Publications

Lead Laboratory

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ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design

Tao, X., LaFrance, S., Xing, Y., Nava, A., Garcia Martin, H., Keasling, J., Backman, T. (2022). Nucleic Acids Research.

Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems

Pandey, N., Davison, S., Krishnamurthy, M., Trettel, D., Lo, C., Starkenburg, S., Wozniak, K., Kern, T., Reardon, S., Unkefer, C., Hennelly, S., Dale, T. (2022). ACS Synthetic Biology.

Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production

Czajka, J., Banerjee, D., Eng, T., Menasalvas, J., Yan, C., Munoz, N., Poirier, B., Kim, Y., Baker, S., Tang, Y., Mukhopadhyay, A. (2022). Metabolic Engineering Communications.

Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus

Pomraning, K., Dai, Z., Munoz, N., Kim, Y., Gao, Y., Deng, S., Lemmon, T., Swita, M., Zucker, J., Kim, J., Mondo, S., Panisko, E., Burnet, M., Webb-Robertson, B., Hofstad, B., Baker, S., Burnum-Johnson, K., Magnuson, J. (2022). Metabolic Engineering Communications .

Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering

Ling, C., Peabody, G.L., Salvachúa, D., Kim, Y., Kneucker, C.M., Calvey, C.H., Monninger, M.A., Munoz, N., Poirier, B.C., Ramirez, K.J., St. John, P.C., Woodworth, S.P., Magnuson, J.K., Burnum-Johnson, K.E., Guss, A.M., Johnson, C.W., Beckham, G.T. (2022). Nature Communications.

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Lim, H.G., Rychel, K., Sastry, A.V., Bentley, G.J., Mueller, J., Schindel, H.S., Larsen, P., Laible, P.D., Guss, A.M., Niu, W., Johnson, C.W., Beckham, G.T., Feist, A.M., Palsson, B.O. (2022). Metabolic Engineering.

Production of β-ketoadipic acid from glucose in Pseudomonas putida KT2440 for use in performance-advantaged nylons

Rorrer, N.A., Notonier, S.F., Knott, B.C., Black, B.A., Singh, A., Nicholson, S.R., Kinchin, C.P., Schmidt, G.P., Carpenter, A.C., Ramirez, K.J., Johnson, C.W., Salvachua, D., Crowley, M., Beckham, G.T. (2022). Cell Reports Physical Science.

Modular automated bottom-up proteomic sample preparation for high-throughput applications

Chen, Y., Kaplan Lease, N., Gin, J., Ogorzalek, T., Adams, P., Hillson, N., Petzold, C. (2022). PLOS ONE.

Making Security Viral: Shifting Engineering Biology Culture and Publishing

Mackelprang, R., Adamala, K., Aurand, E., Diggans, J., Ellington, A., Weiss Evans, S., Fortman, C., Hillson, N., Hinman, A., Isaacs, F., Medford, J., Mamaghani, S., Seok Moon, T., Palmer, M., Peccoud, J., Vitalis, E., Hook-Barnard, I., and Friedman, D. (2022). ACS Synthetic Biology.

Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing

Kim, Y., Petzold, C., Kerkhoven, E., Baker, S. (2021). Frontiers in Bioengineering and Biotechnology .

BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform

Plahar, H., Rich, T., Lane, S., Morrell, W., Springthorpe, L., Nnadi, O., Aravina, E., Dai, T., Fero, M., Hillson, N., Petzold, C (2021). ACS Synthetic Biology.

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.

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

Kim, J., Coradetti, S., Kim, Y., Gao, Y., Yaegashi, J., Zucker, J., Munoz, N., Zink, E., Burnum-Johnson, K., Baker, S., Simmons, B., Skerker, J., Gladden, J., Magnuson, J. (2021). Frontiers in Bioengineering and Biotechnology.

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.