Aindrila Mukhopadhyay, Ph.D. - Publications

2002 University of Chicago, Chicago, IL 
 2002- Lawrence Berkeley National Laboratory, Berkeley, CA, USA 
supramolecular self-assembly

111 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Czajka JJ, Banerjee D, Eng T, Menasalvas J, Yan C, Munoz NM, Poirier BC, Kim YM, Baker SE, Tang YJ, Mukhopadhyay A. Tuning a high performing multiplexed-CRISPRi strain to further enhance indigoidine production. Metabolic Engineering Communications. 15: e00206. PMID 36158112 DOI: 10.1016/j.mec.2022.e00206  0.786
2022 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. e0243021. PMID 35285712 DOI: 10.1128/aem.02430-21  0.511
2022 Liu Z, Huang J, Gu Y, Clark DS, Mukhopadhyay A, Keasling JD, Hartwig JF. Assembly and Evolution of Artificial Metalloenzymes within Nissle 1917 for Enantioselective and Site-Selective Functionalization of C─H and C═C Bonds. Journal of the American Chemical Society. 144: 883-890. PMID 34985270 DOI: 10.1021/jacs.1c10975  0.399
2021 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 in Bioreactor Cultivation Under Ionic Liquid Stress. Frontiers in Bioengineering and Biotechnology. 9: 766674. PMID 34869279 DOI: 10.3389/fbioe.2021.766674  0.75
2021 Huang J, Liu Z, Bloomer BJ, 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. PMID 34650235 DOI: 10.1038/s41557-021-00801-3  0.504
2021 Keasling J, Garcia Martin H, Lee TS, Mukhopadhyay A, Singer SW, Sundstrom E. Microbial production of advanced biofuels. Nature Reviews. Microbiology. PMID 34172951 DOI: 10.1038/s41579-021-00577-w  0.491
2021 Eng T, Banerjee D, Lau AK, Bowden E, Herbert RA, Trinh J, Prahl JP, Deutschbauer A, Tanjore D, Mukhopadhyay A. Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor. Metabolic Engineering. PMID 33964456 DOI: 10.1016/j.ymben.2021.04.015  0.736
2021 Kim J, Baidoo EEK, Amer B, Mukhopadhyay A, Adams PD, Simmons BA, Lee TS. Engineering Saccharomyces cerevisiae for isoprenol production. Metabolic Engineering. PMID 33581331 DOI: 10.1016/j.ymben.2021.02.002  0.322
2020 Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl JP, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nature Communications. 11: 5385. PMID 33097726 DOI: 10.1038/s41467-020-19171-4  0.757
2020 Mohamed ET, Werner AZ, Salvachúa D, Singer CA, Szostkiewicz K, Rafael Jiménez-Díaz M, Eng T, Radi MS, Simmons BA, Mukhopadhyay A, Herrgård MJ, Singer SW, Beckham GT, Feist AM. Adaptive laboratory evolution of KT2440 improves -coumaric and ferulic acid catabolism and tolerance. Metabolic Engineering Communications. 11: e00143. PMID 32963959 DOI: 10.1016/J.Mec.2020.E00143  0.736
2020 Thompson MG, Incha MR, Pearson AN, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, et al. Functional analysis of the fatty acid and alcohol metabolism of using RB-TnSeq. Applied and Environmental Microbiology. PMID 32826213 DOI: 10.1128/Aem.01665-20  0.481
2020 Wehrs M, Thompson MG, Banerjee D, Prahl JP, 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. 19: 167. PMID 32811554 DOI: 10.1186/S12934-020-01423-Z  0.54
2020 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. 11: 1742. PMID 32793173 DOI: 10.3389/Fmicb.2020.01742  0.703
2020 Gauttam R, Mukhopadhyay A, Singer SW. Construction of a novel dual-inducible duet-expression system for gene (over)expression in Pseudomonas putida. Plasmid. 102514. PMID 32504628 DOI: 10.1016/J.Plasmid.2020.102514  0.325
2020 Zargar A, Lal R, Valencia LE, Wang J, Backman TWH, Cruz-Morales P, Kothari A, Werts M, Wong A, Bailey CB, Loubat A, Liu Y, Chen Y, Chang S, Benites VT, ... ... Mukhopadhyay A, et al. Chemoinformatic-guided engineering of polyketide synthases. Journal of the American Chemical Society. PMID 32412752 DOI: 10.1021/Jacs.0C02549  0.541
2020 Chen Y, Banerjee D, Mukhopadhyay A, Petzold CJ. Systems and synthetic biology tools for advanced bioproduction hosts. Current Opinion in Biotechnology. 64: 101-109. PMID 31927061 DOI: 10.1016/J.Copbio.2019.12.007  0.359
2020 Eng T, Sasaki Y, Herbert RA, Lau A, Trinh J, Chen Y, Mirsiaghi M, Petzold CJ, Mukhopadhyay A. Production of tetra-methylpyrazine using engineered . Metabolic Engineering Communications. 10: e00115. PMID 31890587 DOI: 10.1016/J.Mec.2019.E00115  0.763
2020 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. 22: 5677-5690. DOI: 10.1039/D0Gc01663B  0.76
2019 Wehrs M, Prahl JP, Moon J, Li Y, Tanjore D, Keasling JD, Pray T, Mukhopadhyay A. Correction to: Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae. Microbial Cell Factories. 18: 218. PMID 31884968 DOI: 10.1186/s12934-019-1262-2  0.411
2019 Thompson MG, Pearson AN, 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 . Acs Synthetic Biology. PMID 31841635 DOI: 10.1021/Acssynbio.9B00292  0.459
2019 Langley S, Eng T, Wan KH, Herbert RA, Klein AP, Yoshikuni Y, Tringe SG, Brown JB, Celniker SE, Mortimer JC, Mukhopadhyay A. Complete Genome Sequence of sp. Strain 33MFTa1.1, Isolated from Roots. Microbiology Resource Announcements. 8. PMID 31515332 DOI: 10.1128/MRA.00432-19  0.694
2019 Rodrigues AV, Tantillo DJ, Mukhopadhyay A, Keasling JD, Beller H. Insights into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme. Chembiochem : a European Journal of Chemical Biology. PMID 31512343 DOI: 10.1002/Cbic.201900560  0.461
2019 Kang A, Mendez-Perez D, Goh EB, 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. PMID 31499175 DOI: 10.1016/J.Ymben.2019.09.003  0.523
2019 Barajas JF, Wehrs M, To M, Cruickshanks L, Urban R, McKee A, Gladden J, Goh EB, Brown ME, Pierotti D, Carothers JM, Mukhopadhyay A, Keasling JD, Fortman JL, Singer SW, et al. Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course. Journal of Microbiology & Biology Education. 20. PMID 31388393 DOI: 10.1128/Jmbe.V20I2.1723  0.711
2019 Nora LC, Wehrs M, Kim J, Cheng JF, Tarver A, Simmons BA, Magnuson J, Harmon-Smith M, Silva-Rocha R, Gladden JM, Mukhopadhyay A, Skerker JM, Kirby J. A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides. Microbial Cell Factories. 18: 117. PMID 31255171 DOI: 10.1186/S12934-019-1167-0  0.306
2019 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. PMID 31107972 DOI: 10.1002/Etc.4501  0.743
2019 Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A. LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. Plos One. 14: e0214960. PMID 30964892 DOI: 10.1371/Journal.Pone.0214960  0.336
2019 Sasaki Y, Eng T, Herbert RA, Trinh J, Chen Y, Rodriguez A, Gladden J, Simmons BA, Petzold CJ, Mukhopadhyay A. Engineering to produce the biogasoline isopentenol from plant biomass hydrolysates. Biotechnology For Biofuels. 12: 41. PMID 30858878 DOI: 10.1186/S13068-019-1381-3  0.762
2019 Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A. Engineering Robust Production Microbes for Large-Scale Cultivation. Trends in Microbiology. PMID 30819548 DOI: 10.1016/J.Tim.2019.01.006  0.751
2019 Kothari A, Wu YW, Chandonia JM, 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. 10. PMID 30808697 DOI: 10.1128/Mbio.02899-18  0.346
2019 Wehrs M, Gladden JM, Liu Y, Platz L, Prahl J, 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. 21: 3394-3406. DOI: 10.1039/C9Gc00920E  0.486
2019 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. 7: 15434-15444. DOI: 10.1021/Acssuschemeng.9B02928  0.32
2019 Baral NR, Sundstrom ER, Das L, Gladden J, Eudes A, Mortimer JC, Singer SW, Mukhopadhyay A, Scown CD. Approaches for More Efficient Biological Conversion of Lignocellulosic Feedstocks to Biofuels and Bioproducts Acs Sustainable Chemistry & Engineering. 7: 9062-9079. DOI: 10.1021/Acssuschemeng.9B01229  0.39
2019 Wang S, Cheng G, Dong J, Tian T, Lee TS, Mukhopadhyay A, Simmons BA, Yuan Q, Singer SW. NaCl enhances Escherichia coli growth and isoprenol production in the presence of imidazolium-based ionic liquids Bioresource Technology Reports. 6: 1-5. DOI: 10.1016/J.Biteb.2019.01.021  0.338
2018 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. 17: 193. PMID 30545355 DOI: 10.1186/S12934-018-1045-1  0.55
2018 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. 17: 159. PMID 30296937 DOI: 10.1186/S12934-018-1006-8  0.74
2018 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. Scientific Reports. 8: 1590. PMID 29371642 DOI: 10.1038/S41598-018-20016-W  0.507
2018 Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan N, Luk J, Novichkov PS, Mukhopadhyay A. Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs. Molecular Microbiology. PMID 29341298 DOI: 10.1111/Mmi.13909  0.307
2018 Wang S, Cheng G, Dong J, Tian T, Lee TS, Mukhopadhyay A, Simmons BA, Yuan Q, Singer SW. Tolerance Characterization and Isoprenol Production of Adapted Escherichia coli in the Presence of Ionic Liquids Acs Sustainable Chemistry & Engineering. 7: 1457-1463. DOI: 10.1021/Acssuschemeng.8B05144  0.336
2018 Xu F, Sun J, Wehrs M, Kim KH, 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 Chemistry & Engineering. 6: 8914-8919. DOI: 10.1021/Acssuschemeng.8B01271  0.323
2017 Dossani ZY, Apel AR, Middleton HS, Hillson NJ, Deutch S, Keasling JD, Mukhopadhyay A. A combinatorial approach to Synthetic Transcription Factor-Promoter combinations for yeast strain engineering. Yeast (Chichester, England). PMID 29084380 DOI: 10.1002/Yea.3292  0.503
2017 Jensen HM, Eng T, Chubukov V, Herbert RA, Mukhopadhyay A. Improving membrane protein expression and function using genomic edits. Scientific Reports. 7: 13030. PMID 29026162 DOI: 10.1038/S41598-017-12901-7  0.768
2017 Morrell W, Birkel G, Forrer M, Lopez T, Backman T, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso Gutierrez J, George K, Mukhopadhyay A, Vaino I, Keasling JD, et al. The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization. Acs Synthetic Biology. PMID 28826210 DOI: 10.1021/Acssynbio.7B00204  0.47
2017 Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EE, Petzold CJ, Keasling JD, Mukhopadhyay A. Engineering glucose metabolism of Escherichia coli under nitrogen starvation. Npj Systems Biology and Applications. 3: 16035. PMID 28725483 DOI: 10.1038/npjsba.2016.35  0.783
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, García Martín H, et al. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metabolic Engineering. PMID 28606738 DOI: 10.1016/J.Ymben.2017.06.004  0.56
2017 Shymansky CM, Wang G, Baidoo EEK, Gin J, Apel AR, Mukhopadhyay A, García Martín H, Keasling JD. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. Frontiers in Bioengineering and Biotechnology. 5: 31. PMID 28596955 DOI: 10.3389/Fbioe.2017.00031  0.512
2017 Parisutham V, Chandran SP, Mukhopadhyay A, Lee SK, Keasling JD. Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries. Bioresource Technology. PMID 28535986 DOI: 10.1016/J.Biortech.2017.05.001  0.552
2017 Liang Y, Richardson SM, Yan J, Benites VT, Cheng-Yue C, Tran T, Mortimer J, Mukhopadhyay A, Keasling JD, Loque D. Endoribonuclease-based two-component repressor systems for tight gene expression control in plants. Acs Synthetic Biology. PMID 28094975 DOI: 10.1021/Acssynbio.6B00295  0.587
2016 Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. Npj Systems Biology and Applications. 2: 16009. PMID 28725470 DOI: 10.1038/npjsba.2016.9  0.786
2016 Reider Apel A, d'Espaux L, Wehrs M, Sachs D, Li RA, Tong GJ, Garber M, Nnadi O, Zhuang W, Hillson NJ, Keasling JD, Mukhopadhyay A. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae. Nucleic Acids Research. PMID 27899650 DOI: 10.1093/Nar/Gkw1023  0.571
2016 Eudes A, Mouille M, Robinson DS, Benites VT, Wang G, Roux L, Tsai YL, Baidoo EE, Chiu TY, Heazlewood JL, Scheller HV, Mukhopadhyay A, Keasling JD, Deutsch S, Loqué D. Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast. Microbial Cell Factories. 15: 198. PMID 27871334 DOI: 10.1186/S12934-016-0593-5  0.53
2016 Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EE, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ. Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants. Biotechnology For Biofuels. 9: 212. PMID 27766116 DOI: 10.1186/S13068-016-0630-Y  0.637
2016 Kothari A, Charrier M, Wu YW, 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. PMID 27664055 DOI: 10.1093/Femsle/Fnw224  0.366
2016 Brown ME, Mukhopadhyay A, Keasling JD. Engineering bacteria to catabolize the carbonaceous component of sarin: teaching E. coli to eat isopropanol. Acs Synthetic Biology. PMID 27403844 DOI: 10.1021/Acssynbio.6B00115  0.533
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. Scientific Reports. 6: 19512. PMID 26781725 DOI: 10.1038/Srep19512  0.538
2016 Frederix M, Mingardon F, Hu M, 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. 18: 4189-4197. DOI: 10.1039/C6Gc00642F  0.499
2015 Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS. σ(54)-dependent regulome in Desulfovibrio vulgaris Hildenborough. Bmc Genomics. 16: 919. PMID 26555820 DOI: 10.1186/S12864-015-2176-Y  0.339
2015 García Martín H, Kumar VS, Weaver D, Ghosh A, Chubukov V, Mukhopadhyay A, Arkin A, Keasling JD. A Method to Constrain Genome-Scale Models with 13C Labeling Data. Plos Computational Biology. 11: e1004363. PMID 26379153 DOI: 10.1371/Journal.Pcbi.1004363  0.767
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. Journal of Bacteriology. PMID 26283774 DOI: 10.1128/Jb.00319-15  0.337
2015 Mukhopadhyay A. Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends in Microbiology. 23: 498-508. PMID 26024777 DOI: 10.1016/J.Tim.2015.04.008  0.455
2015 Chubukov V, Mingardon F, Schackwitz W, Baidoo EE, Alonso-Gutierrez J, Hu Q, Lee TS, Keasling JD, Mukhopadhyay A. Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC. Applied and Environmental Microbiology. 81: 4690-6. PMID 25934627 DOI: 10.1128/Aem.01102-15  0.79
2015 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. 112: 879-88. PMID 25450012 DOI: 10.1002/Bit.25511  0.385
2014 Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS, Leong S, Mukhopadhyay A. Improving microbial biogasoline production in Escherichia coli using tolerance engineering. Mbio. 5: e01932. PMID 25370492 DOI: 10.1128/Mbio.01932-14  0.811
2014 Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. Plos Computational Biology. 10: e1003827. PMID 25188426 DOI: 10.1371/Journal.Pcbi.1003827  0.48
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: 382. PMID 25120537 DOI: 10.3389/Fmicb.2014.00382  0.532
2014 Rajeev L, Luning EG, Mukhopadhyay A. DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. Journal of Visualized Experiments : Jove. PMID 25079303 DOI: 10.3791/51715  0.314
2014 Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, 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. 9: e101115. PMID 24983352 DOI: 10.1371/Journal.Pone.0101115  0.723
2014 Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson JJ, Auer M, Wall JD, Mukhopadhyay A. Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. Frontiers in Microbiology. 5: 77. PMID 24639670 DOI: 10.3389/Fmicb.2014.00077  0.31
2013 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. Nature Biotechnology. 31: 1039-46. PMID 24142050 DOI: 10.1038/Nbt.2689  0.795
2013 Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS. New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. Journal of Bacteriology. 195: 4466-75. PMID 23913324 DOI: 10.1128/Jb.00679-13  0.31
2013 Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. The Isme Journal. 7: 2178-91. PMID 23739051 DOI: 10.1038/Ismej.2013.83  0.355
2013 Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The Isme Journal. 7: 1790-802. PMID 23575373 DOI: 10.1038/Ismej.2013.60  0.529
2013 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 Chemical Engineering Science. 103: 68-73. DOI: 10.1016/J.Ces.2013.06.044  0.556
2012 Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling JD. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metabolic Engineering. 14: 653-60. PMID 23026122 DOI: 10.1016/J.Ymben.2012.08.009  0.709
2012 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. The Isme Journal. 6: 2045-55. PMID 22739494 DOI: 10.1038/Ismej.2012.60  0.519
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, et al. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. Plos One. 7: e37010. PMID 22649505 DOI: 10.1371/Journal.Pone.0037010  0.789
2012 Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, 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. 13: 138. PMID 22507456 DOI: 10.1186/1471-2164-13-138  0.787
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, ... ... Mukhopadhyay A, et al. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnology Journal. 10: 609-20. PMID 22458713 DOI: 10.1111/J.1467-7652.2012.00692.X  0.507
2012 Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, et al. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiology. 159: 12-26. PMID 22430844 DOI: 10.1104/Pp.111.193151  0.334
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 Physiology. 158: 654-65. PMID 22158675 DOI: 10.1104/Pp.111.187187  0.475
2012 Juminaga D, Baidoo EE, Redding-Johanson AM, Batth TS, Burd H, Mukhopadhyay A, Petzold CJ, Keasling JD. Modular engineering of L-tyrosine production in Escherichia coli. Applied and Environmental Microbiology. 78: 89-98. PMID 22020510 DOI: 10.1128/Aem.06017-11  0.567
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, et al. A pie chart showing the percent relative abundance of each taxon in the McCel-adapted thermophilic bacterial consortia. Plos One. DOI: 10.1371/Journal.Pone.0037010.G002  0.761
2011 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. 12: R99. PMID 21992415 DOI: 10.1186/Gb-2011-12-10-R99  0.362
2011 Peralta-Yahya PP, Ouellet M, Chan R, Mukhopadhyay A, Keasling JD, Lee TS. Identification and microbial production of a terpene-based advanced biofuel. Nature Communications. 2: 483. PMID 21952217 DOI: 10.1038/Ncomms1494  0.774
2011 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. Nature Reviews. Microbiology. 9: 452-66. PMID 21572460 DOI: 10.1038/Nrmicro2575  0.341
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. Molecular Systems Biology. 7: 487. PMID 21556065 DOI: 10.1038/Msb.2011.21  0.76
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. The Plant Cell. 23: 1373-90. PMID 21478444 DOI: 10.1105/Tpc.111.083931  0.304
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. Metabolic Engineering. 13: 194-203. PMID 21215324 DOI: 10.1016/J.Ymben.2010.12.005  0.584
2011 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. Journal of Proteome Research. 10: 1571-82. PMID 21166475 DOI: 10.1021/Pr1009433  0.36
2011 Ouellet M, Datta S, Dibble DC, Tamrakar PR, Benke PI, Li C, Singh S, Sale KL, Adams PD, Keasling JD, Simmons BA, Holmes BM, Mukhopadhyay A. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production Green Chemistry. 13: 2743-2749. DOI: 10.1039/C1Gc15327G  0.528
2010 Dunlop MJ, Keasling JD, Mukhopadhyay A. A model for improving microbial biofuel production using a synthetic feedback loop. Systems and Synthetic Biology. 4: 95-104. PMID 20805930 DOI: 10.1007/S11693-010-9052-5  0.742
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, Arkin AP, et al. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 12: 2645-57. PMID 20482586 DOI: 10.1111/J.1462-2920.2010.02234.X  0.498
2010 Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD. Functional genomic study of exogenous n-butanol stress in Escherichia coli. Applied and Environmental Microbiology. 76: 1935-45. PMID 20118358 DOI: 10.1128/Aem.02323-09  0.766
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, et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Applied and Environmental Microbiology. 76: 1574-86. PMID 20038696 DOI: 10.1128/Aem.02141-09  0.526
2010 Shaikh AS, Tang YJ, Mukhopadhyay A, Martín HG, Gin J, Benke PI, Keasling JD. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnology Progress. 26: 52-6. PMID 19899123 DOI: 10.1002/Btpr.325  0.62
2010 Rajeev L, Luning E, Dehal P, Joachimiak M, Mukhopadhyay A. Mapping the Two-component Regulatory Networks in Desulfovibrio vulgaris Lawrence Berkeley National Laboratory. DOI: 10.2172/985735  0.304
2010 Ray J, Keller K, Krierim B, Auer M, Keasling J, Wall J, Mukhopadhyay A. Investigating the role of CheA-3 in Dusulfovibrio Vulgaris Hildenborough Lawrence Berkeley National Laboratory. DOI: 10.2172/985233  0.498
2009 Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A. A rapid and inexpensive labeling method for microarray gene expression analysis. Bmc Biotechnology. 9: 97. PMID 19939278 DOI: 10.1186/1472-6750-9-97  0.469
2009 Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, 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. 37: 2926-39. PMID 19293273 DOI: 10.1093/Nar/Gkp164  0.777
2009 Borglin S, Joyner D, Jacobsen J, Mukhopadhyay A, Hazen TC. Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. Journal of Microbiological Methods. 76: 159-68. PMID 18996155 DOI: 10.1016/J.Mimet.2008.10.003  0.346
2008 Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Current Opinion in Biotechnology. 19: 228-34. PMID 18515068 DOI: 10.1016/J.Copbio.2008.05.003  0.812
2008 Fortman JL, Chhabra S, Mukhopadhyay A, Chou H, Lee TS, Steen E, Keasling JD. Biofuel alternatives to ethanol: pumping the microbial well. Trends in Biotechnology. 26: 375-81. PMID 18471913 DOI: 10.1016/J.Tibtech.2008.03.008  0.786
2008 Gaucher SP, Redding AM, Mukhopadhyay A, Keasling JD, Singh AK. Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins. Journal of Proteome Research. 7: 2320-31. PMID 18416566 DOI: 10.1021/Pr700772S  0.778
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 Chemistry. 80: 886-90. PMID 18179240 DOI: 10.1021/Ac071445+  0.635
2007 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, et al. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 189: 5996-6010. PMID 17545284 DOI: 10.1128/Jb.00368-07  0.759
2007 Tang Y, Pingitore F, Mukhopadhyay A, Phan R, Hazen TC, Keasling JD. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry. Journal of Bacteriology. 189: 940-9. PMID 17114264 DOI: 10.1128/Jb.00948-06  0.627
2006 Gao R, Mukhopadhyay A, Fang F, Lynn DG. Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens. Journal of Bacteriology. 188: 5204-11. PMID 16816192 DOI: 10.1128/Jb.00387-06  0.627
2006 Redding AM, Mukhopadhyay A, Joyner DC, Hazen TC, Keasling JD. Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics. Briefings in Functional Genomics & Proteomics. 5: 133-43. PMID 16772278 DOI: 10.1093/Bfgp/Ell025  0.781
2006 Mukhopadhyay A, He Z, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, et al. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. Journal of Bacteriology. 188: 4068-78. PMID 16707698 DOI: 10.1128/Jb.01921-05  0.783
2004 Mukhopadhyay A, Gao R, Lynn DG. Integrating input from multiple signals: the VirA/VirG two-component system of Agrobacterium tumefaciens. Chembiochem : a European Journal of Chemical Biology. 5: 1535-42. PMID 15515087 DOI: 10.1002/Cbic.200300828  0.474
2000 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. 242: 105-14. PMID 10721702 DOI: 10.1016/S0378-1119(99)00541-7  0.489
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