Aindrila Mukhopadhyay

Vice President for Biofuels and Bioproducts, and Director of Host Engineering

Research Focus

Dr. Mukhopadhyay received a Masters in Chemistry from the Indian Institute of Technology, Mumbai, and a PhD in Organic Chemistry from the University of Chicago.  She is a Senior Scientist of the Biological Systems and Engineering Division at the Lawrence Berkeley National Laboratory.

At JBEI, Dr. Mukhopadhyay is the Vice President of the Biofuels and Bioproducts Division and the Director of the Host Engineering group. Her group develops tools to engineer a variety of microbial platforms including P. putida, E. coli, S. cerevisiae, and other microbial strains. Her group specifically focuses on developing robust strains that show high tolerance and productivity during biofuels and chemicals production and the optimization required to achieve scalability. Visit the M-group website for more on her group’s work.


  • P. putida, E. coli, C. glutamicum and other yeast bacterial strains: Improve strain tolerance to solvent-like biofuels and chemicals, develop methods to optimize gene expression in production strains, and understand the bottlenecks to scalability.

Featured Media

Improving Membrane Protein Expression Using Genome Wide Edits

New Cas9-based Toolkit Eases Obstacles in Genetic Engineering

Berkeley Lab Scientists Brew Jet Fuel in One-Pot Recipe

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KQED Quest Career Spotlight: Microbiologist

Tolerance Engineering boosts biogasoline production in bacteria


Women @ Energy: Aindrila Mukhopadhyay


Aindrila’s Mission: JBEI Scientist Sketches Her SF Neighborhood

Featured Publications

Complete list from Google Scholar

  • Jensen, H. M., Eng, T., Chubukov, V., Herbert, R. A. & Mukhopadhyay, A*. Improving membrane protein expression and function using genomic edits. Nature Scientific Reports 2017. online
  • Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EEK, Petzold CJ, Keasling JD, Mukhopadhyay A* Engineering glucose metabolism of Escherichia coli under nitrogen starvation. Nature Systems Biology and Applications 2017 online
  • 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 online
  • 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 online
  • 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 online
  • Mukhopadhyay A* Tolerance engineering in bacteria for the production of advanced biofuels and chemicals Trends in Microbiology 2015 online
  • 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
  • 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
  • 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 online
  • Engineering microbial biofuel tolerance and export using efflux pumps”.  Mol Syst Biol. 2011 online
  • Rutherford BJ, Dahl R, Price R, Szmidt HL, Benke PI, Mukhopadhyay A*, and Keasling JD. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. 2010 online
  • Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. 2008 online

Featured Intellectual Property