Publications

Ferrara, M., Gallo, A., Cervini, C., Gambacorta, L., Solfrizzo, M., Baker, S. E., & Perrone, G. (2021). Evidence of the Involvement of a Cyclase Gene in the Biosynthesis of Ochratoxin A in Aspergillus carbonarius. Toxins (Basel), 13(12). https://doi.org/10.3390/toxins13120892

Zhao, Y., Yu, X.-H., & Liu, C.-J. (2021). The Inducible Accumulation of Cell Wall-Bound p-Hydroxybenzoates Is Involved in the Regulation of Gravitropic Response of Poplar. Frontiers in Plant Science, 12(2861). https://doi.org/10.3389/fpls.2021.755576

Carruthers, D. N., & Lee, T. S. (2021). Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms. Front Microbiol, 12(3725). https://doi.org/10.3389/fmicb.2021.791089

Tian, Y., Lin, C.-Y., Park, J.-H., Wu, C.-Y., Kakumanu, R., Pidatala, V. R., Vuu, K. M., Rodriguez, A., Shih, P. M., Baidoo, E. E. K., Temple, S., Simmons, B. A., Gladden, J. M., Scheller, H. V., & Eudes, A. (2021). Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolor. Biotechnology for Biofuels, 14(1), 217. https://doi.org/10.1186/s13068-021-02068-9

Rahaman, M. S., Tulaphol, S., Hossain, M. A., Jasinski, J. B., Sun, N., George, A., Simmons, B. A., Maihom, T., Crocker, M., & Sathitsuksanoh, N. (2021). Cooperative Brønsted-Lewis acid sites created by phosphotungstic acid encapsulated metal–organic frameworks for selective glucose conversion to 5-hydroxymethylfurfural. Fuel, 122459. https://doi.org/https://doi.org/10.1016/j.fuel.2021.122459

Pérez-Pimienta, J. A., García-López, R. M., Méndez-Acosta, H. O., González-Álvarez, V., Simmons, B. A., Méndoza-Pérez, J. A., & Arreola-Vargas, J. (2021). Ionic liquid-water mixtures enhance pretreatment and anaerobic digestion of agave bagasse. Industrial Crops and Products, 171, 113924. https://doi.org/https://doi.org/10.1016/j.indcrop.2021.113924

Banerjee, D., Eng, T., Sasaki, Y., Srinivasan, A., Oka, A., Herbert, R. A., Trinh, J., Singan, V. R., Sun, N., Putnam, D., Scown, C. D., Simmons, B., & Mukhopadhyay, A. (2021). Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress. Frontiers in Bioengineering and Biotechnology, 9(1119). https://doi.org/10.3389/fbioe.2021.766674

Scavuzzo-Duggan, T., Varoquaux, N., Madera, M., Vogel, J. P., Dahlberg, J., Hutmacher, R., Belcher, M., Ortega, J., Coleman-Derr, D., Lemaux, P., Purdom, E., & Scheller, H. V. (2021). Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions. Frontiers in Plant Science, 12(2537). https://doi.org/10.3389/fpls.2021.747225

Pang, B., Li, J., Eiben, C. B., Oksen, E., Barcelos, C., Chen, R., Englund, E., Sundstrom, E., & Keasling, J. D. (2021). Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels. Metab Eng, 68, 210–219. https://doi.org/10.1016/j.ymben.2021.10.007

Leggieri, P. A., Kerdman-Andrade, C., Lankiewicz, T. S., Valentine, M. T., & O’Malley, M. A. (2021). Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture. Microbial Cell Factories, 20(1), 199. https://doi.org/10.1186/s12934-021-01684-2

Huang, J., Liu, Z., Bloomer, B. J., Clark, D. S., Mukhopadhyay, A., Keasling, J. D., & Hartwig, J. F. (2021). Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme. Nature Chemistry. https://doi.org/10.1038/s41557-021-00801-3

Wang, Y., Meng, X., Tian, Y., Kim, K. H., Jia, L., Pu, Y., Leem, G., Kumar, D., Eudes, A., Ragauskas, A. J., & Yoo, C. G. (2021). Engineered Sorghum Bagasse Enables a Sustainable Biorefinery with p-Hydroxybenzoic Acid-Based Deep Eutectic Solvent. ChemSusChem, n/a(n/a). https://doi.org/https://doi.org/10.1002/cssc.202101492

Rodriguez, A., Meadows, J. A., Sun, N., Simmons, B. A., & Gladden, J. M. (2021). Evaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenol. Microbial Cell Factories, 20(1), 181. https://doi.org/10.1186/s12934-021-01670-8

Plahar, H. A., Rich, T. N., Lane, S. D., Morrell, W. C., Springthorpe, L., Nnadi, O., Aravina, E., Dai, T., Fero, M. J., Hillson, N. J., & Petzold, C. J. (2021). BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.1c00263

Baral, N. R., Yang, M., Harvey, B. G., Simmons, B. A., Mukhopadhyay, A., Lee, T. S., & Scown, C. D. (2021). Production Cost and Carbon Footprint of Biomass-Derived Dimethylcyclooctane as a High-Performance Jet Fuel Blendstock. ACS Sustainable Chemistry & Engineering. https://doi.org/10.1021/acssuschemeng.1c03772

Dewhirst, R. A., Handakumbura, P., Clendinen, C. S., Arm, E., Tate, K., Wang, W., Washton, N. M., Young, R. P., Mortimer, J. C., McDowell, N. G., & Jardine, K. J. (2021). High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa. ACS Earth and Space Chemistry, 5(8), 1813–1828. https://doi.org/10.1021/acsearthspacechem.0c00299

Lim, H. G., Eng, T., Banerjee, D., Alarcon, G., Lau, A. K., Park, M.-R., Simmons, B. A., Palsson, B. O., Singer, S. W., Mukhopadhyay, A., & Feist, A. M. (2021). Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution. ACS Sustainable Chemistry & Engineering. https://doi.org/10.1021/acssuschemeng.1c03765

Cole, B., Bergmann, D., Blaby-Haas, C. E., Blaby, I. K., Bouchard, K. E., Brady, S. M., Ciobanu, D., Coleman-Derr, D., Leiboff, S., Mortimer, J. C., Nobori, T., Rhee, S. Y., Schmutz, J., Simmons, B. A., Singh, A. K., Sinha, N., Vogel, J. P., O’Malley, R. C., Visel, A., & Dickel, D. E. (2021). Plant single-cell solutions for energy and the environment. Communications Biology, 4(1), 962. https://doi.org/10.1038/s42003-021-02477-4

Gabriel, R., Mueller, R., Floerl, L., Hopson, C., Harth, S., Schuerg, T., Fleissner, A., & Singer, S. W. (2021). CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars. Biotechnology for Biofuels, 14(1), 169. https://doi.org/10.1186/s13068-021-02018-5

Zhao, Y., Yu, X., Lam, P.-Y., Zhang, K., Tobimatsu, Y., & Liu, C.-J. (2021). Monolignol acyltransferase for lignin p-hydroxybenzoylation in Populus. Nature Plants. https://doi.org/10.1038/s41477-021-00975-1

Swift, C. L., Malinov, N. G., Mondo, S. J., Salamov, A., Grigoriev, I. V., & O’Malley, M. A. (2021). A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction. Frontiers in Fungal Biology, 2(29). https://doi.org/10.3389/ffunb.2021.708358

Leynaud Kieffer Curran, L. M. C., Pham, L. T. M., Sale, K. L., & Simmons, B. A. (2021). Review of advances in the development of laccases for the valorization of lignin to enable the production of lignocellulosic biofuels and bioproducts. Biotechnology Advances, 107809. https://doi.org/https://doi.org/10.1016/j.biotechadv.2021.107809

Liu, C. L., Xue, K., Yang, Y., Liu, X., Li, Y., Lee, T. S., Bai, Z., & Tan, T. (2021). Metabolic engineering strategies for sesquiterpene production in microorganism. Crit Rev Biotechnol, 1–20. https://doi.org/10.1080/07388551.2021.1924112

Chen, T.-C., Chern, M., Steinwand, M., Ruan, D., Wang, Y., Isharani, A., & Ronald, P. (2021). Paladin, a tyrosine phosphatase-like protein, is required for XA21-mediated immunity in rice. Plant Communications, 2(4), 100215. https://doi.org/https://doi.org/10.1016/j.xplc.2021.100215

Eng, T., Banerjee, D., Lau, A. K., Bowden, E., Herbert, R. A., Trinh, J., Prahl, J.-P., Deutschbauer, A., Tanjore, D., & Mukhopadhyay, A. (2021). Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor. Metabolic Engineering, 66, 229–238. https://doi.org/https://doi.org/10.1016/j.ymben.2021.04.015

Keasling, J., Garcia Martin, H., Lee, T. S., Mukhopadhyay, A., Singer, S. W., & Sundstrom, E. (2021). Microbial production of advanced biofuels. Nat Rev Microbiol. https://doi.org/10.1038/s41579-021-00577-w

Leggieri, P. A., Liu, Y., Hayes, M., Connors, B., Seppälä, S., O’Malley, M. A., & Venturelli, O. S. (2021). Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annual Review of Biomedical Engineering. https://doi.org/10.1146/annurev-bioeng-082120-022836

Ing, N., Deng, K., Chen, Y., Aulitto, M., Gin, J. W., Pham, T. L. M., Petzold, C. J., Singer, S. W., Bowen, B., Sale, K. L., Simmons, B. A., Singh, A. K., Adams, P. D., & Northen, T. R. (2021). A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities. Sci Rep, 11(1), 11803. https://doi.org/10.1038/s41598-021-91181-8

Yang, M., Dahlberg, J., Baral, N. R., Putnam, D., & Scown, C. D. (2021). Identifying Forage Sorghum Ideotypes for Advanced Biorefineries. ACS Sustainable Chemistry & Engineering. https://doi.org/10.1021/acssuschemeng.1c01706

Dong, O. X., & Ronald, P. C. (2021). Targeted DNA insertion in plants. Proc Natl Acad Sci U S A, 118(22). https://doi.org/10.1073/pnas.2004834117

Gauttam, R., Mukhopadhyay, A., Simmons, B. A., & Singer, S. W. (2021). Development of dual-inducible duet-expression vectors for tunable gene expression control and CRISPR interference-based gene repression in Pseudomonas putida KT2440. Microbial Biotechnology. https://doi.org/10.1111/1751-7915.13832

Thompson, M. G., Eiben, C. B., Pearson, A. N., & Shih, P. M. (2021). Draft Genome Sequence of Mycobacterium sp. Strain JC1 DSM 3803. Microbiol Resour Announc, 10(19). https://doi.org/10.1128/mra.00150-21

Pham, L. T. M., Deng, K., Northen, T. R., Singer, S. W., Adams, P. D., Simmons, B. A., & Sale, K. L. (2021). Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium. Biotechnol Biofuels, 14(1), 108. https://doi.org/10.1186/s13068-021-01953-7

Lin, C. Y., Vuu, K. M., Amer, B., Shih, P. M., Baidoo, E. E. K., Scheller, H. V., & Eudes, A. (2021). In-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-product. Metab Eng, 66, 148–156. https://doi.org/10.1016/j.ymben.2021.04.011

Podolsky, I. A., Seppälä, S., Xu, H., Jin, Y.-S., & O’Malley, M. A. (2021). A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast. Metabolic Engineering. https://doi.org/https://doi.org/10.1016/j.ymben.2021.04.009

Moore, W. M., Chan, C., Ishikawa, T., Rennie, E. A., Wipf, H. M., Benites, V., Kawai-Yamada, M., Mortimer, J. C., & Scheller, H. V. (2021). Reprogramming sphingolipid glycosylation is required for endosymbiont persistence in Medicago truncatula. Curr Biol. https://doi.org/10.1016/j.cub.2021.03.067

Das, L., Achinivu, E. C., Barcelos, C. A., Sundstrom, E., Amer, B., Baidoo, E. E. K., Simmons, B. A., Sun, N., & Gladden, J. M. (2021). Deconstruction of Woody Biomass via Protic and Aprotic Ionic Liquid Pretreatment for Ethanol Production. ACS Sustainable Chemistry & Engineering, 9(12), 4422–4432. https://doi.org/10.1021/acssuschemeng.0c07925

Yao, A., Choudhary, H., Mohan, M., Rodriguez, A., Magurudeniya, H., Pelton, J. G., George, A., Simmons, B. A., & Gladden, J. M. (2021). Can Multiple Ions in an Ionic Liquid Improve the Biomass Pretreatment Efficacy? ACS Sustainable Chemistry & Engineering, 9(12), 4371–4376. https://doi.org/10.1021/acssuschemeng.0c09330

Mamode Cassim, A., Navon, Y., Gao, Y., Decossas, M., Fouillen, L., Grélard, A., Nagano, M., Lambert, O., Bahammou, D., Van Delft, P., Maneta-Peyret, L., Simon-Plas, F., Heux, L., Jean, B., Fragneto, G., Mortimer, J. C., Deleu, M., Lins, L., & Mongrand, S. (2021). Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation. J Biol Chem, 100602. https://doi.org/10.1016/j.jbc.2021.100602

Barcelos, C. A., Oka, A. M., Yan, J., Das, L., Achinivu, E. C., Magurudeniya, H., Dong, J., Akdemir, S., Baral, N. R., Yan, C., Scown, C. D., Tanjore, D., Sun, N., Simmons, B. A., Gladden, J., & Sundstrom, E. (2021). High-Efficiency Conversion of Ionic Liquid-Pretreated Woody Biomass to Ethanol at the Pilot Scale. ACS Sustainable Chemistry & Engineering, 9(11), 4042–4053. https://doi.org/10.1021/acssuschemeng.0c07920

Gonçalves, D. R. P., Mishra, U., Wills, S., & Gautam, S. (2021). Regional environmental controllers influence continental scale soil carbon stocks and future carbon dynamics. Sci Rep, 11(1), 6474. https://doi.org/10.1038/s41598-021-85992-y

Hodgson-Kratky, K., Perlo, V., Furtado, A., Choudhary, H., Gladden, J. M., Simmons, B. A., Botha, F., & Henry, R. J. (2021). Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. Plant Molecular Biology. https://doi.org/10.1007/s11103-021-01136-w

Mishra, S. K., Gautam, S., Mishra, U., & Scown, C. D. (2021). Performance-Based Payments for Soil Carbon Sequestration Can Enable a Low-Carbon Bioeconomy. Environmental Science & Technology. https://doi.org/10.1021/acs.est.0c06452

Demirer, G. S., Silva, T. N., Jackson, C. T., Thomas, J. B., W. Ehrhardt, D., Rhee, S. Y., Mortimer, J. C., & Landry, M. P. (2021). Nanotechnology to advance CRISPR–Cas genetic engineering of plants. Nature Nanotechnology, 16(3), 243–250. https://doi.org/10.1038/s41565-021-00854-y

Jing, B., Ishikawa, T., Soltis, N., Inada, N., Liang, Y., Murawska, G., Fang, L., Andeberhan, F., Pidatala, R., Yu, X., Baidoo, E., Kawai-Yamada, M., Loque, D., Kliebenstein, D. J., Dupree, P., & Mortimer, J. C. (2021). The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1. Plant Direct, 5(3), e00309. https://doi.org/10.1002/pld3.309

Liu, Y., Cruz-Morales, P., Zargar, A., Belcher, M. S., Pang, B., Englund, E., Dan, Q., Yin, K., & Keasling, J. D. (2021). Biofuels for a sustainable future. Cell. https://doi.org/10.1016/j.cell.2021.01.052

Brunner, M., Imberti, S., Simmons, B. A., Warr, G. G., & Atkin, R. (2021). Liquid Nanostructure of Cholinium Argininate Biomass Solvents. ACS Sustainable Chemistry & Engineering, 9(7), 2880–2890. https://doi.org/10.1021/acssuschemeng.0c08829

Wilken, S. E., Monk, J. M., Leggieri, P. A., Lawson, C. E., Lankiewicz, T. S., Seppala, S., Daum, C. G., Jenkins, J., Lipzen, A. M., Mondo, S. J., Barry, K. W., Grigoriev, I. V., Henske, J. K., Theodorou, M. K., Palsson, B. O., Petzold, L. R., & O’Malley, M. A. (2021). Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. MSystems, 6(1), e00002-21. https://doi.org/10.1128/mSystems.00002-21

Ren, Y., Li, M., Guo, S., Sun, H., Zhao, J., Zhang, J., Liu, G., He, H., Tian, S., Yu, Y., Gong, G., Zhang, H., Zhang, X., Alseekh, S., Fernie, A. R., Scheller, H. V., & Xu, Y. (2021). Evolutionary Gain of Oligosaccharide Hydrolysis and Sugar Transport Enhanced Carbohydrate Partitioning in Sweet Watermelon Fruits. Plant Cell. https://doi.org/10.1093/plcell/koab055

Kim, J., Baidoo, E. E. K., Amer, B., Mukhopadhyay, A., Adams, P. D., Simmons, B. A., & Lee, T. S. (2021). Engineering Saccharomyces cerevisiae for isoprenol production. Metab Eng, 64, 154–166. https://doi.org/10.1016/j.ymben.2021.02.002

Hori, C., Takata, N., Lam, P. Y., Tobimatsu, Y., Nagano, S., Mortimer, J. C., & Cullen, D. (2020). Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus. Sci Rep, 10(1), 22043. https://doi.org/10.1038/s41598-020-78781-6

Yang, X., Medford, J. I., Markel, K., Shih, P. M., De Paoli, H. C., Trinh, C. T., McCormick, A. J., Ployet, R., Hussey, S. G., Myburg, A. A., Jensen, P. E., Hassan, M. M., Zhang, J., Muchero, W., Kalluri, U. C., Yin, H., Zhuo, R., Abraham, P. E., Chen, J.-G., … Tuskan, G. A. (2020). Plant Biosystems Design Research Roadmap 1.0. BioDesign Research, 2020, 1–38. https://doi.org/10.34133/2020/8051764

Yan, J., Liu, Y., Yang, L., He, H., Huang, Y., Fang, L., Scheller, H. V., Jiang, M., & Zhang, A. (2020). Cell Wall beta-1,4-galactan Regulated by BPC1/BPC2-GALS1 Module Aggravates Salt Sensitivity in Arabidopsis thaliana. Mol Plant. https://doi.org/10.1016/j.molp.2020.11.023

Ferrara, M., Gallo, A., Perrone, G., Magistà, D., & Baker, S. E. (2020). Comparative Genomic Analysis of Ochratoxin A Biosynthetic Cluster in Producing Fungi: New Evidence of a Cyclase Gene Involvement. Front Microbiol, 11(3289). https://doi.org/10.3389/fmicb.2020.581309

Gao, Y., Lipton, A. S., Wittmer, Y., Murray, D. T., & Mortimer, J. C. (2020). A grass-specific cellulose-xylan interaction dominates in sorghum secondary cell walls. Nat Commun, 11(1), 6081. https://doi.org/10.1038/s41467-020-19837-z

Gao, Y., Lipton, A. S., Wittmer, Y., Murray, D. T., & Mortimer, J. C. (2020). A grass-specific cellulose–xylan interaction dominates in sorghum secondary cell walls. Nature Communications, 11(1), 6081. https://doi.org/10.1038/s41467-020-19837-z

Aulitto, M., Tom, L. M., Ceja-Navarro, J. A., Simmons, B. A., & Singer, S. W. (2020). Whole-Genome Sequence of Brevibacillus borstelensis SDM, Isolated from a Sorghum-Adapted Microbial Community. Microbiol Resour Announc, 9(48). https://doi.org/10.1128/MRA.01046-20

Lawson, C., Marti, J. M., Radivojevic, T., Jonnalagadda, S. V. R., Gentz, R., Hillson, N. J., Peisert, S., Kim, J., Simmons, B. A., Petzold, C. J., Singer, S. W., Mukhopadhyay, A., Tanjore, D., Dunn, J., & Martin, H. G. (2020). Machine learning for metabolic engineering: A review. Metab Eng. https://doi.org/10.1016/j.ymben.2020.10.005

Geiselman, G. M., Kirby, J., Landera, A., Otoupal, P., Papa, G., Barcelos, C., Sundstrom, E. R., Das, L., Magurudeniya, H. D., Wehrs, M., Rodriguez, A., Simmons, B. A., Magnuson, J. K., Mukhopadhyay, A., Lee, T. S., George, A., & Gladden, J. M. (2020). Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks. Microb Cell Fact, 19(1), 208. https://doi.org/10.1186/s12934-020-01456-4

Garabedian, B. M., Meadows, C. W., Mingardon, F., Guenther, J. M., de Rond, T., Abourjeily, R., & Lee, T. S. (2020). An automated workflow to screen alkene reductases using high-throughput thin layer chromatography. Biotechnology for Biofuels, 13(1), 184. https://doi.org/10.1186/s13068-020-01821-w

Banerjee, D., Eng, T., Lau, A. K., Sasaki, Y., Wang, B., Chen, Y., Prahl, J. P., Singan, V. R., Herbert, R. A., Liu, Y., Tanjore, D., Petzold, C. J., Keasling, J. D., & Mukhopadhyay, A. (2020). Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun, 11(1), 5385. https://doi.org/10.1038/s41467-020-19171-4

Pierce, A., Zheng, Y., Wagner, W. L., Scheller, H. V., Mohnen, D., Ackermann, M., & Mentzer, S. J. (2020). Visualizing pectin polymer-polymer entanglement produced by interfacial water movement. Carbohydrate Polymers, 246, 116618. https://doi.org/10.1016/j.carbpol.2020.116618

Yang, M., Baral, N. R., Anastasopoulou, A., Breunig, H. M., & Scown, C. D. (2020). Cost and Life-Cycle Greenhouse Gas Implications of Integrating Biogas Upgrading and Carbon Capture Technologies in Cellulosic Biorefineries. Environmental Science & Technology. https://doi.org/10.1021/acs.est.0c02816

Baral, N. R., Dahlberg, J., Putnam, D., Mortimer, J. C., & Scown, C. D. (2020). Supply Cost and Life-Cycle Greenhouse Gas Footprint of Dry and Ensiled Biomass Sorghum for Biofuel Production. ACS Sustainable Chemistry & Engineering. https://doi.org/10.1021/acssuschemeng.0c03784

Radivojevic, T., Costello, Z., Workman, K., & Garcia Martin, H. (2020). A machine learning Automated Recommendation Tool for synthetic biology. Nat Commun, 11(1), 4879. https://doi.org/10.1038/s41467-020-18008-4

Zhang, J., Petersen, S. D., Radivojevic, T., Ramirez, A., Perez-Manriquez, A., Abeliuk, E., Sanchez, B. J., Costello, Z., Chen, Y., Fero, M. J., Martin, H. G., Nielsen, J., Keasling, J. D., & Jensen, M. K. (2020). Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism. Nat Commun, 11(1), 4880. https://doi.org/10.1038/s41467-020-17910-1

Wheatley, P., Gupta, S., Pandini, A., Chen, Y., Petzold, C. J., Ralston, C. Y., Blair, D. F., & Khan, S. (2020). Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM. Biophysical Journal, 119(6), 1108–1122. https://doi.org/10.1016/j.bpj.2020.08.009

Achmon, Y., Claypool, J. T., Fernández-Bayo, J. D., Hernandez, K., McCurry, D. G., Harrold, D. R., Su, J., Simmons, B. A., Singer, S. W., Dahlquist-Willard, R. M., Stapleton, J. J., VanderGheynst, J. S., & Simmons, C. W. (2020). Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation. Applied Soil Ecology, 153, 103602. https://doi.org/10.1016/j.apsoil.2020.103602

Banda, D. M., Pereira, J. H., Liu, A. K., Orr, D. J., Hammel, M., He, C., Parry, M. A. J., Carmo-Silva, E., Adams, P. D., Banfield, J. F., & Shih, P. M. (2020). Novel bacterial clade reveals origin of form I Rubisco. Nature Plants. https://doi.org/10.1038/s41477-020-00762-4

Mohamed, E. T., Werner, A. Z., Salvachúa, D., Singer, C., Szostkiewicz, K., Jiménez-Díaz, M., Eng, T., Radi, M. S., Simmons, B. A., Mukhopadhyay, A., Herrgård, M. J., Singer, S. W., Beckham, G. T., & Feist, A. M. (2020). Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Metabolic Engineering Communications, e00143. https://doi.org/10.1016/j.mec.2020.e00143

Calgaro-Kozina, A., Vuu, K. M., Keasling, J. D., Loque, D., Sattely, E. S., & Shih, P. M. (2020). Engineering Plant Synthetic Pathways for the Biosynthesis of Novel Antifungals. ACS Cent Sci, 6(8), 1394–1400. https://doi.org/10.1021/acscentsci.0c00241

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