Lead Laboratory
Publication Date
Perspectives for self-driving labs in synthetic biology
Martin, H.G., et al. (2023). Current Opinion in Biotechnology.
Evaluation of engineered low-lignin poplar for conversion into advanced bioproducts
Lin, Chien-Yuan, et al. (2022). Biotechnology for Biofuels and Bioproducts.
Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides
Otoupal, P., et. al. (2022). Microbial Cell Factories.
Tackling the Catch-22 Situation of Optimizing a Sensor and a Transporter System in a Whole-Cell Microbial Biosensor Design for an Anthropogenic Small Molecule
Shin, S., Jha, R., and Dale, T. (2022). ACS Synthetic Biology.
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.