  18. 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)
  19. 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)
  20. 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!!!
  21. 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
  22. 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
  23. 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
  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


  1. Kazakov A, Rajeev L, Chenn A, Luning EJ, Dubchak I, Mukhopadhyay A, Novichkov P*, σ54-dependent Regulome in Desulfovibrio vulgaris Hildenborough BMC Genomics2015
  2. Garcıa-Martin∗, Kumar VS, Weaver D, Ghosh A, Chubukov V, Mukhopadhyay A, Arkin AP, Keasling JD. A method to constrain genome-scale models with 13C labeling data. PLoS Comput Biol 2015
  3. Rocha UN* , Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR and Brodie EL, Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust Front. Microbiol 2015
  4. Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, García-Martín H.A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. PLoS Comput Biol 2014
  5. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD et al: Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013.
  6. Kazakov A, Rajeev L, Luning EG, Zane G, Siddartha K, Rodionov D, Dubchak I, Arkin A, Wall J, Mukhopadhyay A, Novichkov P. A new family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria" J Bact 2013
  7. Zhou A, Baidoo E E, He Z, Mukhopadhyay A, Baumohl J, Benke P I, Joachimiak M, Xie M, Song R, Arkin A, Hazen T, Keasling J, Wall J, Stahl D, Zhou J Characterization of NaCl-tolerance in Desulfovibrio vulagris Hildenborough through experimental evolution ISME J 2013
  8. Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling J Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng 2012
  9. Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, et al. A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels. PLoS ONE 2012
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. J. Ito, C. J. Petzold, A. Mukhopadhyay, J. Heazlewood The role of proteomics in the development of cellulosic biofuels. Current Proteomics. 2010
  20. 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

M Postdoc and Graduate Research

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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,
  13. A. Mukhopadhyay, R. Gao, D. G. Lynn Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem 2004 link
  14. 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. pdf
  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 pdf


  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
  2. Mukhopadhyay, Aindrila; Mingardon, Florence; Chanal, Angelique. Modified Host Cells Having tolerance to α-Olefins. U.S. Patent Application Ser. No: 61/986,669 30-Apr-2014.
  3. Mukhopadhyay, Aindrila, Reider-Apel Amanda, Keasling JD, Discovery of a hexose transporter variant in Sachharomyces cerevisiae that allows growth on xylose” U.S. Patent Application Ser. No: 62/192,517 14-July-2015

Recent invited talks

  1. Mukhopadhyay A, Sustainable production of biofuels Gordon Conference Green chemistry, Stowe, Vermont, US, July 31-Aug-5, 2016.
  2. Mukhopadhyay A, Engineering bacteria for the production of fuels and chemicals SFSU Depratment of Biology Colloquium in Microbiology and Cell & Molecular Biology, Apr 7th 2016
  3. Mukhopadhyay A, Engineering Microbial Solvent Tolerance Indo-US Bilateral Conference in Cell Factories, Mumbai, India, March 18-20th 2016
  4. Mukhopadhyay A, Studies in signaling, stress and engineering in bacteria, John Lawrence Seminar Series, LBNL, Berkeley, CA Oct 6th 2015
  5. Mukhopadhyay A, Engineering Microbial Solvent Tolerance using efflux pumps, Gordon research Conference, Lucca, Italy April 24-May 1 2015
  6. Mukhopadhyay A, Developing new Transcrip1on factors and promoter systems for S. cerevisiae, Joint Genome Institute, User meeting (Synthetic Biology workshop), Walnut Creek, CA, USA, March 25 2015
  7. Mukhopadhyay A, Engineering Solvent Tolerant Bacteria: A Systems Biology Guided Effort, Genomic Science Contractors-Grantees Meeting XIII/USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, Washington DC, USA, Feb 22-25 2015 link
  8. Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Departmental Seminar, Dept of Chemical engineering, IIT, Mumbai, India, Feb 10th 2015
  9. Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Indo-US Conference and Workshop in Systems and Synthetic Biology, New Delhi, India, Nov 9-12 2014 link
  10. Mukhopadhyay A, Engineering Microbial Solvent Tolerance, SIMB, St Louise MO, USA, Jul 24th 2014
  11. Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Bioenergy and Photosynthesis Seminar, ASU, Tempe, AZ USA Feb 20th 2014
  12. Mukhopadhyay A, Dynamic response of biological soil crust to wetting and drying events, 12th Biennial Conference of Science and Management on the Colorado Plateau Northern Arizona University, Flagstaff, Sept 18th 2013
  13. Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Energy Biosciences Institute Seminar Series, Berkeley CA, USA Sept 3rd 2013 see talk
  14. Mukhopadhyay A Presenting at Science at the Theater event, Eight Big Ideas, Berkeley Repertory Theater, Berkeley CA USA May 13th 2013
  15. Mukhopadhyay A Lecture to ChemE Students (Biofuel production and processing, ChemE 437; Unit Ops II), invited by Prof James Carothers, University of Washington Seattle, USA, Feb 8th 2013
  16. Mukhopadhyay A Advances in Host Engineering for the production of Chemicals and Fuels, Bioenergy and Biotechnology Team, Reliance India Limited, Mumbai, India Jan 3rd 2013
  17. Mukhopadhyay A Advances in Host Engineering for production of Chemicals and Fuels, Special Seminar, DBT-ICT Center for Energy Biosciences, Mumbai, India, Dec 31st 2012
  18. Mukhopadhyay A Signaling and stress in natural and engineered microbes, Departmental Seminar, Washington University at St Louis, Missouri, Sept 21, 2012
  19. Mukhopadhyay A Society for General Microbiology, Fall Conference, Warwick, UK, Sept 3-5 2012 link
  20. Mukhopadhyay A Engineering Solvent Tolerant Microbes for Biofuel production, ITRI forum 2012, Milpitas, CA June 25th 2012
  21. Mukhopadhyay A Resolving Community and Metabolic Dynamics in Colorado Plateau Biological Soil Crusts, ASMCUE, San Mateo, June 15th 2012 link
  22. Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 Plenary session
  23. Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 Link
  24. 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
  25. Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010.
  26. 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
  27. 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.
Personal tools