Preprints in review

Kothari A, Wu Y-W, Charrier M, Rajeev L, Rocha AM, Paradis CJ, Hazen TC, Singer SW, Mukhopadhyay A Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes BioRxIv 2017 doi: 10.1101/113860

Peer Reviewed


Xu F, Sun J, Wehrs M, Kim KHo, Rau SS, Chan AM, Simmons BA, Mukhopadhyay A, Singh S* Biocompatible choline-based deep eutectic solvents enable one-pot production of cellulosic ethanol. ACS Sustainable Chem. Eng, 2018 (in press)

Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan, N, Luk, J, Novichkov PS and Mukhopadhyay A* . Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs. Molecular Microbiology 2018 (OA)

Thompson MG, Sedaghatian N, Barajas JF, Wehrs M, Bailey CB, Kaplan N, Hillson NJ, Mukhopadhyay A &  Keasling JD Isolation and characterization of novel mutations in the pSC101 origin that increase copy number. Nature Scientific Reports 2018 (OA)

Dossani ZY, Reider Apel A, Szmidt-Middleton H, Hillson NJ, Deutsch S, Keasling JD,Mukhopadhyay A* . A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineeringYeast2018 (OA)


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 OA

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. and Garcia Martin, H* The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization. ACS Synthetic Biology 2017.

d’Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, Martín HG, Keasling JD* Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks Metabolic Engineering  2017

Parisutham V, Sathesh-Prabu C, Mukhopadhyay A, Lee SK*, Keasling JD Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries Bioresource Technology 2017

Shymansky CM, Wang G, Baidoo EEK, Gin J, Reider Apel A, Mukhopadhyay A,Martin HG* Keasling JD, Flux-enabled exploration of the role of Sip1 in galactose yeast metabolism, Frontiers in Bioengineering and Biotechnology 2017

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 Syn Bio 2017

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


Reider Apel A, d’Espaux L, Wehrs M, Sachs D, Li R, Tong G, Garber M, Nnadi O, Zhuang W, Hillson N, Keasling JD, Mukhopadhyay, A* A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae NAR 2016

Thorgersen MP, Lancaster WA, Rajeev L, Ge X, Vaccaro BJ, Poole FL, Arkin AP, Mukhopadhyay A, Adams MWW* A Highly Expressed High Molecular Weight S-Layer Complex of Pelosinus Strain UFO1 Binds Uranium and Environmental Microbiology 2016

Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EEK, Keasling JD, Mukhopadhyay A*, Tang YJ* Escherichia coli glycolytic strategies, catabolite repression, and metabolite channeling Biotechnology for biofuels 2016

Kothari A, Charrier M, Wu Y-W, 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 Microbiology Letters 2016

Brown ME, Mukhopadhyay A, Keasling JD*. Engineering bacteria to catabolize the carbonaceous component of sarin: teaching coli to eat isopropanol. ACS Synthetic Biology 2016

Frederix M, Mingardon F, Sun N, Pray T, Singh S, Simmons BA, Keasling JD, Mukhopadhyay A* Development of an coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass. Green Chemistry 2016 OA

Fortman JL and Mukhopadhyay A*, Future of Antibiotics: Emerging technologies, in Science & Society, Trends in Microbiology 2016

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

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


Kazakov A, Rajeev L, Chenn A, Luning EJ, Dubchak I, Mukhopadhyay A, Novichkov P*, σ54-dependent Regulome in Desulfovibrio vulgaris Hildenborough BMC Genomics 2015

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 Bact. 2015

Mukhopadhyay A* Tolerance engineering in bacteria for the production of advanced biofuels and chemicals Trends in Microbiology 2015

Garcıa-Martin H*, 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

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) Appl Environ Microbiol. 2015

Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A* Improving olefin tolerance and production in coli using native and evolved AcrB. Biotechnology and Bioengineering. 2015

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 Microbiol 2015


Jensen HM#, Foo JL#, 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

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

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

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

Rajeev, L.*, Luning, E. G., Mukhopadhyay, A. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems. Vis. Exp. 2014

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 2014

2013 and earlier

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.

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

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

Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A*. Utilizing a highly responsive gene, yhjX, in coli based production of 1,4-Butanediol CES 2013

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

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

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

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

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

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

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

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

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. R. Bhadra.

Rutherford, B.J and Mukhopadhyay, A*. 2012 Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels, In: Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK. ed. Arora, R.

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

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

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

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

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

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

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

Ouellet M, Datta S, Dibble DC, Tamrakar PR, Benke PI, Li CL, Singh S, Sale KL, Adams PD, Keasling JD, Simmons BD, Holmes BM*, Mukhopadhyay A. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. Green Chemistry 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

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.

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

Ito J, Petzold CJ, Mukhopadhyay A, Heazlewood J*. The role of proteomics in the development of cellulosic biofuels. Current Proteomics. 2010

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

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, ArkinAP, Wall JD, Zhou J*. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Environ Microbiol. 2010

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

Dunlop MJ, Keasling JD, Mukhopadhyay A*. A Model for Improving Microbial Biofuel Production using a Synthetic Feedback Loop. Systems and Synthetic Biology 2010.

Ouellet M, Adams PD, Keasling JD and Mukhopadhyay A*. A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology 2009

Shaikh AS#, Tang YJ#, Mukhopadhyay A#, García Martín H, Gin J, Benke PI, Keasling JD* Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnology Progress 2009

Elias DE*, Mukhopadhyay A#, Joachimiak MP#, Redding AM, Yen H-CB, 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 Research 2009

Borglin S, Joyner DC, Jacobsen JS, Mukhopadhyay A, Hazen TC*. Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris J Microbiol Methods. 2009

Gaucher S#, Redding AM#, Mukhopadhyay A, Keasling JD, Singh AK*. Post-translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins. Journal of Proteomic Research 2008

Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD*. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. 2008

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

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. Analytical Chem 2008

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 J Bacteriol. 2007

Tang YJ#, Pingitore F#, Mukhopadhyay A#, Phan R, Hazen TC, Keasling JD*. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. Bacteriol. 2007

Redding A-M, Mukhopadhyay A, Joyner DC, Hazen TC, Keasling JD* Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics. Brief Funct Genomic Proteomic 2006

Mukhopadhyay A, He Z, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman H-Y, Huang K, Huang R, Joyner DC, Katz N, Keller M, Oeller P, Redding AM, Sun J, Wall J, Wei J, Yang J, Yen H-C, Zhou J, Keasling JD*. Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach Bacteriol. 2006

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,

Mukhopadhyay A, Gao R, Lynn DG*. Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem 2004

Wang Y, Mukhopadhyay A, Howitz VR, Binns AN, Lynn DG*. Construction of an efficient expression system for Agrobacterium tumefaciens based on the coliphage T5 promoter. Gene 2000


 Reports and commentaries

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

Lee TS, Keasling JD, Beller HR, Mukhopadhyay A. JBEI Performance Metric for FY16, Q2 Metric report: New methods to modify or control regulation of engineered pathways for biofuel production (2016)

Mukhopadhyay A, Perspective on the future of biofuels using microbial platforms, Biofuels International, Volume 11 (1) Jan 2017

Aindrila’s Theses

Mukhopadhyay A, Initiating lateral gene transfer: analysis of the VirA/VirG two component system in vivo. (Ph. D.) Department of Chemistry, University of Chicago, Chicago, IL, USA

Mukhopadhyay A, Synthesis of chiral bioactive molecules using enzymes and microorganisms. (M. Sc) Department of Chemistry Indian Institute of Technology, Powai, Mumbai, Maharashtra, India, 1996.

M-group Patents

Mukhopadhyay A, Mingardon F Chanal A. Modified Host Cells Having tolerance to α-Olefins. US Patent 20,170,051,317, (2017/02/23)

Mukhopadhyay A, Reider-Apel A, Ouellet M, Keasling JD, Synthetic Polypeptide Having A Xylose Import Activity US Patent 20170015714 A1 (2017/01/19)

Dunlop, MJ. Keasling, JD. Mukhopadhyay, A. Modified Host Cells with Efflux Pumps. S. Patent No. 9428726 (2016/8/30)