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Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida.

Thompson MG, Pearson AN, Barajas JF, Cruz-Morales P, Sedaghatian N, Costello Z, Garber ME, Incha MR, Valencia LE, Baidoo EEK, Martin HG, Mukhopadhyay A, Keasling JD.

ACS Synth Biol. 2020 Jan 17;9(1):53-62. doi: 10.1021/acssynbio.9b00292. Epub 2020 Jan 2.


Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase.

Blake-Hedges JM, Pereira JH, Cruz-Morales P, Thompson MG, Barajas JF, Chen J, Krishna RN, Chan LJG, Nimlos D, Alonso-Martinez C, Baidoo EEK, Chen Y, Gin JW, Katz L, Petzold CJ, Adams PD, Keasling JD.

J Am Chem Soc. 2020 Jan 15;142(2):835-846. doi: 10.1021/jacs.9b09187. Epub 2020 Jan 2.


Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer.

Thompson MG, Valencia LE, Blake-Hedges JM, Cruz-Morales P, Velasquez AE, Pearson AN, Sermeno LN, Sharpless WA, Benites VT, Chen Y, Baidoo EEK, Petzold CJ, Deutschbauer AM, Keasling JD.

Metab Eng Commun. 2019 Aug 10;9:e00098. doi: 10.1016/j.mec.2019.e00098. eCollection 2019 Dec.


Mevalonate Pathway Promiscuity Enables Noncanonical Terpene Production.

Eiben CB, de Rond T, Bloszies C, Gin J, Chiniquy J, Baidoo EEK, Petzold CJ, Hillson NJ, Fiehn O, Keasling JD.

ACS Synth Biol. 2019 Oct 18;8(10):2238-2247. doi: 10.1021/acssynbio.9b00230. Epub 2019 Oct 2.


Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli.

Kang A, Mendez-Perez D, Goh EB, Baidoo EEK, Benites VT, Beller HR, Keasling JD, Adams PD, Mukhopadhyay A, Lee TS.

Metab Eng. 2019 Dec;56:85-96. doi: 10.1016/j.ymben.2019.09.003. Epub 2019 Sep 6.


Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis.

Brenac L, Baidoo EEK, Keasling JD, Budin I.

Mol Microbiol. 2019 Nov;112(5):1564-1575. doi: 10.1111/mmi.14380. Epub 2019 Sep 17.


Production of clovamide and its analogues in Saccharomyces cerevisiae and Lactococcus lactis.

Bouchez P, Teixeira Benites V, Baidoo EEK, Mortimer JC, Sullivan ML, Scheller HV, Eudes A.

Lett Appl Microbiol. 2019 Sep;69(3):181-189. doi: 10.1111/lam.13190. Epub 2019 Jul 16.


A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction.

Liang Y, Eudes A, Yogiswara S, Jing B, Benites VT, Yamanaka R, Cheng-Yue C, Baidoo EE, Mortimer JC, Scheller HV, Loqué D.

Biotechnol Biofuels. 2019 May 23;12:130. doi: 10.1186/s13068-019-1467-y. eCollection 2019.


Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.

Barajas JF, McAndrew RP, Thompson MG, Backman TWH, Pang B, de Rond T, Pereira JH, Benites VT, Martín HG, Baidoo EEK, Hillson NJ, Adams PD, Keasling JD.

J Ind Microbiol Biotechnol. 2019 Aug;46(8):1225-1235. doi: 10.1007/s10295-019-02189-z. Epub 2019 May 21.


Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning.

Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR.

ACS Synth Biol. 2019 Jun 21;8(6):1337-1351. doi: 10.1021/acssynbio.9b00020. Epub 2019 May 24.


Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.

Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD.

mBio. 2019 May 7;10(3). pii: e02577-18. doi: 10.1128/mBio.02577-18.


Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids.

Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW.

Biotechnol Bioeng. 2019 Aug;116(8):1909-1922. doi: 10.1002/bit.26995. Epub 2019 Apr 29.


Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.

Luo X, Reiter MA, d'Espaux L, Wong J, Denby CM, Lechner A, Zhang Y, Grzybowski AT, Harth S, Lin W, Lee H, Yu C, Shin J, Deng K, Benites VT, Wang G, Baidoo EEK, Chen Y, Dev I, Petzold CJ, Keasling JD.

Nature. 2019 Mar;567(7746):123-126. doi: 10.1038/s41586-019-0978-9. Epub 2019 Feb 27.


Discovery of novel geranylgeranyl reductases and characterization of their substrate promiscuity.

Meadows CW, Mingardon F, Garabedian BM, Baidoo EEK, Benites VT, Rodrigues AV, Abourjeily R, Chanal A, Lee TS.

Biotechnol Biofuels. 2018 Dec 28;11:340. doi: 10.1186/s13068-018-1342-2. eCollection 2018.


Characterization, Spatial Variation and Risk Assessment of Heavy Metals and a Metalloid in Surface Soils in Obuasi, Ghana.

Akoto O, Bortey-Sam N, Nakayama SMM, Ikenaka Y, Baidoo E, Apau J, Marfo JT, Ishizuka M.

J Health Pollut. 2018 Aug 20;8(19):180902. doi: 10.5696/2156-9614-8.19.180902. eCollection 2018 Sep.


Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H.

Czajka JJ, Abernathy MH, Benites VT, Baidoo EEK, Deming JW, Tang YJ.

Proc Natl Acad Sci U S A. 2018 Dec 4;115(49):12507-12512. doi: 10.1073/pnas.1807804115. Epub 2018 Nov 16.


Liquid Chromatography and Mass Spectrometry Analysis of Isoprenoid Intermediates in Escherichia coli.

Baidoo EEK, Wang G, Joshua CJ, Benites VT, Keasling JD.

Methods Mol Biol. 2019;1859:209-224. doi: 10.1007/978-1-4939-8757-3_11.


Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications.

Baidoo EEK, Teixeira Benites V.

Methods Mol Biol. 2019;1859:11-69. doi: 10.1007/978-1-4939-8757-3_2.


Microbial Metabolomics: A General Overview.

Baidoo EEK.

Methods Mol Biol. 2019;1859:1-8. doi: 10.1007/978-1-4939-8757-3_1.


Short-chain ketone production by engineered polyketide synthases in Streptomyces albus.

Yuzawa S, Mirsiaghi M, Jocic R, Fujii T, Masson F, Benites VT, Baidoo EEK, Sundstrom E, Tanjore D, Pray TR, George A, Davis RW, Gladden JM, Simmons BA, Katz L, Keasling JD.

Nat Commun. 2018 Nov 1;9(1):4569. doi: 10.1038/s41467-018-07040-0.


Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli.

Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS.

Biotechnol Biofuels. 2018 Oct 20;11:285. doi: 10.1186/s13068-018-1272-z. eCollection 2018.


Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC.

Eng T, Demling P, Herbert RA, Chen Y, Benites V, Martin J, Lipzen A, Baidoo EEK, Blank LM, Petzold CJ, Mukhopadhyay A.

Microb Cell Fact. 2018 Oct 8;17(1):159. doi: 10.1186/s12934-018-1006-8.


Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification.

Li G, Jones KC, Eudes A, Pidatala VR, Sun J, Xu F, Zhang C, Wei T, Jain R, Birdseye D, Canlas PE, Baidoo EEK, Duong PQ, Sharma MK, Singh S, Ruan D, Keasling JD, Mortimer JC, Loqué D, Bartley LE, Scheller HV, Ronald PC.

BMC Biotechnol. 2018 Sep 4;18(1):54. doi: 10.1186/s12896-018-0464-8.


Engineering the oleaginous yeast Yarrowia lipolytica to produce the aroma compound β-ionone.

Czajka JJ, Nathenson JA, Benites VT, Baidoo EEK, Cheng Q, Wang Y, Tang YJ.

Microb Cell Fact. 2018 Sep 1;17(1):136. doi: 10.1186/s12934-018-0984-x.


Increased drought tolerance in plants engineered for low lignin and low xylan content.

Yan J, Aznar A, Chalvin C, Birdseye DS, Baidoo EEK, Eudes A, Shih PM, Loqué D, Zhang A, Scheller HV.

Biotechnol Biofuels. 2018 Jul 18;11:195. doi: 10.1186/s13068-018-1196-7. eCollection 2018.


Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B2 Biosynthesis.

Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD.

Chembiochem. 2018 Jul 4;19(13):1391-1395. doi: 10.1002/cbic.201800169. Epub 2018 May 14.


Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli.

George KW, Thompson MG, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS.

Metab Eng. 2018 May;47:60-72. doi: 10.1016/j.ymben.2018.03.004. Epub 2018 Mar 9.


Production of muconic acid in plants.

Eudes A, Berthomieu R, Hao Z, Zhao N, Benites VT, Baidoo EEK, Loqué D.

Metab Eng. 2018 Mar;46:13-19. doi: 10.1016/j.ymben.2018.02.002. Epub 2018 Feb 21.


Association between human exposure to heavy metals/metalloid and occurrences of respiratory diseases, lipid peroxidation and DNA damage in Kumasi, Ghana.

Bortey-Sam N, Ikenaka Y, Akoto O, Nakayama SMM, Asante KA, Baidoo E, Obirikorang C, Mizukawa H, Ishizuka M.

Environ Pollut. 2018 Apr;235:163-170. doi: 10.1016/j.envpol.2017.12.005. Epub 2017 Dec 27.


Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts.

Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM.

Biotechnol Biofuels. 2017 Oct 23;10:241. doi: 10.1186/s13068-017-0927-5. eCollection 2017.


Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase.

Yuzawa S, Bailey CB, Fujii T, Jocic R, Barajas JF, Benites VT, Baidoo EEK, Chen Y, Petzold CJ, Katz L, Keasling JD.

ACS Chem Biol. 2017 Nov 17;12(11):2725-2729. doi: 10.1021/acschembio.7b00714. Epub 2017 Oct 17.


Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme.

de Rond T, Stow P, Eigl I, Johnson RE, Chan LJG, Goyal G, Baidoo EEK, Hillson NJ, Petzold CJ, Sarpong R, Keasling JD.

Nat Chem Biol. 2017 Nov;13(11):1155-1157. doi: 10.1038/nchembio.2471. Epub 2017 Sep 11.


Contamination Levels and Sources of Heavy Metals and a Metalloid in Surface Soils in the Kumasi Metropolis, Ghana.

Akoto O, Bortey-Sam N, Ikenaka Y, Nakayama SMM, Baidoo E, Yohannes YB, Ishizuka M.

J Health Pollut. 2017 Sep 7;7(15):28-39. doi: 10.5696/2156-9614-7.15.28. eCollection 2017 Sep.


The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization.

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, Garcia Martin H.

ACS Synth Biol. 2017 Dec 15;6(12):2248-2259. doi: 10.1021/acssynbio.7b00204. Epub 2017 Sep 8.


Engineering glucose metabolism of Escherichia coli under nitrogen starvation.

Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EE, Petzold CJ, Keasling JD, Mukhopadhyay A.

NPJ Syst Biol Appl. 2017 Jan 5;3:16035. doi: 10.1038/npjsba.2016.35. eCollection 2017.


Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism.

Shymansky CM, Wang G, Baidoo EEK, Gin J, Apel AR, Mukhopadhyay A, García Martín H, Keasling JD.

Front Bioeng Biotechnol. 2017 May 24;5:31. doi: 10.3389/fbioe.2017.00031. eCollection 2017.


SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum.

Eudes A, Dutta T, Deng K, Jacquet N, Sinha A, Benites VT, Baidoo EEK, Richel A, Sattler SE, Northen TR, Singh S, Simmons BA, Loqué D.

PLoS One. 2017 Jun 8;12(6):e0178160. doi: 10.1371/journal.pone.0178160. eCollection 2017.


Oxidative stress and respiratory symptoms due to human exposure to polycyclic aromatic hydrocarbons (PAHs) in Kumasi, Ghana.

Bortey-Sam N, Ikenaka Y, Akoto O, Nakayama SMM, Asante KA, Baidoo E, Obirikorang C, Saengtienchai A, Isoda N, Nimako C, Mizukawa H, Ishizuka M.

Environ Pollut. 2017 Sep;228:311-320. doi: 10.1016/j.envpol.2017.05.036. Epub 2017 May 25.


Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis.

Zhang J, Barajas JF, Burdu M, Wang G, Baidoo EE, Keasling JD.

ACS Synth Biol. 2017 May 19;6(5):884-890. doi: 10.1021/acssynbio.6b00372. Epub 2017 Apr 30.


Production of jet fuel precursor monoterpenoids from engineered Escherichia coli.

Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams PD, Petzold CJ, Keasling JD, Lee TS.

Biotechnol Bioeng. 2017 Aug;114(8):1703-1712. doi: 10.1002/bit.26296. Epub 2017 May 18.


Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence.

Wan N, DeLorenzo DM, He L, You L, Immethun CM, Wang G, Baidoo EEK, Hollinshead W, Keasling JD, Moon TS, Tang YJ.

Biotechnol Bioeng. 2017 Jul;114(7):1593-1602. doi: 10.1002/bit.26287. Epub 2017 Mar 30.


Production of Odd-Carbon Dicarboxylic Acids in Escherichia coli Using an Engineered Biotin-Fatty Acid Biosynthetic Pathway.

Haushalter RW, Phelan RM, Hoh KM, Su C, Wang G, Baidoo EE, Keasling JD.

J Am Chem Soc. 2017 Apr 5;139(13):4615-4618. doi: 10.1021/jacs.6b11895. Epub 2017 Mar 21.


Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions.

He L, Xiu Y, Jones JA, Baidoo EEK, Keasling JD, Tang YJ, Koffas MAG.

Metab Eng. 2017 Jan;39:247-256. doi: 10.1016/j.ymben.2016.12.008. Epub 2016 Dec 23.


Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae.

Kirby J, Dietzel KL, Wichmann G, Chan R, Antipov E, Moss N, Baidoo EEK, Jackson P, Gaucher SP, Gottlieb S, LaBarge J, Mahatdejkul T, Hawkins KM, Muley S, Newman JD, Liu P, Keasling JD, Zhao L.

Metab Eng. 2016 Nov;38:494-503. doi: 10.1016/j.ymben.2016.10.017. Epub 2016 Oct 27.


Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis.

Fang L, Ishikawa T, Rennie EA, Murawska GM, Lao J, Yan J, Tsai AY, Baidoo EE, Xu J, Keasling JD, Demura T, Kawai-Yamada M, Scheller HV, Mortimer JC.

Plant Cell. 2016 Dec;28(12):2991-3004. doi: 10.1105/tpc.16.00186. Epub 2016 Nov 28.


Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast.

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.

Microb Cell Fact. 2016 Nov 21;15(1):198.


Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants.

Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EE, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ.

Biotechnol Biofuels. 2016 Oct 10;9:212. eCollection 2016.


13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids.

Ghosh A, Ando D, Gin J, Runguphan W, Denby C, Wang G, Baidoo EE, Shymansky C, Keasling JD, García Martín H.

Front Bioeng Biotechnol. 2016 Oct 5;4:76. eCollection 2016.


Glycosylation of inositol phosphorylceramide sphingolipids is required for normal growth and reproduction in Arabidopsis.

Tartaglio V, Rennie EA, Cahoon R, Wang G, Baidoo E, Mortimer JC, Cahoon EB, Scheller HV.

Plant J. 2017 Jan;89(2):278-290. doi: 10.1111/tpj.13382. Epub 2017 Jan 25.


Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production.

Yuzawa S, Deng K, Wang G, Baidoo EE, Northen TR, Adams PD, Katz L, Keasling JD.

ACS Synth Biol. 2017 Jan 20;6(1):139-147. doi: 10.1021/acssynbio.6b00176. Epub 2016 Sep 6.


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