146. Srinivasan A, Chen-Xiao K, Banerjee D, Oka A, Pidatala V, Eudes A, Simmons BA, Eng TE, Mukhopadhyay A * 2024 Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum using statistical design of experiments (in press JIMB) BioRxiv

145.Yunus IS, Hudson GA, Chen Y, Gin JW, Kim J, Baidoo EEK, Petzold CJ, Adams PD,. Simmons BA, Mukhopadhyay A, Keasling JD, Lee TS*, 2024 Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida, Metabolic Engineering,

144. Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H 2024 Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

143. Baral NR, Banerjee D, Mukhopadhyay A, Simmons BA, Singer BA, Scown CD* 2024 Integration of Genome-Scale Metabolic Model with Biorefinery Process Model Reveals Market-Competitive Carbon-Negative Sustainable Aviation Fuel Utilizing Microbial Cell Mass Lipids and Biogenic CO2 BioResources DOI:10.15376/biores.19.3.4056-4086

142. Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Garcia Martin H, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim JH, Lee TS*, Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida, Metabolic Engineering, 2024,

141. Baral NR, Banerjee D, Mukhopadhyay A, Simmons BA, Singer SW, Scown CD * Economic and Environmental Trade-Offs of Simultaneous Sugar and Lignin Utilization for Biobased Fuels and Chemicals, ACS Sustainable Chem. Eng. 2024 doi: 10.1021/acssuschemeng.3c05541

140. Garber ME, Frank V, Kazakov AE, Incha MR, Nava AA, Zhang H, Valencia LE, Keasling JD, Rajeev L, Mukhopadhyay A. 2023. REC protein family expansion by the emergence of a new signaling pathway. 2023 mBio org/10.1128/mbio.02622-23

139. Kulakowski, S, Banerjee, D, Scown, CD, Mukhopadhyay, A* Improving microbial bioproduction under low-oxygen conditions COBIOT 2023 org/10.1016/j.copbio.2023.103016

138. Camargo AP*, Call L, Roux S, Nayfach S, Huntemann M, Palaniappan K, Ratner A, Chu K, Mukherjee S, Reddy T B K, Chen I-M A, Ivanova NN, Eloe-Fadrosh EA, Woyke T, Baltrus, Castañeda-Barba DAS, de la Cruz F, Funnell BE, Hall JPJ, Mukhopadhyay A, Rocha EPC, Stalder T, Top E, Kyrpides NC, IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata, Nucleic Acids Research, 2024,


137. Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen J-H, Ekman A, Kakumanu R, Liu Diercks Y, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A*, Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering, Cell Reports, 2023,

136. Garcia VE, Pidatala V, Barcelos CA, Liu D, Otoupal P, Wendt, O, Choudhary H, Sun N, Eudes A, Sundstrom ER, Scheller HV, Putnam DH, Mukhopadhyay A, Gladden JM, Simmons BA, Rodriguez A* Enhanced microbial production of protocatechuate from engineered sorghum using an integrated feedstock-to-product conversion technology Green Chemistry 2023 doi 10.1039/D3GC01481A

135. Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS*, Balskus EP, Hartwig JF*, Mukhopadhyay A*, Keasling JD* Complete integration of carbene-transfer chemistry into biosynthesis Nature 2023

134. Gauttam R., Eng T., Zhao Z., ul ain Rana Q., Simmons B.A., Yoshikuni Y., Mukhopadhyay A., Singer S.W. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microbial Biotechnology. 2023

133. Zha J*, Zhao Z, Xiao Z, Eng T, Mukhopadhyay A, Koffas MAG*, Tang Y* Biosystems Design of Corynebacterium glutamicum for Bio-Production, COBIOT 2023

132. Banerjee D, Mukhopadhyay A* Perspectives in Growth Production Trade-off in Microbial Bioproduction RSC Sustainability, 2023


131. Zhao R, Sengupta A, Tan AX, Whelan R, Pinkerton T, Menasalvas J, Eng T, Mukhopadhyay A, Jun Y-S, Pakrasi HB, Tang Y Photobiological production of high-value pigments via compartmentalized co-cultures using Ca-alginate hydrogels npg Sci Rep 2022 

130. Wang X, Baidoo EEK, Kakumanu R, Xie S, Mukhopadhyay A, Lee TS* Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida, Biotechnology for Biofuels and Bioproducts 2022

129. Park M-R, Gauttam R, Fong B, Chen Y, Lim H-Y, Feist, A, Mukhopadhyay A, Petzold CJ, Simmons BD, Singer SW Revealing Oxidative Pentose Metabolism in New Pseudomonas putida Isolates Environmental Microbiology 2022

128. Otoupal PB, Geiselman GM, Oka A, Barcelos CA, Choudhary H, Dinh D, Zhong W, Hwang H, Keasling JD, Mukhopadhyay A, Sundstrom E, Haushalter RW, Sun N, Simmons BA Gladden* Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides Microbial Cell Factories 2022

127. Lin H-H, Mendez‐Perez D, Park J, Wang X, Cheng Y, Huo J, Mukhopadhyay A, Lee TS, Shanks BH* Precursor Prioritization for p-Cymene Production through Synergistic Integration of Biology and Chemistry, Biotechnology for Biofuels and Bioproducts 2022

126. Iwai K, Wehrs M, Garber M, Sustarich J, Washburn L, Costello Z, Kim PW, Ando D, Gaillard WR, Hillson NJ, Adams PD, Mukhopadhyay A, Martin HG, Singh AK. Scalable and Automated CRISPR-Based Strain Engineering Using Droplet Microfluidics. Microsystems and Nanoengineering 2022

125. Liu Z, Huang J, Gu Y, Clark DS, Mukhopadhyay A, Keasling JD, Hartwig JF. Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C─ H and C═ C Bonds. Journal of the American Chemical Society 2022 

124. Czajka JJ, Banerjee D, Eng TT, Menasalvas J, Yan C, Munoz NM, Poirier BC, Kim Y-M, Baker SE, Tang YJ, Mukhopadhyay A* Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production MEC 2022

123. Schmidt M, Pearson AN, Incha MR, Thompson MG, Baidoo EEK, Kakumanu R, Mukhopadhyay A, Shih PM, Deutschbauer AM, Blank LM, Keasling JD Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing Applied and Environmental Microbiology 2022

122. Garber ME, Fregoso R, Lake J, Kakouridis A, Mukhopadhyay A* Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation Scientific reports 2022


121. Banerjee D, Eng T, Sasaki Y, Srinivasan A, Oka A, Herbert RA, Trinh J, Singan VR, Sun N, Putnam D, Scown CD, Simmons B, Mukhopadhyay A*. Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress. Frontiers in bioengineering and biotechnology 2021

120. Huang J, Liu Z, Bloomer B, Clark DS*, Mukhopadhyay, A*, Keasling JD*, Hartwig JF*. Unnatural Biosynthesis by an Engineered Microorganism with Heterologously Expressed Natural Enzymes and an Artificial Metalloenzyme Nature Chemistry 2021

119. Keasling JD*, Martin HG, Lee TS, Mukhopadhyay A, Singer SW, Sundstrom E. Microbial production of advanced biofuels Nature Microbiology Reviews 2021

118. Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia J-M, Spencer S, Wu X, Sara Altenburg, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A* Ecogenomics of groundwater phages suggests niche differentiation linked to specific environmental tolerance mSystems 2021

117. Eng T, Banerjee D, Lau AK, Herbert RA, Prahl JP, Deutschbauer AM, Tanjore D, and Mukhopadhyay A*. Determinants of Bioreactor Fitness in Pseudomonas putida KT2440 Via Fitness Profiling Enables Optimized Indigoidine Production from Lignin-Derived Monomers. Metabolic Engineering 2021

116. Lim HY, Eng T, Banerjee D, Alarcon G, Lau AK, Park MR, Simmons BA, Palsson BO, Singer SW, Mukhopadhyay A, and Feist AM*. Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution. ACS Sus Chemistry & Engineering 2021

115. Baral NR, Yang M, Harvey BG, Simmons BA, Mukhopadhyay A, Lee TS, Scown CD* Production Cost and Carbon Footprint of Biomass-Derived Dimethylcyclooctane as a High-Performance Jet Fuel Blendstock ACS Sus Chemistry & Engineering 2021

114. Gauttam R, Mukhopadhyay A, Simmons BA, Singer SW* Development of dual‐inducible duet‐expression vectors for tunable gene expression control and CRISPR interference‐based gene repression in Pseudomonas putida KT2440 Microbial Biotechnology 2021

113.Wang X, Pereira, JH, Tsutakawa S, Fang X, Adams PD, Mukhopadhyay A, Lee T S Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450 Metabolic Engineering 2021

112. Kim J, Baidoo EEK, Amer B, Mukhopadhyay A, Adams PD, Simmons BA, Lee TS Engineering Saccharomyces cerevisiae for isoprenol production, Metabolic Engineering, 2021


111. Geiselman GM and Kirby J Landera A, Otoupal P, Papa G, Barcelos C, Sundstrom ER, Das L, Magurudeniya HD, Wehrs M, Mukhopadhyay A, Blake Simmons, Gladden JD, Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks Microbial cell factories 2020

110. Banerjee, D.§, Eng, T.§, Lau, A.K., Sasaki, Y., Wang, B., Chen, Y., Prahl, J.-P., Singan, .R., Herbert, RA., Liu, Y., Tanjore, D., Petzold, CJ., Keasling, JD., Mukhopadhyay, A* 2020. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat. Commun. 11, 5385. OA

109. Wehrs, M.§, Thompson, MG.§, Banerjee, D.§, Prahl, J-P., Morella, NM., Barcelos, CA., Moon, J., Costello, Z., Keasling, JD., Shih, PM., Tanjore D*, Mukhopadhyay A* Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation Microbial cell factories 2020 OA

108. Thompson, MG., Incha, MR., Pearson, AN., Schmidt, M., Sharpless, WA., Eiben, C.B., Cruz-Morales, P., Blake-Hedges, JM., Liu, Y., Adams, CA., Haushalter, RW., Krishna, RN,, Lichtner, P., Blank, LM., Mukhopadhyay, A., Deutschbauer, AM., Shih, PM., Keasling JD* Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq AEM 2020

107. Lim, HG., Fong, B., Alarcon, G., Magurudeniya, HD., Eng, T., Szubin, R., Olson, CA., Palsson, BO., Gladden, JM., Simmons, BA., Mukhopadhyay, A, Singer, SW., Feist AM., Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution Green Chemistry 2020

106. Mohamed, ET., Werner, Allison Z; Salvachúa, D., Singer, C., Szostkiewicz, K., Jiménez-Díaz, M., Eng, T., Radi, MS., Simmons, BA, Mukhopadhyay A, Herrgård, MJ., Singer, SW., Beckham, GT., Feist AM., Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance, Metabolic Engineering Communications 2020

105. Eng T§, Herbert RA§, Martinez U, Wang B, Chen JC., Brown JB., Deutschbauer AM., Bissell MJ., Mortimer JC.*, Mukhopadhyay A* Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria  Frontiers in Microbiology  2020 OA

104. Rajeev L, Garber, ME and Mukhopadhyay A*. Tools to map target genes of bacterial two‐component system response regulators. Environmental Microbiology Reports. 2020 OA

103. Chiniquy, J., Garber, ME, Mukhopadhyay A, Hillson N*. Fluorescent amplification for next-generation sequencing (FA-NGS) library preparation. BMC Genomics 2020

102. Chen Y, Banerjee D, Mukhopadhyay A, Petzold CJ* Systems and synthetic biology tools for advanced bioproduction hosts, Current Opinion in Biotechnology, 2020

101. Eng T§, Sasaki Y§, Herbert RA, Lau A, Trinh J, Chen Y, Mirsiaghi M, Petzold CJ, Mukhopadhyay A* Production of tetra-methylpyrazine using engineered Corynebacterium glutamicum, Met Eng Comm, 2020

100. Thompson MG, Pearson AM, Barajas JF, Cruz-Morales P, Sedaghatian N, Costello Z, Garber ME, Incha MR, Valencia LE, Baidoo EEK, Garcia-Martin H, Mukhopadhyay A, Keasling JD* Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida ACS Synthetic Biology 2020


99. Kothari A, Soneja D, Tang A, Carlson H, Deutschbauer AM, Mukhopadhyay A* Native plasmid-encoded mercury resistance genes are functional and demonstrate natural transformation in environmental bacterial isolates mSphere 2019

98. Rigual V, Papa G, Rodriguez A, Wehrs M, Kim K, Oliet M, Alonso M, Gladden J, Mukhopadhyay A, Simmons B, Singh S, Evaluating protic ionic liquid for woody biomass one-pot pretreatment + saccharification, followed by Rhodosporidium toruloides cultivation ACS Sus Chem & Eng 2019

97. Rodrigues AV, Tantillo DJ, Mukhopadhyay A, Keasling JD, Beller HR* Insights into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme. Chembiochem 2019

96. Kang A, Mendez-Perez D, Goh E-B, Baidoo EEK. Benites VT, Beller HR, Keasling JD, Adams PD, Mukhopadhyay A, Lee TS* Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli Metabolic Engineering 2019

95. Langley S, Eng T, Wan K, Herbert RA, Klein A, Yoshikuni Y, Tringe S, Brown JB, Celniker S, Mortimer JC*, and Mukhopadhyay A*. Complete Genome Sequence of Agrobacterium sp. 33MFTa1.1 isolated from the roots of Thlaspi arvense. Microbiology Resource Announcements 2019

94. Baral, NR, Kavvada, O, Mendez-Perez, D, Mukhopadhyay, A, Lee, TS, Simmons, BA Scown, CD* Greenhouse Gas Footprint, Water-Intensity, and, Production Cost of Bio-Based Isopentenol as a Renewable Transportation Fuel ACS Sustainable Chemistry & Engineering 2019

93. Czamanski Nora L, Wehrs M, Kim J-H, Cheng J-F, Tarver A, Simmons BA, Magnuson J, Harmon-Smith M, Silva-Rocha R, Gladden JM, Mukhopadhyay A, Skerker JM*, Kirby J* A toolset of promoters for metabolic engineering of Rhodosporidium toruloides Microbial Cell Factories 2019 

92. Wehrs, M., Gladden JM, Liu Y, Platz L, Prahl J-P, Moon J, Papa G, Sundstrom E, Geiselman GM, Tanjore D, Keasling JD, Pray TR, Simmons BA Mukhopadhyay A* Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides Green Chemistry 2019 OA

91. Herbert RA, Eng T, Martinez U, Wang B, Langley S, Wan K, Pidatala V, Hoffman E, Chen JC, Bissell MJ, Brown JB, Mukhopadhyay A* Mortimer JC* Rhizobacteria mediate the phytotoxicity of a range of biorefinery‐relevant compounds. Environmental Toxicology and Chemistry 2019 

90. Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkoc P, Wall J, Mukhopadhyay A* LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. PLOS ONE 2019.

89. Dong J, Chen Y, Benites VT, Baidoo EE, Petzold CJ, Beller HR, Eudes A, Mukhopadhyay A, Singer SW* Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids, Biotech and Bioeng 2019

88. Barajas JF, Wehrs M, To M, Cruickshanks L, Urban R, McKee A, Gladden J, Goh E-B, Brown ME, Pierotti D, Carothers JM, Mukhopadhyay A, Keasling JD, Fortman JL, Singer SW*, Bailey CB* Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course” Journal of Microbiology and Biology Education 2019

87. Baral, NR, Sundstrom E, Das L, Gladden J, Eudes, A, Mortimer JC, Singer SW, Mukhopadhyay A, Scown CS* Approaches for More Efficient Biological Conversion of Lignocellulosic Feedstocks to Biofuels and Bioproducts ACS Sustainable Chemistry & Engineering 2019

86. Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A* Engineering robust production microbes for large scale cultivation Trends in Microbiology 2019

85. Sasaki Y, Eng T, Herbert RA, Trinh J, Chen Y, Rodriguez, A, Gladden, JM, Simmons BA, Petzold CJ, Mukhopadhyay, A* Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates. Biotechnology for Biofuels. 2019

84. Kothari A, Wu Y-W, Chandonia J-M, Charrier M, Rajeev L, Rocha AM, Joyner DC, Hazen TC, Singer SW, Mukhopadhyay A* Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes mBio 2019 

83. Baral, N. R., Kavvada, O., Mendez-Perez, D., Mukhopadhyay, A., Lee, T. S., Simmons, B. A., Scown, C. D., Techno-economic analysis and life-cycle greenhouse gas mitigation cost of five routes to bio-jet fuel blendstocks. Energy & Environmental Science 2019



82. Wehrs M, Prahl JP, Moon J, Li Y, Tanjore D, Keasling JD, Pray T, Mukhopadhyay A* Production efficiency of the bacterial non- ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae Microbial Cell Factories 2018  (OA)

81. Rajeev L, Garber M, Zane G, Wall JD, Dubchak I, Novichkov P, Mukhopadhyay A, Kazakov A* A new family of transcriptional regulators of tungston enzymes and molybdate/tungstate transport Environmental Microbiology, 2018

80. Wang S, Cheng G, Dong J, Tian T, Lee TS, Mukhopadhyay A, Simmons BA, Yuan Q, Singer S Tolerance characterization and isoprenol production of adapted Escherichia coli in the presence of ionic liquids ACS Sustainable Chem. Eng, 2018

79. Eng T, Demling P, Herbert RA, Chen Y, Benites V, Martin J, Lipzen A, Baidoo EEK, Blank LM, Petzold CJ, Mukhopadhyay A* Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC Microbial Cell Factories 2018 (OA)

78. 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 

77. 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)

76. 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. npj Scientific Reports 2018 (OA)

75. 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)


74. Jensen, H. M., Eng, T., Chubukov, V., Herbert, R. A. & Mukhopadhyay, A*. Improving membrane protein expression and function using genomic edits. npj Scientific Reports 2017 OA

73. 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.

72. 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

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

70. 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

69. 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

68. 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. npj Systems Biology and Applications 2017


67. 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

66. 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

65. 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

64. 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

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

62. 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

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

60. Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Garcia-Martín HG* Synthetic and systems biology for microbial production of commodity chemicals, npj Systems Biology and Applications 2016

59. 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, npj Sci Rep 2016


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

57. 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

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

55. 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

54. 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

53. 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

52. 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


51. 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

50. 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

49. 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

48. 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

47. 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

46. 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

45. 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.

44. 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

43. 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

42. 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

41. 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

40. 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

39. 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

38. 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

37. 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

36. 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

35. 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

34. 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

33. 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.

32. 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.

31. 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

30. 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

29. 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

28. 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

27. 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

26. 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

25. 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

24. 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

23. 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

22. 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.

21. 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

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

19. 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

18. 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

17. 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

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

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

14. 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

13. 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

12. 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

11. 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

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

9. 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

8. 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

7. 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

6. 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

5. 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

4. 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

3. 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,

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

1. 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 (Link to article)

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

JC Mortimer, RA Herbert, A Mukhopadhyay, TT Eng Use of cholinium lysinate as an herbicide US Patent 11,160,277, 2021

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)

Preprints in review

Sequence-space expansion is driven by the emergence of new signaling pathways
Megan E. GarberVered FrankAlexey E. KazakovMatthew R. InchaAlberto A. NavaHanqiao ZhangJay D. KeaslingLara RajeevAindrila Mukhopadhyay
Photobiological production of high-value pigments via compartmentalized co-cultures using Ca-alginate hydrogels  Zhao R, Sengupta A, Tan AX, Whelan R, Pinkerton T, Menasalvas J, Eng T, Mukhopadhyay A, Jun Y, Pakrasi HB, Tang Y
Preprint from Research Square, 29 Sep 2022 DOI: 10.21203/