Publications

Lead Laboratory

Publication Date

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Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

Pomraning, K., Dai, Z., Munoz, N., Kim, Y., Gao, Y., Deng, S., Kim, J., Hofstad, B., Swita, M., Lemmon, T., Collett, J., Panisko, E., Webb-Robertson, B., Zucker, J., Nicora, C., De Paoli, H., Baker, S., Burnum-Johnson, K., Hillson, N., and Magnuson, J. (2021). Frontiers in Bioengineering and Biotechnology.

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering

Roy, S., Radivojevic, T., Forrer, M., Marti, J. M., Jonnalagadda, V., Backman, T., Morrell, W., Plahar, H., Kim, J., Hillson, N., Garcia Martin, H. (2021). Front. Bioeng. Biotechnol..

Approaches to genetic tool development for rapid domestication of non-model microorganisms

Riley, L.A. and Guss, M. (2021). Biotechnology for Biofuels.

High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440

Gao, Y., Fillmore, T. L., Munoz, N., Bentley, G. J., Johnson, C. W., Kim, J., Meadows, J. A., Zucker, J. D., Burnet, M. C., A. K. Lipton, Bilbao, A., Orton, D. J., Kim, Y., Moore, R. J., Robinson, E. W., Baker, S. E., Webb-Robertson, B. M., Guss, A. M., Gladden, J. M., Beckham, G. T., Magnuson, J. K., Burnum-Johnson, K. E. (2020). Frontiers in Bioengineering and Biotechnology.

Machine learning for metabolic engineering: A review

Lawson, C. E., Martí, 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. G., Martin, H. G. (2020). Metabolic Engineering.

Economic and environmental assessment of biological conversions of Agile BioFoundry bio-derived chemicals

Thathiana Benavides, P., Klein, B., Davis, R. (2020). 2nd Bioenergy Sustainability Conference.

Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1

Pardo, I., Jha, R. K., Bermel, R. E., Bratti, F., Gaddis, M., McIntyre, M. W., Neidle, E.L., Dale, T., Beckham, G. T., Johnson, C. W. (2020). Metabolic Engineering.

A machine learning Automated Recommendation Tool for synthetic biology

Radivojević, T., Costello, Z., Workman, K., Garcia Martin, H. (2020). Nature Communications.

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Zhang, J., Petersen, S. D., Radivojevic, T., Ramirez, A., Pérez-Manríquez, A., Abeliuk, E., Sánchez, B. J., Costello, Z., Chen, Y., Fero, M. J., Garcia Martin, H., Nielsen, J., Keasling, J. D. & Jensen, M. K. (2020). Nature Communications.

Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid

Elmorea, J. R., Dexter, G. N., Salvachúa, D., O'Brien, M., Klingeman, D. M., Gorday, K., Michener, J. K., Peterson, D. J., Beckham, G. T., Guss, A. M. (2020). Metabolic Engineering.

DNA Scanner: a web application for comparing DNA synthesis feasibility, price, and turnaround time across vendors

Doçi, G., Fuchs, L., Kharbanda, Y., Schickling, P., Zulkower, V., Hillson, N., Oberortner, E., Swainston, N., Kabisch, J. (2020). Synthetic Biology.

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

Thompson, M. G., Blake-Hedges, J. M., Henrique Pereira, J., Hangasky, J. A., Belcher, M. S., Moore, W. M., Barajas, J. F., Cruz-Morales, P., Washington, L. J., Haushalter, R. W., Eiben, C. B., Liu, Y., Skyrud, W., Benites, V. T., Barnum, T. P., Baidoo, E. E. K., Scheller, H. V., Marletta, M. A., Shih, P. M., Adams, P. D., Keasling, J. D. (2020). Nature Communications.

Chemoinformatic-Guided Engineering of Polyketide Synthases

Zargar, A., Lal, R., Valencia, L., Wang, J., Backman, T. W. H., Cruz-Morales, P., Kothari, A., Werts, M., Wong, A. R., Bailey, C. B., Loubat, A., Liu, Y., Chen, Y., Chang, S., Benites, V. T., Hernández, A. C., Barajas, J. F., Thompson, M. G., Barcelos, C., Anayah, R., Garcia Martin, H., Mukhopadhyay, A., Petzold, C. J., Baidoo, E. E. K., Katz, L., and Keasling, J. D. (2020). Journal of the American Chemical Society.

Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol

Eiben, C. B., Tian, T., Thompson, M. G., Mendez-Perez, D., Kaplan, N., Goyal, G., Chiniquy, J., Hillson, N. J., Soon Lee, T., Keasling, J. D. (2020). ACS Synthetic Biology.

Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides

Geiselman, G. M., Zhuang, X., Kirby, J., Tran‑Gyamf, M. B., Prahl, J. P., Sundstrom, E. R., Gao, Y., Munoz, N., Nicora, C. D., Clay, D. M., Papa, G., Burnum‑Johnson, K. E., Magnuson, J. K., Tanjore, D., Skerker, J. M., and Gladden, J. M. (2020). Microbial Cell Factories.

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

Chiniquy, J., Garber, M., Mukhopadhyay, A., Hillson, N. (2020). BMC Genomics.

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

Liu, D., Geiselman, G. M., Coradetti, S., Cheng, Y., Kirby, J., Prahl, J. P., Jacobson, O., Sundstrom, E. R., Tanjore, D., Skerker, J. M., Gladden, J. (2020). Biotechnology and Bioengineering.

Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440

Bentley, G. J., Narayanan, N., Jha, R. K., Salvachúa, D., Elmore, J. R., Peabody, G. L., Black, B. A., Ramirez, K., De Capite, A., Michener, W. E., Werner, A. Z., Klingeman, D. M., Schindel, H. S., Foust, R. N. L., Guss, A. M., Dale, T., Johnson, C. W., Beckham, G. T. (2020). Metabolic Engineering.

Systems and synthetic biology tools for advanced bioproduction hosts

Chen, Y., Banerjee, D., Mukhopadhyay, A., Petzold, C. J. (2020). Current Opinion in Biotechnology.

Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

Peabody, G. L., Elmore, J. R., Martinez-Baird, J., Guss, A. M. (2019). Biotechnology for Biofuels.