Lead Laboratory
Publication Date
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.
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.
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.