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Thomas Eng - Publications

Affiliations: 
Lawrence Berkeley National Laboratory, Berkeley, CA, USA 
Area:
systems biology, genetics
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33 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
2025 Lim HG, Srinivasan A, Menchavez R, Yunus IS, Noh MH, White M, Chen Y, Gin JW, Palsson BO, Lee TS, Petzold CJ, Eng T, Mukhopadhyay A, Feist AM. Evolution-guided tolerance engineering of Pseudomonas putida KT2440 for production of the aviation fuel precursor isoprenol. Metabolic Engineering. PMID 40398593 DOI: 10.1016/j.ymben.2025.05.007  0.534
2025 Zournas A, Incha MR, Radivojevic T, Blay V, Martí JM, Costello Z, Schmidt M, Chung T, Thompson MG, Pearson A, Kinnunen PC, Eng T, Lawson CE, Tan S, Ogorzalek T, et al. Author Correction: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida. Communications Biology. 8: 747. PMID 40360703 DOI: 10.1038/s42003-025-08141-5  0.516
2025 Zournas A, Incha MR, Radivojevic T, Blay V, Martí JM, Costello Z, Schimdt M, Chung T, Thompson MG, Pearson A, Kinnunen PC, Eng T, Lawson CE, Tan S, Ogorzalek T, et al. Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida. Communications Biology. 8: 630. PMID 40251395 DOI: 10.1038/s42003-025-08039-2  0.546
2025 de Siqueira GMV, Srinivasan A, Chen Y, Gin JW, Petzold CJ, Lee TS, Guazzaroni M-E, Eng T, Mukhopadhyay A. Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources in . Applied and Environmental Microbiology. e0212324. PMID 40110994 DOI: 10.1128/aem.02123-24  0.519
2025 Baral NR, Banerjee D, Eng T, Simmons BA, Mukhopadhyay A, Scown CD. Microbial Pathways for Cost-Effective Low-Carbon Renewable Indigoidine. Acs Sustainable Chemistry & Engineering. 13: 3300-3310. PMID 40052115 DOI: 10.1021/acssuschemeng.4c09962  0.449
2025 Banerjee D, Menasalvas J, Chen Y, Gin JW, Baidoo EEK, Petzold CJ, Eng T, Mukhopadhyay A. Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source. Npj Systems Biology and Applications. 11: 8. PMID 39809795 DOI: 10.1038/s41540-024-00480-z  0.521
2024 Priya S, Rossbach S, Eng T, Lin H-H, Andeer PF, Mortimer JC, Northen TR, Mukhopadhyay A. Assessing horizontal gene transfer in the rhizosphere of using fabricated ecosystems (EcoFABs). Applied and Environmental Microbiology. 90: e0150524. PMID 39494898 DOI: 10.1128/aem.01505-24  0.437
2024 Kakouridis A, Diamond S, Eng T, Mills HJ, Gámez Holzhaus O, Summers ML, Garcia-Pichel F, Mukhopadhyay A. Desiccated Cyanobacteria Serve As Efficient Plasmid DNA Carriers in Space Flight. Acs Synthetic Biology. PMID 39150229 DOI: 10.1021/acssynbio.3c00672  0.421
2024 Srinivasan A, Chen-Xiao K, Banerjee D, Oka A, Pidatala VR, Eudes A, Simmons BA, Eng T, Mukhopadhyay A. Sustainable production of 2,3,5,6-tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum. Journal of Industrial Microbiology & Biotechnology. PMID 39013608 DOI: 10.1093/jimb/kuae026  0.497
2023 Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, et al. Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Reports. 42: 113087. PMID 37665664 DOI: 10.1016/j.celrep.2023.113087  0.582
2023 Gauttam R, Eng T, Zhao Z, Ul Ain Rana Q, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer SW. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microbial Biotechnology. PMID 36691869 DOI: 10.1111/1751-7915.14205  0.505
2022 Zhao R, Sengupta A, Tan AX, Whelan R, Pinkerton T, Menasalvas J, Eng T, Mukhopadhyay A, Jun YS, Pakrasi HB, Tang YJ. Photobiological production of high-value pigments via compartmentalized co-cultures using Ca-alginate hydrogels. Scientific Reports. 12: 22163. PMID 36550285 DOI: 10.1038/s41598-022-26437-y  0.439
2022 Zha J, Zhao Z, Xiao Z, Eng T, Mukhopadhyay A, Koffas MA, Tang YJ. Biosystem design of Corynebacterium glutamicum for bioproduction. Current Opinion in Biotechnology. 79: 102870. PMID 36549106 DOI: 10.1016/j.copbio.2022.102870  0.465
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  0.517
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  0.5
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  0.514
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  0.564
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  0.524
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  0.487
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  0.555
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  0.513
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  0.468
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  0.498
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  0.54
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  0.52
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  0.518
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  0.683
2015 Eng T, Guacci V, Koshland D. Interallelic complementation provides functional evidence for cohesin-cohesin interactions on DNA. Molecular Biology of the Cell. 26: 4224-35. PMID 26378250 DOI: 10.1091/Mbc.E15-06-0331  0.588
2015 Orgil O, Matityahu A, Eng T, Guacci V, Koshland D, Onn I. A conserved domain in the scc3 subunit of cohesin mediates the interaction with both mcd1 and the cohesin loader complex. Plos Genetics. 11: e1005036. PMID 25748820 DOI: 10.1371/Journal.Pgen.1005036  0.582
2014 Eng T, Guacci V, Koshland D. ROCC, a conserved region in cohesin's Mcd1 subunit, is essential for the proper regulation of the maintenance of cohesion and establishment of condensation. Molecular Biology of the Cell. 25: 2351-64. PMID 24966169 DOI: 10.1091/Mbc.E14-04-0929  0.594
2012 Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Research. 22: 64-75. PMID 22090375 DOI: 10.1101/Gr.126003.111  0.599
2011 Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, MacAlpine DM, Orr-Weaver TL. Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes & Development. 25: 1384-98. PMID 21724831 DOI: 10.1101/Gad.2043111  0.616
2011 Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Research. 21: 175-81. PMID 21177957 DOI: 10.1101/Gr.114611.110  0.579
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