Publications

At ORNL

  • Cahill JF, Kertesz V, Saint-Vincent P, Valentino H, Drufva E, Thiele N, and Michener JK. High-Throughput Characterization and Optimization of Polyamide Hydrolase Activity Using Open Port Sampling Interface Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2023 June, 34, 7, 1383–1391. Link.
  • Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz K, Burnet M, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim Y-M, Apffel A, Magnuson JK, and Burnum-Johnson KE*. PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements. Nat Comms 2023 April 28; 14: 2461. Link.
  • Allemann MN, Presley GN, Elkins JG, and Michener JK*. Sphingobium lignivorans sp. nov., isolated from river sediment downstream of a paper mill. Int J Syst Evol Microbiol 2023 Feb. Link.
  • Kuatsjah E, Zahn M, Chen X, Kato R, Hinchen DJ, Konev MO, Katahira R, Orr C, Wagner A, Zou Y, Haugen SJ, Ramirez KJ, Michener JK, Pickford AR, Kamimura N, Masai E*, Houk KN*, McGeehan JE*, and Beckham GT*. Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation. Proc Natl Acad Sci USA 2023 Jan; 120 (4) e2212246120. Link.
  • Varner PM, Allemann MN, Michener JK, and Gunsch CK*. The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation. Environ. Technol. Innov. 2022 November; 28: 102910. Link.
  • Bleem A†, Kuatsjah E†, Presley GP†, Hinchen DJ, Zahn M, Garcia DC, Michener WE, König G, Tornesakis K, Allemann MN, Giannone RJ, McGeehan JE*, Beckham GT*, and Michener JK*. Discovery, characterization, and metabolic engineering of Rieske non-heme iron monooxygenases for guaiacol O-demethylation. Chem Cat 18 August 2022; 2 (8) : 1989-2011. Link. 
  • Vasileva DP†, Streich JC†, Burdick LH†, Klingeman DM, Chhetri HB, Brelsford CM, Ellis JC, Close DM, Jacobson DA, and Michener JK*. Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination. Nucleic Acids Res 24 June 2022; 50 (11) : 6211-6223. Link. 
  • Moore JAM, Abraham PE, Michener JK, Muchero W, and Cregger MA*. Ecosystem consequences of introducing plant growth promoting rhizobacteria to managed systems and potential legacy effects. New Phytologist 2022 Jan; 234:1914–1918. Link.
  • Azubuike CC, Allemann MN, and Michener JK*. Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products. Curr Opin Microbiol 2021 Nov 11;65:64-72. Link.
  • Presley GN†, Werner AZ†, Katahira R, Garcia DC, Haugen SJ, Ramirez KJ, Giannone RJ, Beckham GT*, Michener JK*. Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound. Metab Eng 2021 May; 65: 1-10. Link. 
  • Cregger MA, Carper DL, Christel S, Doktycz MJ, Labbé J, Michener JK, Dove NC, Johnston ER, Moore JAM, Vélez JM, Morrell-Falvey J, Muchero W, Pelletier DA, Retterer S, Tschaplinski TJ,  Tuskan GA, Weston DJ, and Schadt CW*. Plant–Microbe Interactions: From Genes to Ecosystems Using Populus as a Model System. Phytobiomes J 2021 Mar; 5 : 29-38. Link.
  • Hatmaker E, Presley G, Cannon O, Michener JK, Guss A, and Elkins J*. Complete genome sequences of four natural Pseudomonas isolates that catabolize a wide range of aromatic compounds relevant to lignin valorization. Microbiol Resour Announc 2020 Dec 3;9(49):e00975-20. Link.
  • Elmore JR, Dexter GN, Salvachúa D, O’Brien M, Klingeman DM, Gorday K, Michener JK, Peterson DJ, Beckham GT, and Guss AM*. Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid. Metab Eng 2020 Nov; 62 : 62-71. Link.
  • Chaves JE, Wilton R, Gao Y, Munoz Munoz N, Burnet MC, Schmitz Z, Rowan J, Burdick LH, Elmore J, Guss A, Close D, Magnuson JK, Burnum-Johnson KE, and Michener JK*, Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design. Met Eng Comm 2020 Jul 19;11:e00139. Link.
  • Gilmour CG*, Bullock Soren A, Gionfriddo CM, Podar M, Wall JD, Brown SD, Michener JK, Soledad Goñi Urriza M, Elias DA. Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment. Int J Syst Evol Microbiol 2019 Jun;71(3). Link.
  • Close D, Cooper CJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle NL, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, and Michener JK*, Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 2019. Link
  • Millet LJ, Velez JM, and Michener JK*. Genetic selection for small molecule production in competitive microfluidic droplets. ACS Synth Biol. Link.
  • Trofimov AA, Pawlicki AA, Borodinov N, Mandal S, Mathews TJ, Hildebrand M, Ziatdinov MA, Hausladen KA, Urbanowicz PK, Steed CA, Ievlev AV, Belianinov A, Michener JK, Vasudevan R, and Ovchinnikova OS*. Deep data analytics for genetic engineering of diatoms linking genotype to phenotype via machine learning. npj Comput Mater 2019 5:67. Link.
  • Chaves JE, Presley GN, and Michener JK*, Modular engineering of biomass degradation pathways. Processes 2019, 7(4), 230. Link.
  • Cecil JH, Garcia DC, Giannone RJ, and Michener JK*, Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds in Novosphingobium aromaticivorans. Appl Environ Microbiol 2018. 84:e01185-18. Link.
  • Tuskan GA*, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart L, Yin T, Aury J-M, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall J, Westbrook J, Grimwod J, Muchero W, Jacobson D, and Michener JK, Hardwood tree genomics: Unlocking woody plant biology. Front Plant Sci. 2018; 9: 1799. Link.
  • Standaert RF, Giannone RJ, and Michener JK*. Identification of parallel and divergent optimization solutions for homologous metabolic enzymes. Metab Eng Comm 2018. 6:56-62. Link.
  • Clarkson SM, Giannone RJ, Kridelbaugh DM, Elkins JG, Guss AM*, and Michener JK*, Construction and optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli enables bioconversion of model aromatic compounds. Appl Env Microbiol 2017 Aug 31;83(18). Link.24

Prior to ORNL

  • Michener JK*, Vuilleumier S, Bringel F, and Marx CJ. Transfer of a catabolic pathway for chloromethane in Methylobacterium strains highlights different limitations for growth with chloromethane or with dichloromethane. Front Microbiol 2016. Link
  • Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, et al. Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation. PLoS Comput Biol 2015; 11(8): e1004400. Link
  • Michener JK, Camargo Neves AAC, Vuilleumier S, Bringel F, and Marx CJ. Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. eLife. 2014;10.7554/eLife.04279 Link.
  • Michener JK, Vuilleumier S, Bringel F, and Marx CJ. Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in Methylobacterium strains. J Bacteriol., June 2014 196:2101-2107 Link.
  • Michener JK and Smolke CD. Synthetic RNA switches for yeast metabolic engineering. Methods in Molecular Biology, Yeast Metabolic Engineering. 2012; 1152:125-36 Link.
  • Michener JK, Nielsen J, and Smolke CD. Identification and treatment of heme depletion due to over-expression of a lineage of evolved P450 monooxygenases. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19504-9. Link.
  • Michener JK and Smolke CD. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metabolic Engineering. 2012 Jul; 14(4):306-16. Link
  • Michener JK, Thodey K, Liang JC, and Smolke CD. (2011) Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metabolic Engineering. 2012 May; 14(3):212-22. Link
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